Title of Invention

MODIFIED HUMAN GROWTH HORMONE

Abstract Modified growth hormone polypeptide and uses thereof are provided.
Full Text

Modified Human Growth Hormone
CROSS-REFERENCE TO RELATED APPLICATIONS
[01] This application claims priority to U.S. provisional patent application 60/638,616
filed December 22, 2004 and U.S. provisional patent application 60/727,996 filed October 17, 2005, the specifications of which are incorporated herein in their entirety.
FIELD OF THE INVENTION
[02] This invention relates to growth hormone polypeptides modified with at least one
non-naturally-encoded amino acid.
BACKGROUND OF THE INVENTION
[03] The growth hormone (GH) supergene family (Bazan, F. Immunology Today 11:
350-354 (1990); Mott, H. R. and Campbell, L D. Current Opinion in Structural Biology 5: 114-121 (1995); Silvennoinen, O. and Ihle, J. N. (1996) SIGNALING BY THE HEMATOPOIETIC CYTOKINE RECEPTORS) represents a set of proteins with similar structural characteristics. Each member of this family of proteins comprises a four helical bundle, the general structure of which is shown in Figure 1. While there are still more members of the family yet to be identified, some members of the family include the following: growth hormone, prolactin, placental lactogen, erythropoietin (EPO), thrombopoietin (TPO), interleukin-2 (IL-2), IL-3, IL-4, IL-5, IL-6, IL-7, IL-9, EL-10, EL-11, EL-12 (p35 subunit), IL-13, EL-15, oncostatin M, ciliary neurotrophic factor, leukemia inhibitory factor, alpha interferon, beta interferon, gamma interferon, omega interferon, tau interferon, epsilon interferon, granulocyte-colony stimulating factor (G-CSF), granulocyte-macrophage colony stimulating factor (GM-CSF), macrophage colony stimulating factor (M-CSF) and cardiotrophin-1 (CT-1) ("the GH supergene family"). Members of the GH supergene family have similar secondary and tertiary structures, despite the fact that they generally have limited amino acid or DNA sequence identity. The shared structural features allow new members of the gene family to be readily identified. The general structures of family members hGH, EPO, IFNa-2, and G-CSF are shown in Figures 2, 3, 4, and 5, respectively.

[04] One member of the GH supergene family is human growth hormone (hGH).
Human growth hormone participates in much of the regulation of normal human growth and development. This naturally-occurring single-chain pituitary hormone consists of 191 amino acid residues and has a molecular weight of approximately 22 kDa. hGH exhibits a multitude of biological effects, including linear growth (somatogenesis), lactation, activation of macrophages, and insulin-like and diabetogenic effects, among others (Chawla, R., et al, Ann. Rev. Med. 34:519-547 (1983); Isaksson, O., et al, Ann. Rev. Physiol, 47:483-499 (1985); Hughes, J. and Friesen, H.,Ann. Rev. Physiol, 47:469-482 (1985)).
105] The structure of hGH is well known (Goeddel, D., et al, Nature 281:544-548
(1979)), and the three-dimensional structure of hGH has been solved by X-ray crystallography (de Vos, A., et al, Science 255:306-312 (1992)). The protein has a compact globular structure, comprising four amphipathic alpha helical bundles, termed A-D beginning from the N-terminus, which are joined by loops. hGH also contains four cysteine residues, which participate in two intramolecular disulfide bonds: C53 is paired with C165 and CI 82 is paired with CI 89. The hormone is not glycosylated and has been expressed in a secreted form in E. coli (Chang, C, et al, Gene 55:189-196 (1987)).
[06] A number of naturally occurring mutants of hGH have been identified. These
include hGH-V (Seeburg, DNA 1: 239 (1982); U.S. Patent. Nos. 4,446,235, 4,670,393, and
4,665,180, which are incorporated by reference herein) and a 20-kDa hGH containing a deletion of
residues 32-46 of hGH (Kostyo et al, Biochem. Biophys. Acta 925: 314 (1987); Lewis, U., et al,
J. Biol Chem., 253:2679-2687 (1978)). hi addition, numerous hGH variants, arising from post-
transcriptional, post-translational, secretory, metabolic processing, and other physiological
processes, have been reported (Baumann, G., Endocrine Reviews 12: 424 (1991)).
[07] The biological effects of hGH derive from its interaction with specific cellular
receptors. The hormone is a member of a family of homologous proteins that include placental lactogens and prolactins. hGH is unusual among the family members,.however, in that it exhibits broad species specificity and binds to either lie cloned somatogenic (Leung, D., et al., Nature 330:537-543 (1987)) or prolactin (Boutin, J., et al., Cell 53:69-77 (1988)) receptor. Based on structural and biochemical studies, functional maps for the lactogenic and somatogenic binding domains have been proposed (Cunningham, B. and Wells, J., Proc. Natl. Acad. Sci. 88: 3407 (1991)). The hGH receptor is a member of the hematopoietic/cytokine/growth factor receptor

family, which includes several other growth factor receptors, such as the interleukin (IL)-3, -4 and
-6 receptors, the granulocyte macrophage colony-stimulating factor (GM-CSF) receptor, the
erythropoietin (EPO) receptor, as well as the G-CSF receptor. See, Bazan, Proc. Natl Acad. Sci
USA 87: 6934-6938 (1990). Members of the cytokine receptor family contain four conserved
cysteine residues and a tryptophan-serhe-X-tryptophan-serine motif positioned just outside the
transmembrane region- The conserved sequences are thought to be involved in protein-protein
interactions. See, e.g., Chiba et al9 Biochim. Biophys. Res. Comrru 184: 485-490 (1992). The
interaction between hGH and extracellular domain of its receptor (hGHbp) is among the most well
understood hormone-receptor interactions. High-resolution X-ray crystallographic data
(Cunningham, B., et ah, Science, 254:821-825 (1991)) has shown that hGH has two receptor
binding sites and binds two receptor molecules sequentially using distinct sites on the molecule.
The two receptor binding sites are referred to as Site I and Site II. Site I includes the carboxy
terminal end of helix D and parts of helix A and the A-B loop, whereas Site II encompasses the
amino terminal region of helix A and a portion of helix C. Binding of GH to its receptor occurs
sequentially, with Site I binding first. Site II. then engages a second GH receptor, resulting in
receptor dimerization and activation of the intracellular signaling pathways that lead to cellular
responses to the hormone. An hGH mutein hi which a G120R substitution has been introduced
into site II is able to bind a single hGH receptor, but is unable to dimerize two receptors. The
mutein acts as an hGH antagonist in vitro, presumably by occupying receptor sites without
activating intracellular signaling pathways (Fuh, G., et al, Science 256:1677-1680 (1992)).
[08] Recombinant hGH is used as a therapeutic and has been approved for the treatment
of a number of indications. hGH deficiency leads to dwarfism, for example, which has been
successfully treated for more than a decade by exogenous administration of the hormone, In
addition to hGH deficiency, hGH has also been approved for the treatment of renal failure (in
children), Turner's Syndrome, and cachexia in AIDS patients. Recently, the Food and Drug
Administration (FDA) has approved hGH for the treatment of non-GH-dependent short stature.
hGH is also currently under investigation for the treatment of aging, frailty in the elderly, short
bowel syndrome, and congestive heart failure. Target populations for hGH treatment include
children with idiopathic short stature (ISS) and adults with GHD-like symptoms.
[091 Recombinant hGH is currently sold as a daily injectable product, with five major
products currently on the market: Humatrope™ (Eli Lilly & Co.), Nutropin™ (Genentech),

Norditropin™ (Novo-Nordisk), Genotropin™ (Pfizer) and Saizen/Serostim™ (Serono). A significant challenge to using growth hormone as a therapeutic, however, is that the protein has a short in vivo half-life and, therefore, it must be administered by daily subcutaneous injection for maximum effectiveness (MacGillivray, et al, J. Clin. Endocrinol Metab. 81: 1806-1809 (1996)). Considerable effort is focused on means to improve the administration of hGH agonists and antagonists, by lowering the cost of production, making administration easier for the patient, improving efficacy and safety profile, and creating other properties that would provide a competitive advantage. For example, Genentech and Alkermes formerly marketed Nutropin Depot™, a depot formulation of hGH, for pediatric growth hormone deficiency. While the depot permits less frequent administration (once every 2-3 weeks rather than once daily), it is also associated with undesirable side effects, such as decreased bioavailability and pain at the injection site and was withdrawn from the market in 2004. Another product, Pegvisomant™ (Pfizer), has also recently been approved by the FDA. Pegvisomant™ is a genetically-engineered analogue of hGH that functions as a highly selective growth hormone receptor antagonist indicated for the treatment of acromegaly (van der Lely, et aL9 The Lancet 358: 1754-1759 (2001). Although ■> several of the amino acid side chain residues in Pegvisomant™ are derivatdzed with polyethylene glycol (PEG) polymers, the product is still administered once-daily, indicating that the ■ pharmaceutical properties are not optimal. In addition to PEGylation and depot formulations, other administration routes, including inhaled and oral dosage forms of hGH, are under early-stage •' pre-clinical and clinical development and none have yet received approval from the FDA. Accordingly, there is a need for a polypeptide that exhibits growth hormone activity but that also provides a longer serum half-life and, therefore, more optimal therapeutic levels of hGH and an increased therapeutic half-life.
[10] Covalent attachment of the hydrophilic polymer polyethylene glycol), abbreviated
PEG, is a method of increasing water solubility, bioavailability, increasing serum half-life, increasing therapeutic half-life, modulating immunogenicity, modulating biological activity, or extending the circulation time of many biologically active molecules, including proteins, peptides, and particularly hydrophobic molecules. PEG has been used extensively in pharmaceuticals, on artificial implants, and in other applications where biocompatibility, lack of toxicity, and lack of immunogenicity are of importance. In order to maximize the desired properties of PEG, the total molecular weight and hydration state of the PEG polymer or polymers attached to the biologically

active molecule must be sufficiently high to impart the advantageous characteristics typically associated with PEG polymer attachment, such as increased water solubility and circulating half life, while not adversely impacting the bioactivity of the parent molecule.
[11] PEG derivatives are frequently linked to biologically active molecules through
reactive chemical functionalities, such as lysine, cysteine and histidine residues, the N-terminus and carbohydrate moieties. Proteins and other molecules often have a limited number of reactive sites available for polymer attachment Often, the sites most suitable for modification via polymer attachment play a significant role in receptor binding, and are necessary for retention of the biological activity of the molecule. As a result, indiscriminate attachment of polymer chains to such reactive sites on a biologically active molecule often leads to a significant reduction or even total loss of biological activity of the polymer-modified molecule. R. Claik et al., (1996), J. Biol. Chem.. 271:21969-21977. To form conjugates having sufficient polymer molecular weight for imparting the desired advantages to a target molecule, prior art approaches have typically involved random attachment of numerous polymer arms to the molecule, thereby increasing the risk of a reduction or even total loss in bioactivity of the parent molecule.
[12] Reactive sites that form the loci for attachment of PEG derivatives to proteins are •
dictated by the protein's structure. Proteins, including enzymes, are composed of various
sequences of alpha-amino acids, which have the general structure H2N—CHR--COOH. The alpha
amino moiety (H2N--) of one amino acid joins to the carboxyl moiety (—COOH) of an adjacent
amino acid to form amide linkages, which can be represented as — (NH—CHR— CO)n —, where the
subscript "n" can equal hundreds or thousands. The fragment represented by R can contain
reactive sites for protein biological activity and for attachment of PEG derivatives.
[13] For example, in the case of the amino acid lysine, there exists an -NH2 moiety in
the epsilon position as well as in the alpha position. The epsilon —NH2 is free for reaction under conditions of basic pH. Much of the art in the field of protein derivatization with PEG has been directed to developing PEG derivatives for attachment to the epsilon —NH2 moiety of lysine residues present in proteins. "Polyethylene Glycol and Derivatives for Advanced PEGylation", Nektar Molecular Engineering Catalog, 2003, pp. 1-17. These PEG derivatives all have the common limitation, however, that they cannot be installed selectively among the often numerous lysine residues present on the surfaces of proteins. This can be a significant limitation in instances where a lysine residue is important to protein activity, existing in an enzyme active site for

example, or in cases where a lysine residue plays a role in mediating the interaction of the protein with other biological molecules, as in the case of receptor binding sites.
[14] A second and equally important complication of existing methods for protein
PEGylation is that the PEG derivatives can undergo undesired side reactions with residues other
than those desired. Histidine contains a reactive imino moiety, represented structurally as --N(H>
-, but many chemically reactive species that react with epsilon --NH2 can also react with -N(H)~.
Similarly, the side chain of the amino acid cysteine bears a free sulfhydryl group, represented
structurally as -SH. In some instances, the PEG derivatives directed at the epsilon --NH2 group of
lysine also react with cysteine, histidine or other residues. This can create complex,
heterogeneous mixtures of PEG-derivatized bioactive molecules and risks destroying the activity
of the bioactive molecule being targeted. It would be desirable to develop PEG derivatives that
permit a chemical functional group to be introduced at a single site within the protein that would
then enable the selective coupling of one or more PEG polymers to the bioactive molecule at
specific sites on the protein surface that are both well-defined and predictable.
[151 In addition to lysine residues, considerable effort in the art has been directed toward
the development of activated PEG reagents that target other amino acid side chains, including
cysteine, histidine and the N-terminus. See, e.g., U.S. Pat. No. 6,610,281 which is incorporated by
reference herein, and "Polyethylene Glycol and Derivatives for Advanced PEGylation", Nektar
Molecular Engineering Catalog, 2003, pp. 1-17. A cysteine residue can be introduced site-
selectively into the structure of proteins using site-directed mutagenesis and other techniques
known in the art, and the resulting free sulfhydryl moiety can be reacted with PEG derivatives that
bear thiol-reactive functional groups. This approach is complicated, however, in that the
introduction of a free sulfhydryl group can complicate the expression, folding and stability of the
resulting protein. Thus, it would be desirable to have a means to introduce a chemical functional
group into bioactive molecules that enables the selective coupling of one or more PEG polymers
to the protein while simultaneously being compatible with (i.e., not engaging in undesired side
reactions with) sulfhydryls and other chemical functional groups typically found in proteins.
[16] As can be seen from a sampling of the art, many of these derivatives that have been
developed for attachment to the side chains of proteins, in particular, the — NH2 moiety on the lysine amino acid side chain and the -SH moiety on the cysteine side chain, have proven problematic in their synthesis and use. Some form unstable linkages with the protein that are

subject to hydrolysis and therefore decompose, degrade, or are otherwise unstable in aqueous environments, such as in the bloodstream. Some form more stable linkages, but are subject to hydrolysis before the linkage is formed, which means that the reactive group on the PEG derivative may be inactivated before the protein can be attached. Some are somewhat toxic and are therefore less suitable for use in vivo. Some are too slow to react to be practically useful. Some result in a loss of protein activity by attaching to sites responsible for the protein's activity. Some are not specific in the sites to which they will attach, which can also result in a loss of desirable activity and in a lack of reproducibility of results. In order to overcome the challenges associated with modifying proteins with poly(efhylene glycol) moieties, PEG derivatives have been developed that are more stable (e.g., U.S. Patent 6,602,498, which is incorporated by reference herein) or that react selectively with thiol moieties on molecules and surfaces (e.g., U.S. Patent 6,610,281, which is incorporated by reference herein). There is clearly a need in the art for PEG derivatives that are chemically inert in physiological environments until called upon to react ' selectively to form stable chemical bonds.
[171 Recently, an entirely new technology in the protein sciences has been reported, ;
which promises to overcome many of the limitations associated with site-specific modifications of ; proteins. Specifically, new components have been added to the protein biosynthetic machinery of • the prokaryote Escherichia coli (E. colt) (e.g., L. Wang, et al, (2001), Science 292:498-500) and ■: the eukaryote Sacchromyces cerevisiae (& cerevisiae) (e.g,, J. Chin et al., Science 301:964-7 (2003)), which has enabled the incorporation of non-genetically encoded amino acids to proteins in vivo. A number of new amino acids with novel chemical, physical or biological properties, including photoaffinity labels and photoisomerizable amino acids, photocrosslinking amino acids (see, e.g., Chin, J. W., et al. (2002) Proc. Natl. Acad. Sci. U. S. A. 99:11020-11024; and, Chin, J. W., et al., (2002) J. Am. Chem. Soc. 124:9026-9027), keto amino acids, heavy atom containing amino acids, and glycosylated amino acids have been incorporated efficiently and with high fidelity into proteins in E. coli and in yeast in response to the amber codon, TAG, using this methodology. See, e.g., J. W. Chin et al., (2002), Journal of the American Chemical Society 124:9026-9027; J. W. Chin, & P. G. Schultz, (2002), ChemBioChem 3(11):1135-1137; J. W. Chin, et al., (2002), PNAS United States of America 99:11020-11024; and, L. Wang, & P. G. Schultz, (2002), Chem. Comm., 1:1-11. All references are incorporated by reference in their entirety. These studies have demonstrated that it is possible to selectively and routinely introduce

chemical functional groups, such as ketone groups, alkyne groups and azide moieties, that are not found in proteins, that are chemically inert to all of the functional groups found in the 20 common, genetically-encoded amino acids and that may be used to react efficiently and selectively to form stable covalent linkages.
[18] The ability to incorporate non-genetically encoded amino acids into proteins
permits the introduction of chemical functional groups that could provide valuable alternatives to the naturally-occuaring functional groups, such as the epsilon -NH2 of lysine, the sulfhydryl -SH of cysteine, the imino group of histidine, etc. Certain chemical functional groups are known to be inert to the functional groups found in the 20 common, genetically-encoded amino acids but react cleanly and efficiently to form stable linkages. Azide and acetylene groups, for example, are known in the art to undergo a Huisgen [3+2] cycloaddition reaction in aqueous conditions in the presence of a catalytic amount of copper. See, e.g., Tornoe, et al., (2002) J. Org. Chemu 67:3057-3064; and, Rostovtsev, et al., (2002) Angew. Chem. Int. Ed. 41:2596-2599. By introducing an azide moiety into a protein structure, for example, one is able to incorporate a functional group that is chemically inert to amines, sulfhydryls, carboxylic acids, hydroxy! groups found in proteins, but that also reacts smoothly and efficiently with an acetylene moiety to form a : cycloaddition product Importantly, in the absence of the acetylene moiety, the azide remains chemically inert and unreactive in the presence of other protein side chains and under physiological conditions.
[19] The present invention addresses, among other things, problems associated with the
activity and production of GH polypeptides, and also addresses the production of a hGH polypeptide with improved biological or pharmacological properties, such as improved therapeutic half-life.
BRIEF SUMMARY OF THE INVENTION
[20] This invention provides GH supergene family members, including GH, e.g., hGH
polypeptides, comprising one or more non-naturally encoded amino acids.
[21] In some embodiments, the GH, e.g., hGH polypeptide comprises one or more post-
translational modifications. In some embodiments, the GH, e.g., hGH polypeptide is linked to a linker, polymer, or biologically active molecule. In some embodiments, the GH, e.g., hGH

polypeptide is linked to a bifunctional polymer, bifunctional linker, or at least one additional GH,
e.g., hGH polypeptide.
[22] In some embodiments, the non-naturally encoded amino acid is linked to a water
soluble polymer. In some embodiments, the water soluble polymer comprises a poly(ethylene
glycol) moiety. In some embodiments, the non-naturally encoded amino acid is linked to the
water soluble polymer with a linker or is bonded to the water soluble polymer. In some
embodiments, the poly(ethylene glycol) molecule is a bifunctional polymer. In some
embodiments, the bifunctional polymer is linked to a second polypeptide. In some embodiments,
die second polypeptide is a GH, e.g., hGH polypeptide.
[23] In some embodiments, the GH, e.g., hGH polypeptide comprises at least two amino
acids linked to a water soluble polymer comprising a poly(ethylene glycol) moiety, hi some
embodiments, at least one amino acid is a non-naturally encoded amino acid.
[24] Regions of GH, e.g., hGH can be illustrated as follows, wherein fee amino acid
positions in hGH are indicated in the middle row:
Helix A Helix B Helix C Helix D
[1-5]- [6-33]- [34-74]- [75-96] - [97-105] - [106-129]- [130-153] - [154-183] - [184-191]
N-term A-B loop B-C loop C-D loop C-term
[25] In some embodiments, one or more non-naturally encoded amino acids axe
incorporated at any position in one or more of the following regions corresponding to secondary structures in hGH as follows: 1-5 (N-terminus), 6-33 (A helix), 34-74 (region between A helix and -B helix, the A-B loop), 75-96 (B helix), 97-105 (region between B helix and C helix, the B-C loop), 106-129 (C helix), 130-153 (region between C helix and D helix, the C-D loop), 154-183 (D helix), 184-191 (C-terminus) from SEQ ID NO: 2 or the corresponding amino acids of SEQ ED NO: 1 or 3. In other embodiments, the non-naturally encoded amino acid is substituted at a position selected from the group consisting of residues 1-5, 32-46, 97-105, 132-149, and 184-191 from hGH SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. In some embodiments, one or more non-naturally encoded amino acids are incorporated in one or more of the following positions in GH, e.g., hGH: before position 1 (i.e. at the N-terminus), 1, 2, 3,4, 5,8, 9, 11, 12, 15, 16, 19, 22, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 55, 57, 59, 65, 66, 69, 70, 71, 74, 88, 91, 92, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 111, 112, 113, 115, 116, 119, 120, 122, 123, 126, 127, 129, 130, 131,



(SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3). In some embodiments, the non-naturally occurring amino acid at one or more of these positions is linked to a water soluble polymer: 30, 35, 74, 92, 103, 143, 145 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3). In some embodiments, the non-naturally occurring amino acid at one or more of these positions is linked to a water soluble polymer 35, 92, 143, 145 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3).
[31] Human GH antagonists include, but are not limited to, those with substitutions at
1,2, 3, 4, 5, 8, 9, 11,12, 15, 16, 19, 22, 103,109,112,113,115, 116,119, 120,123, and 127 or an
addition at position 1 (i.e., at the N-terminus), or any combination thereof (SEQ ID NO:2, or the
corresponding amino acid in SEQ ID NO: 1, 3, or any other GH sequence).
[32] In some embodiments, the GH, e.g., hGH polypeptide comprises a substitution,
addition or deletion that modulates affinity of the GH, e.g., hGH polypeptide for a GH, e.g., hGH
polypeptide receptor when compared with the affinity of the corresponding GH, e.g.,hGH without
the substitution, addition, or deletion. In some embodiments, the GH, e.g., hGH polypeptide
comprises a substitution, addition, or deletion that increases the stability of the GH, e.g., hGH
polypeptide when compared with the stability of the corresponding GH, e.g., hGH without the
substitution, addition, or deletion. In some embodiments, the GH, e.g., hGH polypeptide
comprises an amino acid substitution selected from the group consisting of F10A, F10H, F10I;
M14W, M14Q, M14G; H18D; H21N; G120A; R167N; D171S; E174S; F176Y, I179T or any
combination thereof in hGH SEQ ID NO: 2. In some embodiments, the GH, e.g., hGH
polypeptide comprises a substitution, addition, or deletion that modulates the immunogenicity of
the GH, e.g., hGH polypeptide when compared with the immunogenicity of the corresponding
GH, e.g.,hGH without the substitution, addition, or deletion. In some embodiments, the GH, e.g.,
hGH polypeptide comprises a substitution, addition, or deletion that modulates serum half-life or
circulation time of the GH, e.g., hGH polypeptide when compared with the serum half-life or
circulation time of the corresponding GH, e.g., hGH without the substitution, addition, or deletion.
[33] In some embodiments, the GH, e.g., hGH polypeptide comprises a substitution,
addition, or deletion that increases the aqueous solubility of the GH, e.g., hGH polypeptide when compared to aqueous solubility of the corresponding GH, e.g.,hGH without the substitution, addition, or deletion, hi some embodiments, the GH, e.g., hGH polypeptide comprises a substitution, addition, or deletion that increases the solubility of the GH, e.g., hGH polypeptide

produced in a host cell when compared to the solubility of the corresponding GH, e.g., hGH without the substitution, addition, or deletion. In some embodiments, the GH, e.g., hGH polypeptide comprises a substitution, addition, or deletion that increases the expression of the GH, e.g., hGH polypeptide in a host cell or increases synthesis in vitro when compared to the expression or synthesis of the corresponding GH, e.g., hGH without the substitution, addition, or deletion.. In some embodiments, the hGH polypeptide comprises an amino acid substitution G120A. The hGH polypeptide comprising this substitution retains agonist activity and retains or improves expression levels in a host cell. In some embodiments, the GH, e.g., hGH polypeptide comprises a substitution, addition, or deletion that increases protease resistance of the GH, e.g., hGH polypeptide when compared to the protease resistance of the corresponding GH, e.g.,hGH without the substitution, addition, or deletion.
[34] In some embodiments the amino acid substitutions in the GH, e.g., hGH
polypeptide may be with naturally occurring or non-naturally occurring amino acids, provided that
at least one substitution is with a non-naturally encoded amino acid.
[35] In some embodiments, the non-naturally encoded amino acid comprises a carbonyl '
group, an acetyl group, an aminooxy group, a hydrazine group, a hydrazide group, a
semicarbazide group, an azide group, or an alkyne group.
[36] In some embodiments, the non-naturally encoded amino acid comprises a carbonyl
group. In some embodiments, the non-naturally encoded amino acid has the structure:
(CH^COFfe
R3HN COR4
wherein n is 0-10; Ri is an alkyl, aryl, substituted alkyl, or substituted aryl; R2 is H, an alkyl, aryl, substituted alkyl, and substituted aryl; and R3 is H, an amino acid, a polypeptide, or an amino terminus modification group, and R4 is H, an amino acid, a polypeptide, or a carboxy terminus modification group.
[37] In some embodiments, the non-naturally encoded amino acid comprises an
aminooxy group. In some embodiments, the non-naturally encoded amino acid comprises a hydrazide group. In some embodiments, the non-naturally encoded amino acid comprises a hydrazine group. In some embodiments, the non-naturally encoded amino acid residue comprises a semicarbazide group.

[38] In some embodiments, the non-naturally encoded amino acid residue comprises an
azide group. In some embodiments, the non-naturally encoded amino acid has the structure:
(CHaWWCHaW^
R2HN TK)R3
wherein n is 0-10; Ri is an alkyl, aryl, substituted alkyl, substituted aryl or not present; X is O, N,
S or not present; m is 0-10; R2 is H, an amino acid, a polypeptide, or an amino terminus
modification group, and R3 is H, an amino acid, a polypeptide, or a carboxy terminus modification
group.
[39] In some embodiments, the non-naturally encoded amino acid comprises an alkyne
group. In some embodiments, the non-naturally encoded amino acid has the structure:
(CH^XtCH^CCH
R2HN COR3
wherein n is 0-10; R\ is an alkyl, aryl, substituted alkyl, or substituted aryl; X is O, N, S or not
present; m is 0-10, R2 is H, an amino acid, a polypeptide, or an amino terminus modification
group, and R3 is H, an amino acid, a polypeptide, or a carboxy terminus modification group.
[40] In some embodiments, the polypeptide is a GH, e.g., hGH polypeptide agonist,
partial agonist, antagonist, partial antagonist, or inverse agonist. In some embodiments, the GH, e.g., hGH polypeptide agonist, partial agonist, antagonist, partial antagonist, or inverse agonist comprises a non-naturally encoded amino acid linked to a water soluble polymer. In some embodiments, the water soluble polymer comprises a poly(ethylene glycol) moiety. In some embodiments, the GH, e.g., hGH polypeptide agonist, partial agonist, antagonist, partial antagonist, or inverse agonist comprises a non-naturally encoded amino acid and one or more post-translational modification, linker, polymer, or biologically active molecule. In some embodiments, the non-naturally encoded amino acid linked to a water soluble polymer is present within the Site II region (the region of the protein encompassing the AC helical-bundle face, amino terminal region of helix A and a portion of helix C) of the GH, e.g., hGH polypeptide. In some embodiments, the GH, e.g., hGH polypeptide comprising a non-naturally encoded amino acid linked to a water soluble polymer prevents dimerization of the GH, e.g., hGH polypeptide receptor by preventing the GH, e.g., hGH polypeptide antagonist from binding to a second GH, e.g., hGH polypeptide receptor molecule. In some embodiments, an amino acid other than glycine

is substituted for G120 in SEQ ID NO: 2 (hGH). In some embodiments, arginine is substituted for
G120 in SEQ ID NO: 2. In some embodiments, a non-naturally encoded amino acid is substituted
for G120 in SEQ ID NO: 2. In some embodiments, the non-naturally encoded amino acid linked
to a water soluble polymer is present within the receptor binding region of the GH, e.g., hGH
polypeptide or interferes with the receptor binding of the GH, e.g., hGH polypeptide.
[41] The present invention also provides isolated nucleic acids comprising a
polynucleotide that hybridizes under stringent conditions to SEQ ID NO: 21 or 22 wherein the polynucleotide comprises at least one selector codon. In some embodiments, the selector codon is selected from the group consisting of an amber codon, ochre codon, opal codon, a unique codon, a rare codon, a five-base codon, and a four-base codon.
[42] The present invention also provides methods of making a GH, e.g., hGH
polypeptide linked to a water soluble polymer. In some embodiments, the method comprises contacting an isolated GH, e.g., hGH polypeptide comprising a non-naturally encoded amino acid with a water soluble polymer comprising a moiety that reacts with the non-naturally encoded " amino acid. In some embodiments, the non-naturally encoded amino acid incorporated into the ^ GH, e.g., hGH polypeptide is reactive toward a water soluble polymer that is otherwise unreactive toward any of the 20 common amino acids. In some embodiments, the non-naturally encoded' '.! amino acid incorporated into the GH, e.g., hGH polypeptide is reactive toward a linker, polymer, [43J In some embodiments, the GH, e.g., hGH polypeptide linked to the water soluble
polymer is made by reacting a GH, e.g., hGH polypeptide comprising a carbonyl-containing
amino acid with a polyethylene glycol) molecule comprising an aminooxy, hydrazine, hydrazide
or semicarbazide group. In some embodiments, the aminooxy, hydrazine, hydrazide or
semicarbazide group is linked to the poly(ethylene glycol) molecule through an amide linkage.
[44] In some embodiments, the GH, e.g., hGH polypeptide linked to the water soluble
polymer is. made by reacting a polyethylene glycol) molecule comprising a carbonyl group with a polypeptide comprising a non-naturally encoded amino acid that comprises an aminooxy, hydrazine, hydrazide or semicarbazide group.
[45] In some embodiments, the GH, e.g., hGH polypeptide linked to the water soluble
polymer is made by reacting a GH, e.g., hGH polypeptide comprising an alkyne-containing amino

acid with a poly(ethylene glycol) molecule comprising an azide moiety. In some embodiments,
the azide or alkyne group is linked to the poly(ethylene glycol) molecule through an amide
linkage.
[46] In some embodiments, the GH, e.g., hGH polypeptide linked to the water soluble
polymer is made by reacting a GH, e.g., hGH polypeptide comprising an azide-containing amino
acid with a poly(ethylene glycol) molecule comprising an alkyne moiety. In some embodiments,
the azide or alkyne group is linked to the polyethylene glycol) molecule through an amide
linkage.
[47] In some embodiments, the poly(ethylene glycol) molecule has a molecular weight
of between about 0.1 kDa and about 100 kDa. In some embodiments, the poly(ethylene glycol)
molecule has a molecular weight of between 0.1 kDa and 50 kDa.
[48] In some embodiments, the poly(ethylene glycol) molecule is a branched polymer.
In some embodiments, each branch of the polyethylene glycol) branched polymer has a molecular ;
weight of between 1 kDa and 100 kDa, or between 1 kDa and 50 kDa.
[49] In some embodiments, the water soluble polymer linked to the GH, e.g., hGH
polypeptide comprises a polyalkylene glycol moiety, hi some embodiments, the non-naturally
encoded amino acid residue incorporated into the GH, e.g., hGH polypeptide comprises a carbonyl group, an aminooxy group, a hydrazide group, a hydrazine, a semicarbazide group, an azide group, .
or an alkyne group. In some embodiments, the non-naturally encoded amino acid residue ;
incorporated into the GH, e.g., hGH polypeptide comprises a carbonyl moiety and the water
soluble polymer comprises an aminooxy, hydrazide, hydrazine, or semicarbazide moiety. In some
embodiments, the non-naturally encoded amino acid residue incorporated into the GH, e.g., hGH
polypeptide comprises an alkyne moiety and the water soluble polymer comprises an azide
moiety. In some embodiments, the non-naturally encoded amino acid residue incorporated into
the GH, e.g., hGH polypeptide comprises an azide moiety and the water soluble polymer
comprises an alkyne moiety.
[SO] The present invention also provides compositions comprising a GH, e.g., hGH
polypeptide comprising a non-naturally encoded amino acid and a pharmaceutically acceptable
carrier. In some embodiments, the non-naturally encoded amino acid is linked to a water soluble
polymer.

[51] The present invention also provides cells comprising a polynucleotide encoding the
GH, e.g., hGH polypeptide comprising a selector codon. In some embodiments, the cells comprise an orthogonal RNA synthetase and/or an orthogonal tRNA for substituting a non-naturally encoded amino acid into the GH, e.g., hGH polypeptide.
[52] The present invention also provides methods of making a GH, e.g., hGH
polypeptide comprising a non-naturally encoded amino acid. In some embodiments, the methods comprise culturing cells comprising a polynucleotide or polynucleotides encoding a GH, e.g., hGH polypeptide, an orthogonal RNA synthetase and/or an orthogonal tRNA under conditions to permit expression of the GH, e.g., hGH polypeptide; and purifying the GH, e.g., hGH polypeptide from the cells and/or culture medium.
[53] The present invention also provides methods of increasing therapeutic half-life,
serum half-life or circulation time of GH, e.g., hGH polypeptides. The present invention also provides methods of modulating immunogenicity of GH, e.g;, hGH polypeptides. In some ' embodiments, the methods comprise substituting a non-naturally encoded amino acid for any one or more amino acids in naturally occurring GH, e.g., hGH polypeptides and/or linking the GH, e.g., hGH polypeptide to a linker, a polymer, a water soluble polymer, or a biologically active molecule.
[54] The present invention also provides methods of treating a patient in need of such
treatment with an effective amount of a GH, e.g., hGH molecule of the present invention. In some --
embodiments, the methods comprise administering to the patient a therapeutically-effective1
amount of a pharmaceutical composition comprising a GH, e.g., hGH polypeptide comprising a
non-naturally-encoded amino acid and a pharmaceutical^ acceptable carrier. In some
embodiments, the non-naturally encoded amino acid is linked to a water soluble polymer.
[55] The present invention also provides GH, e.g., hGH polypeptides comprising a
sequence shown in SEQ ID NO: 1, 2,3, or any other GH polypeptide sequence, except that at least one amino acid is substituted by a non-naturally encoded amino acid. In some embodiments, the non-naturally encoded amino acid is linked to a water soluble polymer. In some embodiments, the water soluble polymer comprises a poly(ethylene glycol) moiety. In some embodiments, the non-naturally encoded amino acid comprises a carbonyl group, an aminooxy group, a hydrazide group, a hydrazine group, a semicarbazide group, an azide group, or an alkyne group. In some

embodiments, the non-naturally encoded amino acid is substituted at a position selected from the
group consisting of residues 1-5, 82-90, 117-134, and 169-176 from SEQ ID NO: 3 (hGH).
[56] The present invention also provides pharmaceutical compositions comprising a
pharmaceutical^ acceptable carrier and a GH, e.g., hGH polypeptide comprising the sequence shown in SEQ ID NO: 1,2, 3, or any other GH polypeptide sequence, wherein at least one amino acid is substituted by a non-naturally encoded amino acid. In some embodiments, the non-naturally encoded amino acid comprises a saccharide moiety. In some embodiments, the water soluble polymer is linked to the polypeptide via a saccharide moiety. In some embodiments, a linker, polymer, or biologically active molecule is linked to the GH, e.g., hGH polypeptide via a saccharide.moiety.
[57] The present invention also provides a GH, e.g., hGH polypeptide comprising a
water soluble polymer linked by a covalent bond to the GH, e.g., hGH polypeptide at a single
amino acid. In some embodiments, the water soluble polymer comprises a poly(ethylene glycol)
moiety. In some embodiments, the amino acid covalently linked to the water soluble polymer is a
non-naturally encoded amino acid present in the polypeptide. In some embodiments the non- '/
naturally encoded amino acid is substituted at position 35, 92,143, or 145 of SEQ ID NO 2.
[58] The present invention provides a GH, e.g., hGH polypeptide comprising at least
one linker, polymer, or biologically active molecule, wherein said linker, polymer, or biologically active molecule is attached to the polypeptide through a functional group of a non-naturally encoded amino acid ribosomally incorporated into the polypeptide. In some embodiments, the polypeptide is monoPEGylated. The present invention also provides a GH, e.g., hGH polypeptide comprising a linker, polymer, or biologically active molecule that is attached to one or more non-naturally encoded amino acid wherein said non-naturally encoded amino acid is ribosomally incorporated into the polypeptide at pre-selected sites.
[59] In another embodiment, conjugation of the hGH polypeptide comprising one or
more non-naturally occurring amino acids to another molecule, including but not limited to PEG, provides substantially purified hGH due to the unique chemical reaction utilized for conjugation to the non-natural amino acid. Conjugation of hGH comprising one or more non-naturally encoded amino acids to another molecule, such as PEG, may be performed with other purification techniques performed prior to or following the conjugation step to provide substantially pure hGH.

[60] The present invention further provides a hormone composition containing a growth
hormone (GH) linked to at least one water-soluble polymer by a covalent bond, where the covalent bond is an oxime bond In some embodiments, the GH is a human growth hormone (hGH), such as a sequence that is at least about 80% identical to SEQ ID NO: 2; in some embodiments the sequence is the sequence of SEQ ID NO: 2. The GH can include one or more non-naturally encoded amino acids (NEAAs), such as a NEAA that includes a carbonyl group, e.g., a ketone, such as an NEAA that is para-acetylphenylalanine. In some embodiments the oxime bond is between the NEAA and the water-soluble polymer. The GH can be substituted with a para-acetylphenylalanine at a position corresponding to position 35 of SEQ ID NO: 2. In some embodiments, the water-soluble polymer includes one or more polyethylene glycol (PEG) molecules. The PEG can be linear, e.g., a linear PEG of MW of about 0.1 and about 100 kDa, or about 1 and about 60 kDa, or about 20 and about 40 kDa, or about 30 kDa. In some embodiments, the PEG is a branched PEG, e.g., a branched PEG that has a molecular weight between about 1 and about 100 kDa, or about 30 and about 50 kDa, or about 40 kDa. In some embodiments the GH is linked by a plurality of covalent bonds to a plurality of water-soluble polymers, where at least one of the covalent bonds are oxime bonds. In some of these embodiments, the GH is a human growth hormone (GH, e.g., hGH), e.g., a GH, e.g., hGH with a sequence that is at least about 80% identical to SEQ ID NO: 2; in some embodiments the sequence is that of SEQ ID NO: 2. In some embodiments in which the GH, e.g., hGH, is linked to a plurality of water-soluble polymers, the GH comprises a plurality of NEAAs.
[61] In certain embodiments, the invention provides a GH composition that contains a
GH, e.g., hGH that comprises the sequence of SEQ ID NO: 2, where the GH, e.g., hGH is linked
via an oxime bond to a 30 kDa linear PEG, and where the oxime bond is formed with a para-
acetylphenylalanine substituted at a position corresponding to position 35 of SEQ ID NO: 2.
[62] In some embodiments, the invention provides a hormone composition containing a
GH, e.g., hGH linked via an oxime bond to at least one linear PEG, where the GH, e.g., hGH comprises the amino acid sequence of SEQ ID NO: 2 and contains at least one NEAA substituted at one or more positions selected from the group consisting of residues 1-5, 6-33, 34-74, 75-96, 97-105, 106-129, 130-153, 154-183, and 184-191. Li some embodiments, the NEAA(s) is substituted at one or more positions selected from the group consisting of residues before position 1 (i.e. at the N-tenninus), 1, 2, 3, 4, 5, 8, 9, 11, 12, 15, 16, 19, 22, 29, 30, 32, 33, 34, 35, 36, 37,

38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 55, 57, 59, 65, 66, 69, 70, 71, 74, 88, 91, 92, 94,
95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 111, 112, 113, 115, 116, 119,
120, 122, 123, 126, 127, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,
143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 159, 161, 168, 172,
183,184,185, 186,187, 188, 189,190,191, and 192 (i.e., at the carboxyl terminus of the protein).
In some embodiments, the NEAA(s) is substituted at one or more positions selected from the
group consisting of residues 35, 92, 131,134, 143, and 145. In some embodiments, theNEAA(s)
is substituted at one or more positions selected from the group consisting of residues 30, 35, 74,
92,103,143, and 145. In some embodiments, theNEAA(s) is substituted at one or more positions
selected from the group consisting of residues 35, 92, 143, and 145. In some embodiments, the
NEAA is substituted at position 35. At least one of the NEAA is a para-acetylphenylalanine in
some embodiments. In some embodiments, the PEG has a molecular weight between about 0.1
and about 100 kDa, or about 1 and about 60 kDa, or about 20 and about 40 kDa, or about 30 kDa.
[63] hi yet other embodiments, the invention provides a method of making a GH, e.g.,
hGH linked via an oxime bond to a water-soluble polymer comprising contacting a GH, e.g., hGH -that comprises a NEAA comprising a carbonyl group with a PEG oxyamine under conditions •'■ suitable for formation of an oxime bond. The NEAA can contain a ketone group, e.g., a caibonyl. "■' The NEAA can be para-acetylphenylalanine. In some embodiments containing a para-acetylphenylalanine, the para-acetylphenylalanine is substituted at a position in the GH, e.g., hGH ; corresponding to amino acid 35 in SEQ ID NO: 2. In some embodiments, the PEG oxyamine is a monomethoxyPEG (MPEG) oxyamine. In some embodiments, the MPEG oxyamine is linear, e.g., a linear MPEG of about 20-40 kDa, or about 30 kDa. In some embodiments, the MPEG oxyamine is a linear 30 kDa monomethoxy-PEG-2-aminooxy ethylamine carbamate hydrochloride, hi some embodiments, the GH, e.g., hGH comprising an NEAA is made by introducing (i) a nucleic acid encoding a GH, e.g., hGH wherein the nucleic acid has been modified to provide a selector codon for incorporation of the NEAA; and (ii) the NEAA; to an organism whose cellular machinery is capable of incorporating the NEAA into a protein in response to the selector codon of the nucleic acid of (i). In some embodiments, the reaction conditions for forming the oxime bond include mixing the MPEG and GH, e.g., hGH to produce a MPEG-GH, e.g., hGH mixture with a MPEG.GH, e.g., hGH ratio of about 5 to 10, a pH of about 4 to 6; and gentle stirring of the MPEG-GH, e.g., MPEG-hGH mixture for about 10 to 50 hours at room temperature. In some

embodiments, the method further includes purifying the GH, e.g., hGH, e.g., to at least about 99% pure.
[64] Cellular machinery includes, but is not limited to, an orthogonal tRNA and/or
aminoacyl tRNA synthetase.
[65] In still yet further embodiments, the invention provides a pharmaceutical
composition that contains a hormone composition comprising a growth hormone linked by a covalent bond to at least one water-soluble polymer, wherein the covalent bond is an oxime bond, and a pharmaceutically acceptable excipient In some embodiments, the GH is a GH, e.g., hGH. In some embodiments, the GH comprises a NEAA. In some embodiments, the water-soluble polymer comprises a PEG, such as a linear PEG. In some embodiments the PEG is a linear PEG of about 30 kDa and the GH is an GH, e.g., hGH substituted at a position corresponding to amino acid 35 of SEQ ID NO: 2 with a para-acetylphenylalanine, and the oxime bond is formed between the para-acetylphenylalanine and the PEG.
[66] In some embodiments, the invention provides a method of treatment by *
administering to an individual in need of treatment an effective amount of a hormone composition H containing a growth hormone (GH) linked by covalent bond(s) to at least one water-soluble *: polymer, where the covalent bond(s) is an oxime bond. In some embodiments, the GH is hGH. In . some embodiments, the GH comprises a NEAA. In. some embodiments, the water-soluble * polymer comprises a PEG, such as a linear PEG. In some embodiments, the PEG is a linear PEG of about 30 kDa and the GH is hGH substituted at a position corresponding to amino acid 35 of SEQ ID NO: 2 with a para-acetylphenylalanine, and the oxime bond is formed between the para-acetylphenylalanine and the PEG. In some embodiments, the individual that is treated is a human. In some embodiments, the individual that is treated suffers from pediatric growth hormone deficiency, idiopathic short stature, adult growth hormone deficiency of childhood onset, adult growth hormone deficiency of adult onset, or secondary growth hormone deficiency. In some embodiments, the GH is hGH. In some embodiments, the GH comprises a NEAA. In some embodiments, the water-soluble polymer comprises a PEG, such as a linear PEG. In some embodiments, the PEG is a linear PEG of about 30 kDa and the GH e.g., hGH substituted at a position corresponding to amino acid 35 of SEQ ID NO: 2 with a para-acetylphenylalanine, and the oxime bond is formed between the paTa-acetylphenylalanine and the PEG.

[67] In some embodiments, the invention provides a method of treatment by
administering to an individual in need of treatment an effective amount of a hormone composition
comprising a growth hormone (GH) linked by covalent bond(s) to at least one water-soluble
polymer, where the water-soluble polymer is a linear polymer, and where the hormone
composition is given at a frequency of no more than once per week, once per two weeks, or once
per month. In some embodiments, the polymer is a PEG. In some embodiments, the GH
comprises a NEAA In some embodiments, the polymer is linked to the GH via an oxime bond.
[68] In some embodiments, the invention provides a hormone composition comprising a
GH, e.g., hGH, wherein the GH, e.g., hGH has an average serum half-life of at least about 12 hours when administered to a mammal subcutaneously. In some embodiments, the GH, e.g., hGH comprises a NEAA. In some embodiments, the hormone composition further contains a water-soluble polymer, such as a PEG, e.g., a linear PEG.
[69] In some embodiments, the invention provides a hormone composition comprising a
GH, e.g., hGH linked to a PEG, wherein the GH, e.g., hGH has an average serum half-life of at least about 7-fold the serum half-life of a composition comprising the GH, e.g., hGH without the PEG, when administered to a mammal subcutaneously.
BRIEF DESCRIPTION OF THE DRAWINGS
[70] Figure 1 - A diagram of the general structure for four helical bundle proteins is
shown.
[71] Figure 2 - A diagram of the general structure for the four helical bundle protein
Growth Hormone (GH) is shown.
[72] Figure 3 - A diagram of the general structure for the four helical bundle protein
Erythropoietin (EPO) is shown.
[73] Figure 4 - A diagram of the general structure for the four helical bundle protein
Interferon alpha-2 (IFNa-2) is shown.
[74] Figure 5 - A diagram of the general structure for the four helical bundle protein
Granulocyte Colony Stimulating Factor (G-CSF) is shown.
[75] Figure 6 - A Coomassie blue stained SDS-PAGE is shown demonstrating the
expression of hGH comprising the non-naturally encoded amino acid p-acetyl phenylalanine at
each of the following positions: Y35, F92, Yl 11, G131, R134, K140, Y143, or K145.

[76] Figure 7, Panels A and B - A diagram of the biological activity of the hGH
comprising a non-naturally encoded amino acid (Panel B) and wild-type hGH (Panel A) on IM9
cells is shown.
[771 Figure 8 - A Coomassie blue stained SDS-PAGE is shown demonstrating the
production of hGH comprising a non-naturally encoded amino acid that is PEGylated by covalent
linkage of PEG (5,20 and 30 kDa) to the non-naturally encoded amino acid.
[78] Figure 9 - A diagram is shown demonstrating the biological activity of the various
PEGylated forms of hGH comprising a non-naturally encoded amino acid on IM9 cells.
[79] Figure 10, Panel A - This figure depicts the primary structure of hGH with the
trypsin cleavage sites indicated and the non-natural amino acid substitution, F92pAF, specified
with an arrow (Figure modified from Becker et al. Biotechnol Appl Biochem. (1988) 10(4):326-
337). Figure 10, Panel B — Superimposed tryptic maps are shown of peptides generated from a
hGH polypeptide comprising a non-naturally encoded amino acid that is PEGylated (labeled A),
peptides generated from a hGH polypeptide comprising a non-naturally encoded amino acid
(labeled B), and peptides generated from WHO rhGH (labeled C). Figure 10, Panel C - A
magnification of peak 9 from Panel B is shown.
[80] Figure 11, Panel A and Panel B show Coomassie blue stained SDS-PAGE analysis
of purified PEG-hGH polypeptides.
[81] Figure 12 - A diagram of the biological activity of a hGH dimer molecule on IM9
cells is shown.
[82] Figure 13, Panel A - A diagram is shown of the IM-9 assay data measuring
phosphorylation of pSTAT5 by hGH antagonist with the G120R substitution. Figure 13, Panel B
- A diagram is shown of the IM-9 assay data measuring phosphorylation of pSTAT5 by a hGH
polypeptide with a non-natural amino acid incorporated at the same position (G120).
[83] Figure 14 — A diagram is shown indicating that a dimer of the hGH antagonist
shown in Figure 13, Panel B also lacks biological activity in fee IM-9 assay.
[84] Figure 15 — A diagram is shown comparing the serum half-life in rats of hGH
polypeptide comprising a non-naturally encoded amino acid that is PEGylated with hGH
polypeptide that is not PEGylated.
[85] Figure 16 - A diagram is shown comparing the serum half-life in rats of hGH
polypeptides comprising a non-naturally encoded amino acid that is PEGylated.

[86] Figure 17 - A diagram is shown comparing the serum half-life in rats of hGH
polypeptides comprising a non-naturally encoded amino acid that is PEGylated. Rats were dosed once with 2.1 mg/kg.
[87] Figure 18, Panel A - A diagram is shown of the effect on rat body weight gain after
administration of a single dose of hGH polypeptides comprising a non-naturally encoded amino acid that is PEGylated (position 35, 92). Figure 18, Panel B - A diagram is shown of the effect on circulating plasma IGF-1 levels after administration of a single dose of hGH polypeptides comprising a non-naturally encoded amino acid that is PEGylated (position 35, 92). Figure 18, Panel C - A diagram is shown of the effect on rat body weight gain after administration of a single dose of hGH polypeptides comprising a non-naturally encoded amino acid that is PEGylated (position 92, 134, 145, 131, 143). Figure 18, Panel D - A diagram is shown of the effect on circulating plasma IGF-1 levels after administration of a single dose of hGH polypeptides comprising a non-naturally encoded amino acid that is PEGylated (position 92, 134, 145, 131, 143). Figure 18, Panel E - A diagram is shown comparing the serum half-life in rats of hGH polypeptides comprising a non-naturally encoded amino acid that is PEGylated (position 92, 134, 145, 131, 143).
[88] Figure 19 — A diagram is shown of the structure of linear, 30 kDa monomethoxy-
poly(ethylene glycol)-2-aminooxy ethylamine carbamate hydrochloride.
[89] Figure 20- A diagram is shown illustrating synthesis of carbamate-linked
oxyamino-derivatized PEG
[90] Figure 21 presents illustrative, non-limiting examples of PEG-containing reagents
that can be used to modify non-natural amino acid polypeptides to form PEG-containing, oxime-linked non-natural amino acid polypeptides.
[91] Figure 22 presents illustrative, non-limiting examples of the synthesis of PEG-
containing reagents that can be used to rciodify non-natural amino acid polypeptides to form PEG-containing, oxime-linked non-natural amino acid polypeptides.
[92] Figure 23 presents an illustrative, non-limiting example of the synthesis of an
amide-based hydroxylamine PEG-containing reagent that can be used to modify non-natural amino acid polypeptides to form PEG-containing, oxime-linked non-natural amino acid polypeptides.

[93] Figure 24 presents an illustrative, non-limiting example of the synthesis of a
carbamate-based PEG-containing reagent that can be used to modify non-natural amino acid
polypeptides to form PEG-containing, oxime-linked non-natural amino acid polypeptides.
[94] Figure 25 presents an illustrative, non-limiting example of the synthesis of a
carbamate-based PEG-containing reagent that can be used to modify non-natural amino acid
polypeptides to form PEG-containing, oxime-linked non-natural amino acid polypeptides.
[95] Figure 26 presents illustrative, non-limiting examples of the synthesis of simple
PEG-containing reagents that can be used to modify non-natural amino acid polypeptides to form
PEG-containing, oxime-linked non-natural amino acid polypeptides.
[96] Figure 27 presents illustrative, non-limiting examples of branched PEG-containing
reagents that can be used to modify non-natural amino acid polypeptides to form PEG-containing,
oxime-linked non-natural amino acid polypeptides, and the use of one such reagent to modify a
carbonyl-based non-natural amino acid polypeptide.
[97] Figure 28 presents a graph illustrating IGF-1 plasma concentration in
hypophysectomized rats treated weekly with placebo or increasing dose of PEG-ahGH, or daily
with placebo or Genotropin.
[98] Figure 29 presents a graph illustrating tibial bone length in hypophysectomized rats
treated weekly with placebo or PEG-BhGH, or daily with placebo or Genotropin.
[99] Figure 30 presents a graph illustrating percent bodyweight change in
hyposphysectomized rats treated weekly with placebo or PEG-ahGH, or daily with placebo or
Genotropin.
[100] Figure 31 presents a graph illustrating plasma concentration versus time for PEG-
TiGH administered subcutaneously on days 0 and 7.
[101] Figure 32 presents a graph illustrating plasma concentration versus time for PEG-
a(met)hGH administered as a single subcutaneous or intravenous dose.
DEFINITIONS
[102] It is to be understood that this invention is not limited to the particular
methodology, protocols, cell lines, constructs, and reagents described herein and as such may vary. It is also to be understood that the terminology used herein is for the purpose of describing

particular embodiments only, and is not intended to limit the scope of the present invention, which will be limited only by the appended claims.
[103) As used herein and in the appended claims, the singular forms "a," "an," and "the"
include plural reference unless the context clearly indicates otherwise. Thus, for example, reference to a "hGH" is a reference to one or more such proteins and includes equivalents thereof known to those of ordinary skill in the art, and so forth.
1104] Unless defined otherwise, all technical and scientific terms used herein have the
same meaning as commonly understood to one of ordinary skill in the art to which this invention belongs. Although any methods, devices, and materials similar or equivalent to those described herein can be used in the practice or testing of the invention, the preferred methods, devices and materials are now described.
[105] All publications and patents mentioned herein are incorporated herein by reference
for the purpose of describing and disclosing, for example, the constructs and methodologies that are described in the publications, which might be used in connection with the presently described invention. The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention or for any other reason.
[106] The term "substantially purified" refers to a GH, e.g., hGH polypeptide that may be
substantially or essentially free of components that normally accompany or interact with the protein as found in its naturally occurring environment, i.e. a native cell, or host cell in the case of recombinantly produced GH, e.g., hGH polypeptides. GH, e.g., hGH polypeptide that may be substantially free of cellular material includes preparations of protein having less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 10%, less than' about 5%, less than about 4%, less than about 3%, less than about 2%, or less than about 1% (by dry weight) of contaminating protein. When the GH, e.g., hGH polypeptide or variant thereof is recombinantly produced by the host cells, the protein may be present at about 30%, about 25%, about 20%, about 15%, about 10%, about 5%, about 4%, about 3%, about 2%, or about 1% or less of the dry weight of the cells. When the GH, e.g., hGH polypeptide or variant thereof is recombinantly produced by the host cells, the protein may be present in the culture medium at about 5g/L, about 4g/L, about 3g/L, about 2g/L, about Ig/L, about 750mg/L, about 500mg/L,

about 250mg/L, about lOOmg/L, about 50mg/L, about lOmg/L, or about lmg/L or less of the dry weight of the cells. Thus, "substantially purified" GH, e.g., hGH polypeptide as produced by the methods of the present invention may have a purity level of at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, specifically, a purity level of at least about 75%, 80%, 85%, and more specifically, a purity level of at least about 90%, a purity level of at least about 95%, a purity level of at least about 99% or greater as determined by appropriate methods such as SDS/PAGE analysis, RP-HPLC, SEC, and capillary electrophoresis.
[107} A "recombinant host cell" or "host cell" refers to a cell that includes an exogenous
polynucleotide, regardless of the method used for insertion, for example, direct uptake, transduction, f-mating, or other methods known in the art to create recombinant host cells. The exogenous polynucleotide may be maintained as a nonintegrated vector, for example, a plasmid, or alternatively, may be integrated into the host genome.
[108] As used herein, the term "medium" or "media" includes any culture medium,
solution, solid, semi-solid, or rigid support that may support or contain any host cell, including
bacterial host cells, yeast host cells, insect host cells, plant host cells, eukaryotic host cells,
mammalian host cells, CHO cells, prokaryotic host cells, E. coli, or Pseudomonas host cells, and
cell contents. Thus, the term may encompass medium in which the host cell has been grown, e.g.,
medium into which the GH, e.g., hGH polypeptide has been secreted, including medium either
before or after a proliferation step. The term also may encompass buffers or reagents that contain
host cell lysates, such as in the case where the GH, e.g., hGH polypeptide is produced
intracellularly and the host cells are lysed or disrupted to release the GH, e.g., hGH polypeptide.
[109] "Reducing agent," as used herein with respect to protein refolding, is defined as any
compound or material which maintains sulfhydryl groups in the reduced state and reduces intra- or intermolecular disulfide bonds. Suitable reducing agents include, but are not limited to, dithiothreitol (DTT), 2-mercaptoethanol, dithioerythritol, cysteine, cysteamine (2-aminoethanethiol), and reduced glutathione. It is readily apparent to those of ordinary skill in the art that a wide variety of reducing agents are suitable for use in the methods and compositions of , the present invention.
[110] "Oxidizing agent," as used hereinwith respect to protein refolding, is defined as any
compound or material which is capable of removing an electron from a compound being oxidized.

Suitable oxidizing agents include, but are not limited to, oxidized glutathione, cystine, cystamine, oxidized dithiothreitol, oxidized erythreitol, and oxygen. It is readily apparent to those of ordinary skill in the art that a wide variety of oxidizing agents are suitable for use in the methods of the present invention,
[111] "Denaturing agent" or "denaturant," as used herein, is defined as any compound or
material which will cause a reversible unfolding of a protein. The strength of a denaturing agent
or denaturant will be determined both by the properties and the concentration of the particular
denaturing agent or denaturant. Suitable denaturing agents or denaturants may be chaotropes,
detergents, organic solvents, water miscible solvents, phospholipids, or a combination of two or
more such agents. Suitable chaotropes include, but are not limited to, urea, guanidine, and sodium
thiocyanate. Useful detergents may include, but are not limited to, strong detergents such as
sodium dodecyl sulfate, or polyoxyethylene ethers (e.g. Tween or Triton detergents), Sarkosyl,
mild non-ionic detergents (e.g., digitonin), mild cationic detergents such as N->2,3-
(Dioleyoxy)-propyl-N,N,N-tximethylammomum, mild ionic detergents (e.g. sodium cholate or sodium deoxycholate) or zwitterionic detergents including, but not limited to, sulfobetaines (Zwittergent), 3-(3-chlolamidopropyl)dimethylammonio-l-propane sulfate (CHAPS), and 3-(3» chlolamidopropyl)dimefliylammonio-2-hydroxy-l-propane sulfonate (CHAPSO). Organic, water miscible solvents such as acetonitrile, lower alkanols (especially C2 - C4 alkanols such as ethanol or isopropanol), or lower alkandiols (especially C2 - C4 alkandiols such as ethylene-glycol) maybe used as denaturants. Phospholipids useful in the present invention may be naturally occurring phospholipids such as phosphatidylethanolamine, phosphatidylcholine, phosphatidylserine, and phosphatidylinositol or synthetic phospholipid derivatives or variants such as . dihexanoylphosphatidylcholine or diheptanoylphosphatidylcholine.
[112] "Refolding," as used herein describes any process, reaction or method which
transforms disulfide bond containing polypeptides from an improperly folded or unfolded state to a native or properly folded conformation with respect to disulfide bonds.
[113] "Cofolding," as used herein, refers specifically to refolding processes, reactions, or
methods which employ at least two polypeptides which interact with each other and result in the transformation of unfolded or improperly folded polypeptides to native, properly folded polypeptides.

[114] As used herein, "growth hormone" or "GH" shall include those polypeptides and
proteins that have at least one biological activity of a growth hormone from any mammalian
species including but not limited to, human (hGH), bovine (bGH), porcine, and from other
livestock or farm animals including but not limited to, chicken, as well as GH analogs, GH
isoforms, GH mimetics, GH fragments, hybrid GH proteins, fusion proteins, oligomers and
multimers, homologies, glycosylation pattern variants, variants, splice variants, and muteins,
thereof regardless of the biological activity of same, and further regardless of the method of
synthesis or manufacture thereof including, but not limited to, recombinant (whether produced
from cDNA, genomic DNA, synthetic DNA or other form of nucleic acid), in vitro, in vivo, by
microinjection of nucleic acid molecules, synthetic, transgenic, and gene activated methods.
[115] The term "hGH polypeptide" encompasses hGH polypeptides comprising one or
more amino acid substitutions, additions or deletions. Exemplary substitutions include, e.g., substitution of the lysine at position 41 or the phenylalanine at position 176 of native hGH. It some cases, the substitution may be an isoleucine or arginine residue if die substitution is ai position 41 or is a tyrosine residue if the position is 176. Position F10 can be substituted with e.g., A, H or I. Position M14 may be substituted with, e.g., W, Q or G. Other exemplar) substitutions include any substitutions or combinations thereof including but not limited to: R167N, D171S, E174S, F176Y, I179T; R167E, D171S, E174S, F176Y; F10A, M14W, H18D, H21N;
F10A, M14W, H18D, H21N, R167N, D171S, E174S, F176Y, I179T; F10A, M14W, H18D, H21N, R167N, D171A, E174S, F176Y, I179T; F10H, M14G, H18N, H21N;
F10A, M14W, H18D, H21N, R167N, D171A, T175T, I179T; or
F10I, M14Q, H18E, R167N, D171S, I179T. See, eg., U.S. Patent No. 6,143,523, which is incorporated by reference herein.
[116] Exemplary substitutions in a wide variety of amino acid positions in naturally-
occurring hGH have been described, including substitutions that increase agonist activity, increase protease resistance, convert the polypeptide into an antagonist, etc. and are encompassed by the term "hGH polypeptide."

[117] Agonist GH, e.g., hGH sequences include, e.g., the naturally-occurring hGH
sequence comprising the following modifications H18D, H21N, R167N, D171S, E174S, I179T. See, e.g., U.S. Patent No. 5,849,535, which is incorporated by reference herein. Additional agonist hGH sequences include
H18D, Q22A, F25A, D26A, Q29A, E65A, K168A, E174S; H18A, Q22A, F25A, D26A, Q29A, E65A, K168A, E174S; or
H18D, Q22A, F25A, D26A, Q29A, E65A, K168A, E174A. See, e.g. U.S. Patent 6,022,711, which is incorporated by reference herein. hGH polypeptides comprising substitutions at H18A, Q22A, F25A, D26A, Q29A, E65A, K168A, E174A enhance affinity for the hGH receptor at site I. See, e.g. U.S. Patent 5,854,026, which is incorporated by reference herein. hGH sequences with increased resistance to proteases include, but are not limited to, hGH polypeptides comprising one or more amino acid substitutions within the C-D loop. In some embodiments, substitutions include, but are not limited to, R134D, T135P, K140A, and any combination thereof. See, e.g, Alam etal (1998) J. BiotechnoL 65:183-190. .
[118] Human Growth Hormone antagonists include, e.g., those with a substitution at
G120 (e.g., G120R, G120K, G120W, G120Y, G120F, or G120E) and sometimes further including the following substitutions: H18A, Q22A, F25A, D26A, Q29A, E65A, K168A, E174A. See, e.g. U.S. Patent No. 6,004,931, which is incorporated by reference herein. In some embodiments, hGH antagonists comprise at least one substitution in the regions 106-108 or 127-129 that cause GH to act as an antagonist. See, e.g., U.S. Patent No. 6,608,183, which is incorporated by reference herein. In some embodiments, the hGH antagonist comprises a non-naturally encoded amino acid linked to a water soluble polymer that is present in the Site II binding region of the hGH molecule. In some embodiments, the hGH polypeptide further comprises the following substitutions: H18D, H21N, R167N, K168A, D171S, K172R, E174S, I179T with a substitution at G120. (See, e.g, U.S. Patent 5,849,535)
[119] For the complete full-length naturally-occurring human GH amino acid sequence as
well as the mature naturally-occurring GH amino acid sequence and naturally occurring mutant, see SEQ ID NO: 1, SEQ ID NO: 2 and SEQ ID NO: 3, respectively, herein. In some embodiments, GH polypeptides e.g., hGH polypeptides of the invention are substantially identical to SEQ ID NO: 1, or SEQ ID NO: 2, or SEQ ID NO: 3 or any other sequence of a growth hormone polypeptide. For example, in some embodiments, GH polypeptides e.g., hGH

polypeptides of the invention are at least about 60%, at least about 65%, at least about 70%, at
least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% or
at least about 99% identical to SEQ ID NO: 1, or SEQ ED NO: 2, or SEQ ID NO: 3 or any other
sequence of a growth hormone polypeptide. In some embodiments, GH polypeptides e.g., hGH
polypeptides of the invention are at least about 60%, at least about 65%, at least about 70%, at
least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% or
at least about 99% identical to SEQ ID NO: 2. A number of naturally occurring mutants of hGH
have been identified. These include hGH-V (Seeburg, DNA 1: 239 (1982); U.S. Patent. Nos.
4,446,235, 4,670,393, and 4,665,180, which are incorporated by reference herein) and a 20-kDa
hGH containing a deletion of residues 32-46 of hGH (SEQ ID NO: 3) (Kostyo et aL, Biochem.
Biophys. Acta 925: 314 (1987); Lewis, U., et aL, J. Biol Chem., 253:2679-2687 (1978)). Placental
growth hormone is described in Igout, A., et aL, Nucleic Acids Res. 17(10):3998 (1989)). Iu
addition, numerous hGH variants, arising from post-transcriptional, post-translational, secretory,
metabolic processing, and other physiological processes, have been reported including
proteolytically cleaved or 2 chain variants (Baumann, G., Endocrine Reviews 12: 424 (1991)).
hGH dimers linked directly via Cys-Cys disulfide linkages are described in Lewis, U. J., et aL, J.
Biol Chem. 252:3697-3702 (1977); Brostedt, P. and Roos, P., Prep. Biochem. 19:217-229
(1989)). Nucleic acid molecules encoding hGH mutants and mutant hGH polypeptides are well
known and include, but are not limited to, those disclosed in U.S. Patent Nos.: 5,534,617;
5,580,723; 5,688,666; 5,750,373; 5,834,250; 5,834,598; 5,849,535; 5,854,026; 5,962,411;
5,955,346; 6,013,478; 6,022,711; 6,136,563; 6,143,523; 6,428,954; 6,451,561; 6,780,613 and U.S.
Patent Application Publication 2003/0153003; which are incorporated by reference herein.
[120] Commercial preparations of hGH are sold under the names: Humatrope™ (Eli Lilly
& Co.), Nutropin™ (Genentech), Norditropin™ (Novo-Nordisk), Genotropin™ (Pfizer) and Saizen/Serostim™ (Serono).
[121] The term tchGH polypeptide" also includes the pharmaceutically acceptable salts
and prodrugs, and prodrugs of the salts, polymorphs, hydrates, solvates, biologically-active fragments, biologically active variants and stereoisomers of the naturally-occurring hGH as well as agonist, mimetic, and antagonist variants of the naturally-occurring hGH and polypeptide fusions thereof. Fusions comprising additional amino acids at the amino terminus, carboxyl terminus, or both, are encompassed by the term "hGH polypeptide." Exemplary fusions include,

but are not limited to, e.g., methionyl growth hormone in which a methionine is linked to the N-
terminus of hGH resulting from the recombinant expression of the mature form of hGH lacking
the secretion signal peptide or portion thereof, fusions for the purpose of purification (including,
but not limited to, to poly-histidine or affinity epitopes), fusions with serum albumin binding
peptides and fusions with serum proteins such as serum albumin. U.S. Patent No. 5,750,373,
which is incorporated by reference herein, describes a method for selecting novel proteins such as
growth hormone and antibody fragment variants having altered binding properties for their
respective receptor molecules. The method comprises fusing a gene encoding a protein of interest
to the carboxy terminal domain of the gene HI coat protein of the filamentous phage M13.
[122] Various references disclose modification of polypeptides by polymer conjugation
or glycosylation. The term "hGH polypeptide" includes polypeptides conjugated to a polymer
such as PEG and may be comprised of one or more additional derivitizations of cysteine, lysine, or
other residues. In addition, the hGH polypeptide may*comprise a linker or polymer, wherein the
amino acid to which the linker or polymer is conjugated may be a non-natural amino acid
according to the present invention, or may be conjugated to a naturally encoded amino acid ■
utilizing techniques known in the art such as coupling to lysine or cysteine.
[1231 Polymer conjugation of hGH polypeptides has been reported. See, e.g. U.S. Pat.
Nos. 5,849,535, 6,136,563 and 6,608,183, which are incorporated by reference herein. U.S. Pat No. 4,904,584 discloses PEGylated lysine depleted polypeptides, wherein at least one lysine residue has been deleted or replaced with any other amino acid residue. WO 99/67291 discloses a process for conjugating a protein with PEG, wherein at least one amino acid residue on the protein is deleted and the protein is contacted with PEG under conditions sufficient to achieve conjugation to the protein. WO 99/03887 discloses PEGylated variants of polypeptides belonging to the growth hormone superfamily, wherein a cysteine residue has been substituted with a non-essential amino acid residue located in a specified region of the polypeptide. WO 00/26354 discloses a method of producing a glycosylated polypeptide variant with reduced allergenicity, which as compared to a corresponding parent polypeptide comprises at least one additional glycosylation site. U.S. Pat No. 5,218,092, which is incorporated by reference herein, discloses modification of granulocyte colony stimulating factor (G-CSF) and other polypeptides so as to introduce at least one additional carbohydrate chain as compared to the native polypeptide.

[124] The term "hGH polypeptide" also includes glycosylated hGH, as well as but not
limited to, polypeptides glycosylated at any amino acid position, N-linked or O-linked glycosylated forms of the polypeptide. Variants containing single nucleotide changes are also considered as biologically active variants of hGH polypeptide. In addition, splice variants are also included. The term "hGH polypeptide" also includes GH, e.g., hGH polypeptide heterodimers, homodimers, heteromultimers, or homomultimers of any one or more GH, e.g., hGH polypeptides or any other polypeptide, protein, carbohydrate, polymer, small molecule, linker, ligand, or other biologically active molecule of any type, linked by chemical means or expressed as a fusion protein, as well as polypeptide analogues containing, for example, specific deletions or other modifications yet maintain biological activity.
[125] All references to amino acid positions in GH, e.g., hGH described herein are based
on the position in SEQ ID NO: 2, unless otherwise specified (i.e., when it is stated that the comparison is based on SEQ ID NO: 1, 3, or other hGH sequence). Those of skill in the art will appreciate that amino acid positions corresponding to positions in SEQ ID NO: 1, 2, 3, or any other GH sequence can be readily identified in any other GH, e.g., hGH molecule such as GH, or ! hGH fusions, variants, fragments, etc. For example, sequence alignment programs such as '■' BLAST can be used to align and identify a particular position in a protein that corresponds with a ' * position in SEQ ID NO: 1, 2, 3, or other GH sequence. Substitutions, deletions or additions of v [126] The term "hGH polypeptide" or "hGH" encompasses hGH polypeptides
comprising one or more amino acid substitutions, additions or deletions. hGH polypeptides of the present invention may be comprised of modifications with one or more natural amino acids in conjunction with one or more non-natural amino acid modification. Exemplary substitutions in a wide variety of amino acid positions in naturally-occurring hGH polypeptides have been described, including but not limited to substitutions that modulate one or more of the biological activities of the hGH polypeptide, such as but not limited to, increase agonist activity, increase solubility of the polypeptide, decrease protease susceptibility, convert the polypeptide into an antagonist, etc. and are encompassed by the term " hGH polypeptide."

[127] Human GH antagonists include, but are not limited to, those with substitutions at:
1, 2, 3,4, 5, 8,9, 11,12, 15,16, 19, 22, 103,109,112,113,115,116,119,120, 123, and 127 or an addition at position 1 (i.e., at the N-terminus), or any combination thereof (SEQ ID NO:2, or the corresponding amino acid in SEQ ID NO: 1, 3, or any other GH sequence). In some embodiments, hGH antagonists comprise at least one substitution in the regions 1-5 (N-terminus), 6-33 (A helix), 34-74 (region between A helix and B helix, the A-B loop), 75-96 (B helix), 97-105 (region between B helix and C helix, the B-C loop), 106-129 (C helix), 130-153 (region between C helix and D helix, the C-D loop), 154-183 (D helix), 184-191 (C-terminus) that cause GH to act as an antagonist. In other embodiments, the exemplary sites of incorporation of a non-naturally encoded amino acid include residues within the amino terminal region of helix A and a portion of helix C. In another embodiment, substitution of G120 with a non-naturally encoded amino acid such as p-azido-L-phenyalanine or O-propargyl-L-tyrosine. In other embodiments, the above-listed substitutions are combined with additional substitutions that cause the hGH polypeptide to be an hGH antagonist. For instance, a non-naturally encoded amino acid is substituted at one of the positions identified herein and a simultaneous substitution is introduced at G120 (e.g., G120R, |f G120K, G120W, G120Y, G120F, or G120E). In some embodiments, the hGH antagonist t comprises a non-naturally encoded amino acid linked to a'water soluble polymer that is present in 7'-a receptor binding region of the hGH molecule.
[128] In some embodiments, the GH, e.g., hGH polypeptides further comprise an
addition, substitution or deletion that modulates biological activity of the GH or hGH polypeptide. For example, the additions, substitutions or deletions may modulate one or more properties or activities of GH, e.g., hGH. For example, the additions, substitutions or deletions may modulate affinity for the GH, e.g., hGH polypeptide receptor, modulate (including but not limited to, increases or decreases) receptor dimerization, stabilize receptor dimers, circulating half-life, modulate therapeutic half-life, modulate stability of the polypeptide, modulate cleavage by proteases, modulate dose, modulate release or bio-availability, facilitate purification, or improve or alter a particular route of administration. Similarly, GH, e.g., hGH polypeptides may comprise protease cleavage sequences, reactive groups, antibody-binding domains (including but not limited to, FLAG or poly-His) or other affinity based sequences (including but not limited to, FLAG,

poly-His, GST, etc.) or linked molecules (including but not limited to, biotin) that improve
detection (including but not limited to, GFP), purification or other traits of the polypeptide.
[129] The term "hGH polypeptide" also encompasses homodimers, heterodimers,
homomultimers, and heteromultimers that are linked, including but not limited to those linked directly via non-naturally encoded amino acid side chains, either to the same or different non-naturally encoded amino acid side chains, to naturally-encoded amino acid side chains, or indirectly via a linker. Exemplary linkers including but are not limited to, small organic compounds, water soluble polymers of a variety of lengths such as polyethylene glycol) or polydextran or polypeptides of various lengths.
[130] A "non-naturally encoded amino acid" refers to an amino acid that is not one of the
20 common amino acids or pyrrolysine or selenocysteine. Other terms that may be used synonymously with the term "non-naturally encoded amino acid" are "non-natural amino acid," "unnatural amino acid," "non-naturally-occurring amino acid," and variously hyphenated and non-hyphenated versions thereof. The term "non-naturally encoded amino acid" also includes, but is not limited to, amino acids that occur by modification (e.g. post-translational modifications) of a naturally encoded amino acid (including but not limited to, the 20 common amino acids or pyrrolysine and selenocysteine) but are not themselves naturally incorporated into a growing polypeptide chain by the translation complex. Examples of such non-naturally-occurring amino acids include, but are not limited to, JV^acetylglucosaminyl-L-serine, W-acetylglucosaminyl-L-. threonine, and O-phosphotyrosine.
[131] An "amino terminus modification group" refers to any molecule that can be
attached to the amino terminus of a polypeptide. Similarly, a "carboxy terminus modification group" refers to any molecule that can be attached to the carboxy terminus of a polypeptide. Terminus modification groups include, but are not limited to, various water soluble polymers, peptides or proteins such as serum albumin, or other moieties that increase serum half-life of peptides.
[132] The terms "functional group", "active moiety", "activating group", "leaving
group", "reactive site", "chemically reactive group" and "chemically reactive moiety" are used in the art and herein to refer to distinct, definable portions or units of a molecule. The terms are somewhat synonymous in the chemical arts and are used herein to indicate the portions of molecules that perform some function or activity and are reactive with other molecules.
or

[133] The term "linkage" or "linker" is used herein to refer to groups or bonds that
normally are formed as the result of a chemical reaction and typically are covalent linkages. Hydrolytically stable linkages means that the linkages are substantially stable in water and do not react with water at useful pH values, including but not limited to, under physiological conditions for an extended period of time, perhaps even indefinitely. Hydrolytically unstable or degradable linkages mean that the linkages are degradable in water or in aqueous solutions, including for example, blood. Enzymatically unstable or degradable linkages mean that the linkage can be degraded by one or more enzymes. As understood in the art, PEG and related polymers may include degradable linkages in the polymer backbone or in the linker group between the polymer backbone, and one or more of the terminal functional groups of the polymer molecule. For example, ester linkages formed by the reaction of PEG carboxylic acids or activated PEG carboxylic acids with alcohol groups on a biologically active agent generally hydrolyze under physiological conditions to release the agent. Other hydrolytically degradable linkages include, but are not limited to, carbonate linkages; imine linkages resulted from reaction of an amine and an aldehyde; phosphate ester linkages formed by reacting an alcohol with a phosphate group; hydrazone linkages which are reaction product of a hydrazide and an aldehyde; acetal linkages that are the reaction product of an aldehyde and an alcohol; orthoester linkages that are the reaction product of a formate and an alcohol; peptide linkages formed by an amine group, including but not limited to, at an end of a polymer such as PEG, and a carboxyl group of a peptide; and oligonucleotide linkages formed by a phosphoramidite group, including but not limited to, at the end of a polymer, and a 5' hydroxyl group of an oligonucleotide.
[134] The term '^biologically active molecule", "biologically active moiety" or
biologically active agenf' when used herein means any substance which can affect any physical or biochemical properties of a biological system, pathway, molecule, or interaction relating to an organism, including but not limited to, viruses, bacteria, bacteriophage, transposon, prion, insects, fungi, plants, animals, and humans. In particular, as used herein, biologically active molecules include, but are not limited to, any substance intended for diagnosis, cure, mitigation, treatment, or prevention of disease in humans or other animals, or to otherwise enhance physical or mental well-being of humans or animals. Examples of biologically active molecules include, but are not limited to, peptides, proteins, enzymes, small molecule drugs, hard drugs, soft drugs, carbohydrates, inorganic atoms or molecules, dyes, lipids, nucleosides, radionuclides,

oligonucleotides, toxins, cells, viruses, liposomes, microparticles and micelles. Classes of
biologically active agents that are suitable for use with the invention include, but are not limited
to, drugs, prodrugs, radionuclides, imaging agents, polymers, antibiotics, fungicides, anti-viral
agents, anti-inflammatory agents, anti-tumor agents, cardiovascular agents, anti-anxiety agents,
hormones, growth factors, steroidal agents, microbially derived toxins, and the like.
[135] A "bifunctional polymer" refers to a polymer comprising two discrete functional
groups that are capable of reacting specifically with other moieties (including but not limited to, amino acid side groups) to form covalent or non-covalent linkages. A bifunctional linker having one functional group reactive with a group on a particular biologically active component, and another group reactive with a group on a second biological component, may be used to form a conjugate that includes the first biologically active component, the bifunctional linker and the second biologically active component. Many procedures and linker molecules for attachment of various compounds to peptides are known. See, e.g.9 European Patent Application No. 188,256; U.S. Patent Nos. 4,671,958, 4,659,839, 4,414,148, 4,699,784; 4,680,338, and 4,569,789 which are incorporated by reference herein. A "multi-functional polymer" refers to a polymer comprising two or more discrete functional groups that are capable of reacting specifically with other moieties (including but not limited to, amino acid side groups) to form covalent or non-covalent linkages. A bi-functional polymer or multi-functional polymer may be any desired length or molecular weight, and may be selected to provide a particular desired spacing or conformation between one or more molecules linked to the GH e.g. hGH molecule.
[136] Where substituent groups are specified by their conventional chemical formulas,
written from left to right, they equally encompass the chemically identical substituents that would result from writing the structure from right to left, for example, the structure -CHfeO- is equivalent to the structure -OCH2-.
[137] The term "substituents" includes but is not limited to '^on-interfering substituents".

fluoroalkyl, heterocyclic radical, substituted heterocyclic radical, nitroalkyl, ~N02, — CN, — NRC(OHCi-Cio alkyl), -C(O)-(Ci-Cl0 alkyl), C2-C10 alkyl ihioalkyl, «C(0)0~( CrC10 alkyl), -OH, ~S02, =S, --COOH, -NR2, carbonyl, ~-C(OMCrCto alkyl)-CF3, ~C(0)—CF3, -C(0)NR2, -(C1-C10 aryl>S-(C6-Cio aryl), -C(0)-(Ci-Cio aryl), ~(CH2)m --0~HCH2)m~0~-(C1-C10 alkyl) wherein each m is from 1 to 8, ~C(0)NR2, »C(S)NR2, - S02NR2> --NRC(O) NR2, —NRC(S) NR2, salts thereof, and the like. Each R as used herein is H, alkyl or substituted alkyl, aryl or substituted aryl, aralkyl, or alkaryl.
[138] The term "halogen" includes fluorine, chlorine, iodine, and bromine.
[139] The term "alkyl," by itself or as part of another substituent, means, unless
otherwise stated, a straight or branched chain, or cyclic hydrocarbon radical, or combination thereof, which may be fully saturated, mono- or polyunsaturated and can include di- and multivalent radicals, having the number of carbon atoms designated {i.e. Ct-Cio means one to ten carbons). Examples of saturated hydrocarbon radicals include, but are not limited to, groups such as methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, isobutyl, sec-butyl, cyclohexyl, (cyclohexyl)methyl, cyclopropylmethyl, homologs and isomers of, for example, n-pentyl,:n-hexyl, . n-heptyl, n-octyl, and the like. An unsaturated alkyl group is one having one or more double bonds or triple bonds. Examples of unsaturated alkyl groups include, but are not limited to, vinyl, 2-propenyl, crotyl, 2-isopentenyl, 2-(butadienyl), 2,4-pentadienyl, 3-(l,4-pentadienyl), ethynyl, 1-and 3-propynyl, 3-butynyl, and the higher homologs and isomers. The term "alkyl," unless otherwise noted, is also meant to include those derivatives of alkyl defined in more detail below, such as "heteroalkyl." Alkyl groups which are limited to hydrocarbon groups are termed "homoalkyl".
[140] The term "alkylene" by itself or as part of another substituent means a divalent
radical derived from an alkane, as exemplified, but not limited, by the structures -CH2CH2- and -CH2CH2CH2CH2-, and further includes those groups described below as "heteroalkylene." Typically, an alkyl (or alkylene) group will have from 1 to 24 carbon atoms, with those groups having 10 or fewer carbon atoms being a particular embodiment of the methods and compositions described herein. A "lower alkyl" or 'lower alkylene" is a shorter chain alkyl or alkylene group, generally having eight or fewer carbon atoms.

[141] The terms "alkoxy," "alkylamino" and "alkylthio" (or thioalkoxy) are used in their
conventional sense, and refer to those alkyl groups attached to the remainder of the molecule via an oxygen atom, an amino group, or a sulfur atom, respectively.
[142] The term "heteroalkyl," by itself or in combination with another term, means,
unless otherwise stated, a stable straight or branched chain, or cyclic hydrocarbon radical, or combinations thereof, consisting of the stated number of carbon atoms and at least one heteroatom selected from the group consisting of O, N, Si and S, and wherein the nitrogen and sulfur atoms may optionally be oxidized and the nitrogen heteroatom may optionally be quatemizeA The heteroatom(s) O, N and S and Si may be placed at any interior position of the heteroalkyl group or at the position at which the alkyl group is attached to the remainder of the molecule. Examples include, but are not limited to, -CH2-CH2-0-CH3, -CH2-CH2-NH-CH3, -CH2-CH2-N(CH3)-CH3, -CH2-S-CH2-CH3, -CH2-CH2rS(0)-CH3, -CH^CH^O^-Ofe, -CH=CH-0-CH3, -Si(CH3)3, CH2-CH=N-OCH3, and -CH=CH-N(CH3)-CH3. Up to two heteroatoms may be consecutive, sue! as, for example, -CH2-NH-OCH3 and -CH2-0-Si(CH3)3. Similarly, the term "heteroalkylene" b; itself or as part of another substituent means a divalent radical derived from heteroalkyl, a exemplified, but not limited by, -CH2-CH2-S-CH2-CH2- and -CH2-S-CH2-CH2-NH-CH2-. Fo heteroalkylene groups, the same or different heteroatoms, can also occupy either or both of th chain termini (including but not limited to, alkyleneoxy, alkylenedioxy, alkyleneamino alkylenediamino, aminooxyalkylene, and the like). Still further, for alkylene and heteroalkylem linking groups, no orientation of the linking group is implied by the direction in which the formuL of the linking group is written. For example, the formula -C^O^R'- represents both -0(0^11' and-R'CCO^-.
[143] The terms "cycloalkyl" and "heterocycloalkyl", by themselves or in combination
with other terms, represent, unless otherwise stated, cyclic versions of "alkyl" and "heteroalkyl", respectively. Thus, a cycloalkyl or heterocycloalkyl may include saturated, partially and fully unsaturated ring linkages. Additionally, for heterocycloalkyl, a heteroatom can occupy the position at which the heterocycle is attached to the remainder of the molecule. Examples of cycloalkyl include, but are not limited to, cyclopentyl, cyclohexyl, 1-cyclohexenyl, 3-cyclohexenyl, cycloheptyl, and the like. Examples of heterocycloalkyl include, but are not limited to, l-(l,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2-piperidinyl, 3-piperidinyl, 4-morpholinyl, 3-morpholinyl, tetrahydrofuran-2-yl, tetrahydrofuran-3-yl, tetrahydrothien-2-yl, tetrahydrothien-3-

yl, 1-^piperazinyl, 2~piperazinyl, and the like. Additionally, the term encompasses bicyclic and
tricyclic ring structures. Similarly, the term "heterocycloalkylene" by itself or as part of another
substituent means a divalent radical derived from heterocycloalkyl, and the term "cycloalkylene"
by itself or as part of another substituent means a divalent radical derived from cycloalkyl.
[144] As used herein, the term "water soluble polymer" refers to any polymer that is
soluble in aqueous solvents. Linkage of water soluble polymers to GH, e.g., hGH polypeptides can result in changes including, but not limited to, increased or modulated serum half-life, or increased or modulated therapeutic half-life relative to the unmodified form, modulated immunogenicity, modulated physical association characteristics such as aggregation and multimer formation* altered receptor binding, mid altered receptor dimerization or multimerization. The water soluble polymer may or may not have its own biological activity, and may be utilized as a linker for attaching GH, e.g.,hGH to other substances, including but not limited to one or more GH, e.g., hGH polypeptides, or one or more biologically active molecules. Suitable polymers include, but are not limited to, polyethylene glycol, polyethylene glycol propionaldehyde, mono CI-C10 alkoxy or aryloxy derivatives- thereof (described in U.S. Patent No. 5,252,714 which is incorporated by reference herein),, monomethoxy-polyethylene glycol, polyvinyl pyrrolidone, polyvinyl alcohol, polyamino acids, divinylether maleic anhydride, iV-(2-Hydroxypropyl)-methacrylamide, dextran, dextran derivatives including dextran sulfate, polypropylene glycol, polypropylene oxide/ethylene oxide copolymer, polyoxyethylated polyol, heparin, heparin fragments, polysaccharides, oligosaccharides, glycans, cellulose and cellulose derivatives, including but not limited to methylcellulose and carboxymethyl cellulose, starch and starch derivatives, polypeptides, polyalkylene glycol and derivatives thereof, copolymers of polyalkylene glycols and derivatives thereof, polyvinyl ethyl ethers, and alpha-beta-poly[(2-hydroxyethyl)-DL-aspartamide, and the like, or mixtures thereof. Examples of such water soluble polymers include, but are not limited to, polyethylene glycol and serum albumin.
[145] As used herein, the term "polyalkylene glycol" or "poly(alkene glycol)" refers to
polyethylene glycol (poly(ethylene glycol)), polypropylene glycol, polybutylene glycol, and derivatives thereof. The term "polyalkylene glycol" and/or '^polyethylene glycol" encompasses both linear and branched polymers and average molecular weights of between 0.1 kDa and 100 kDa. Other exemplary embodiments are listed, for example, in commercial supplier catalogs, such

as Shearwater Corporation's catalog "Polyethylene Glycol and Derivatives for Biomedical Applications" (2001).
{146J The term "aryl" means, unless otherwise stated, a polyunsaturated, aromatic,
hydrocarbon substituent which can be a single ring or multiple rings (including but not limited to, from 1 to 3 rings) which are fused together or linked covalently. The term "heteroaryl" refers to aryl groups (or rings) that contain from one to four heteroatoms selected from N, O, and S, wherein the nitrogen and sulfur atoms are optionally oxidized, and the nitrogen atom(s) are optionally quaternized. A heteroaryl group can be attached to the remainder of the molecule through a heteroatom. Non-limiting examples of aryl and heteroaryl groups include phenyl, 1-naphthyl, 2-naphthyl, 4-biphenyl, 1-pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 3-pyrazolyl, 2-imidazolyl, 4-imidazolyl, pyrazinyl, 2-oxazolyl, 4-oxazolyl, 2-phenyl-4-oxazolyl, 5-oxazolyl, 3-isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2-thiazolyl, 4-thiazolyl, 5-thiazoIyl, 2-furyl, 3-furyl, 2-thienyl, 3-thienyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidyl, 4-pyrimidyi, 5-benzothiazolyl, purinyl, 2-benzimidazolyl, 5-indoIyl, 1-isoquinolyl, 5-isoquinolyl, 2-quinoxalinyl, 5-quinoxalinyl, 3-quinolyl, and 6-quinolyl. Substituents for each of the above noted aryl and heteroaryl ring systems are selected from the group of acceptable substituents described below.
[147] For brevity, the term "aryl" when used in combination with other terms (including
but not limited to, aryloxy. arylthioxy, arylalkyl) includes both aryl and heteroaryl rings as defined
above. Thus, the term "arylalkyl" is meant to include those radicals in which an aryl group is
attached to an alkyl group (including but not limited to, benzyl, phenethyl, pyridylmethyl and the
like) including those alkyl groups in which a carbon atom (including but not limited to, a
methylene group) has been replaced by, for example, an oxygen atom (including but not limited
to, phenoxymethyl, 2-pyridyloxymethyl, 3-(l-naphthyloxy)propyl, and the like).
[148] Each of the above terms (including but not limited to, "alkyl," "heteroalkyl," "aryl"
and "heteroaryl") are meant to include both substituted and unsubstituted forms of the indicated
radical. Exemplary substituents for each type of radical are provided below.
[149] Substituents for the alkyl and heteroalkyl radicals (including those groups often
referred to as alkylene, alkenyl, heteroalkylene, heteroalkenyl, alkynyl, cycloalkyl, heterocycloalkyl, cycloalkenyl, and heterocycloalkenyl) can be one or more of a variety of groups selected from, but not limited to: -OR', =0, =NR\ =N-ORJ, -NR'R", -SR\ -halogen, -SiR'R"R"5, -OC(0)R\ -C(0)R\ -C02R>, -CONR'R", -OC(0)NR'R", -NR"C(0)R', -NR'-C(0)NR"R"\ -

NR"C(0)2R\ -NR(>fR'R'R,,,)=NR"", -NR-C(NR'R'^NR'", -S(0)R\ -S(0)2RJ, -S(0)2NR'R", -NRS02R\ -CN and -N02 in a number ranging from zero to (2m'+l), where m' is the total number of carbon atoms in such a radical. R', R", R"' and R"" each independently refer to hydrogen, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, including but not limited to, aryl substituted with 1-3 halogens, substituted or unsubstituted alkyl, alkoxy or thioalkoxy groups, or arylalkyl groups. When a compound of the invention includes more than one R group, for example, each of the R groups is independently selected as are each R\ R", R'" and R**" groups when more than one of these groups is present. When R' and R" are attached to the same nitrogen atom, they can be combined with the nitrogen atom to form a 5-, 6-, or 7-membered ring. For example, -NR'R" is meant to include, but not be limited to, 1-pyrrolidinyl and 4-morpholinyl. From the above discussion of substituents, one of skill in the art will understand that the term "alkyl" is meant to include groups including carbon atoms bound to groups other than hydrogen groups, such as haloalkyl (including but not limited to, -CF3 and -CH2CF3) and acyl (including but not limited to, -C(0)CH3, -C(0)CF3, -C(0)CH2OCH3, and the like).
[150] Similar to the substituents described for the alkyl radical, substituents for the aryl
and heteroaryl groups are varied and are selected from, but are not limited to: halogen, -OR', =0, =NR', =N-OR5, -NR'R", -SR', -halogen, -SiR'R'TT5, -OC(0)R>, -C(0)R', -C02R', -CONR'R", -OC(0)NR'R", -NR"C(0)R\ -NR>-C(0)NR,'R'", -NR"C(0)2R', -NR-C(NR'R"R">NR'"\ -NR-CtNR'R^NR'", -S(0)R\ -S(0)2R', -S(0)2NR'R", -NRS02R5, -CN and -N02, -Rs, -N3, -CE^Pbh, fluoro(CrC4)alkoxy, and fluoro(Ci-C4)alkyl, in a number ranging from zero to the total number of open valences on the aromatic ring system; and where R', R", R"' andR"" are independently selected from hydrogen, alkyl, heteroalkyl, aryl and heteroaryl. When a compound of the invention includes more than one R group, for example, each of the R groups is independently selected as are each R\ R", R'" and R"" groups when more than one of these groups is present.
[151] As used herein, the term "modulated serum half-life" means the positive or
negative change in circulating half-life of a modified hGH relative to its non-modified form. Serum half-life is measured by taking blood samples at various time points after administration of hGH, and determining the concentration of that molecule in each sample. Correlation of the serum concentration with time allows calculation of the serum half-life. Increased serum half-life

desirably has at least about two-fold, but a smaller increase may be useful, for example where it
enables a satisfactory dosing regimen or avoids a toxic effect. In some embodiments, the increase
is at least about three-fold, at least about five-fold, or at least about ten-fold.
[152J The term "modulated therapeutic half-life" as used herein means the positive or
negative change in the half-life of the therapeutically effective amount of a modified hGH, relative to its non-modified form. Therapeutic half-life is measured by measuring pharmacokinetic and/or pharmacodynamic properties of the molecule at various time points after administration. Increased therapeutic half-life desirably enables a particular beneficial dosing regimen, a particular beneficial total dose, or avoids an undesired effect. In some embodiments, the increased therapeutic half-life results from increased potency, increased or decreased binding of the modified molecule to its target, increased or decreased breakdown of the molecule by enzymes such as proteases, or an increase or decrease in another parameter or mechanism of action of the non-modified molecule.
[153] The term "isolated," when applied to a nucleic acid or protein, denotes that the
nucleic acid or protein is free of at least some of the cellular components with which it is
associated in the natural state, or that the nucleic acid or protein has been concentrated to a level
greater than the concentration of its in vivo or in vitro production. It can be in a homogeneous
state. Isolated substances can be in either a dry or semi-dry state, or in solution, including but not
limited to, an aqueous solution. It can be a component of a pharmaceutical composition that
comprises additional pharmaceutically acceptable carriers and/or excipients. Purity and
homogeneity are typically determined using analytical chemistry techniques such as
polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein which
is the predominant species present in a preparation is substantially purified. In particular, an
isolated gene is separated from open reading frames which flank the gene and encode a protein
other than the gene of interest The term "purified" denotes that a nucleic acid or protein gives rise
to substantially one band in an electrophoretic gel. Particularly, it may mean that the nucleic acid
or protein is at least 85% pure, at least 90% pure, at least 95% pure, at least 99% or greater pure.
[154] The term "nucleic acid" refers to deoxyribonucleotides, deoxyribonucleosides,
ribonucleosides, or ribonucleotides and polymers thereof in either single- or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogues of natural nucleotides which have similar binding properties as the reference nucleic acid and are

metabolized in a manner similar to naturally occurring nucleotides. Unless specifically limited
otherwise, the term also refers to oligonucleotide analogs including PNA (peptidonucleic acid),
analogs of DNA used in antisense technology (phosphorothioates, phosphoroamidates, and the
like). Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses
conservatively modified variants thereof (including but not limited to, degenerate codon
substitutions) and complementary sequences as well as the sequence explicitly indicated.
Specifically, degenerate codon substitutions may be achieved by generating sequences in which
the third position of one or more selected (or all) codons is substituted with mixed-base and/or
deoxyinosine residues (Batzer et al, Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol
Chem. 260:2605-2608 (1985);Rossolini et al9Mol Cell Probes 8:91-98 (1994)).
[155] The terms "polypeptide," "peptide" and "protein3* are used interchangeably herein
to refer to a polymer of amino acid residues. That is, a description directed to a polypeptide applies equally to a description of a peptide and a description of a protein, and vice versa. The terms apply to naturally occurring amino acid polymers as well as amino acid polymers in which one or more amino acid residues is a non-naturally encoded amino acid. As used herein, the terms encompass amino acid chains of any length, including fiill length proteins, wherein the amino acid residues are linked by covalent peptide bonds.
[156] The term "amino acid" refers to naturally occurring and non-naturally occurring
amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally encoded amino acids are the 20 common amino acids (alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine) and pyrrolysine and selenocysteine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a caiboxyl group, an amino group, and an R group, such as, homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (such as, norleucine) or modified peptide backbones, but retain die same basic chemical structure as a naturally occurring amino acid.
[157] Amino acids may be referred to herein by either their commonly known three letter
symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical

Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
[158] "Conservatively modified variants" applies to both amino acid and nucleic acid
sequences.. With respect to particular nucleic acid sequences,, "conservatively modified variants" refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally . identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are "silent variations," which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of ordinary skill in the art will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.
[159J As to amino acid sequences, one of ordinary skill in the art will recognize that
individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" where the alteration results in the deletion of an amino acid, addition of an amino acid, or substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are known to those of ordinary skill in the ait Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention.
[160] Conservative substitution tables providing functionally similar amino acids are
known to those of ordinary skill in the art. The following eight groups each contain amino acids that are conservative substitutions for one another:
1) Alanine (A), Glycine (G);
2) Aspartic acid (D), Glutamic acid (E);

3) Asparagine (N), Glutamine (Q);
4) Arginine (R), Lysine (K);
5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V);
6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W);
7) Serine (S), Threonine (T); and
8) Cysteine (C), Methionine (M)
(see, e.g., Creighton, Proteins: Structures and Molecular Properties (W H Freeman & Co.; 2nd edition (December 1993)
[161] The terms "identical" or percent "identity," in the context of two or more nucleic
acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same.
Sequences are "substantially identical" if they have a percentage of amino acid residues or
nucleotides that are the same (i.e., at least about 60% identity, at least about 65%, at least about
70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about ■
95%, or at least about 99% identity over a specified region), when compared and aligned for
maximum correspondence over a comparison window, or designated region as measured using
one of the following sequence comparison algorithms (or other algorithms available to persons of :
ordinary skill in the art) or by manual alignment and visual inspection. This definition also refers
to the complement of a test sequence. The identity can exist over a region that is at least about 50
amino acids or nucleotides in length, or over a region that is 75-100 amino acids or nucleotides in *
length, or, where not specified, across the entire sequence of a polynucleotide or polypeptide.
[162] For sequence comparison, typically one sequence acts as a reference sequence, to
which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
[163] A "comparison window", as used herein, includes reference to a segment of any one
of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two

sequences are optimally aligned. Methods of alignment of sequences for comparison are known to
those of ordinary skill in the art. Optimal alignment of sequences for comparison can be
conducted, including but not limited to, by the local homology algorithm of Smith and Waterman
(1970) Adv. Appl Math, 2:482c, by the homology alignment algorithm of Needleman and Wunsch
(1970) J. Mol Biol 48:443, by the search for similarity method of Pearson and Lipman (1988)
Proc. Nat'L Acad. Sci. USA 85:2444, by computerized implementations of these algorithms (GAP,
BESTTTT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics
Computer Group, 575 Science Dr., Madison, WI), or by manual alignment and visual inspection
(see, e.g., Ausubel et al> Current Protocols in Molecular Biology (1995 supplement)).
[164] One example of an algorithm that is suitable for determining percent sequence
identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al (1997) Nuc. Acids Res. 25:3389-3402, and Altschul et al (1990) J. Mol Biol . 215:403-410, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information available at the World Wide Web at '; ncbi.nlm.nih.gov. The BLAST algorithm parameters W, T, and X determine the sensitivity and ,-speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a A wordlength (W) of 11, an expectation (E) or 10, M=5, N=-4 and a comparison of both strands, i For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and 4 expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff (1992) ,', Proc. Natl Acad. Sci. USA 89:10915) alignments (B) of 50, expectation (E) of 10, M=5, N=-4, and a comparison of both strands. The BLAST algorithm is typically performed with the "low complexity" filter turned off.
[165] The BLAST algorithm also performs a statistical analysis of the similarity between
two sequences (see, e.g., Karlin and Altschul (1993) Proc. Natl Acad. Sci. USA 90:5873-5787). Dne measure of similarity provided by the BLAST algorithm is the smallest sum probability |P(N)), which provides an indication of the probability by which a match between two nucleotide :>r amino acid sequences would occur by chance. For example, a nucleic acid is considered similar :o a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to he reference nucleic acid may be less than about 0.2, or less than about 0.01, or less than about 0.001.

[166] The phrase "selectively (or specifically) hybridizes to" refers to the binding,
duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (including but not limited to, total cellular or library DNA or RNA).
[1671 The phrase "stringent hybridization conditions" refers to hybridization of sequences
of DNA, RNA, PNA, or other nucleic acid mimics, or combinations thereof under conditions of low ionic strength and high temperature as is known in the art Typically, under stringent conditions a probe will hybridize to its target subsequence in a complex mixture of nucleic acid (including but not limited to, total cellular or library DNA or RNA) but does not hybridize to other sequences in the complex mixture. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, "Overview of principles of hybridization and the. strategy of nucleic acid assays" (1993). Generally, stringent conditions are selected to be about 5-10° C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength pH. The Tm' is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions may be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30°C for short probes (including but not limited to, 10 to 50 nucleotides) and at least about 60° C for long probes (including but Hot limited to, greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal may be at least two times background, optionally 10 times background hybridization. Exemplary stringent hybridization conditions can be as following; 50% formamide, 5X SSC, and 1% SDS, incubating at 42°C, or 5X SSC, 1% SDS, incubating at 65°C, with wash in 0.2X SSC, and 0.1% SDS at 65°C. Such washes can be performed for 5, 15, 30, 60, 120, or more minutes.
[168] As used herein, the term "eukaryote" refers to organisms belonging to the
phylogenetic domain Eucarya such as animals (including but not limited to, mammals, insects,

reptiles, birds, etc.), ciliates, plants (including but not limited to, monocots, dicots, algae, etc.), fungi, yeasts, flagellates, microsporidia, protists, etc.
[169] As used herein, the term "non-eukaryote" refers to non-eukaryotic organisms. For
example, a non-eukaryotic organism can belong to the Eubacteria (including but not limited to, Escherichia coli9 Thermos thermophilics, Bacillus stearothermophilus, Pseudomonas fluorescens, Pseudomonas aeruginosa, Pseudomonas putida, etc.) phylogenetic domain, or the Archaea (including but not limited to, Methanococcus jannaschii9 Methanobacterium therrnoautotrophicum, Halobacterium such as Haloferax volcanii and Halobacterium species NRC'l, Archaeoglobus julgidus, Pyrococcus furiosus^ Pyrococcus horikoshii> Aeuropyrum pernix, etc.) phylogenetic domain.
[170] The term "subject" as used herein, refers to an animal, in some embodiments a
mammal, and in other embodiments a human, who is the object of treatment, observation or
experiment.
[171] The term "effective amount" as used herein refers to that amount of the modified
non-natural amino acid polypeptide being administered which will relieve to some extent one oi
more of the symptoms of the disease, condition or disorder being treated. Compositions
containing the modified non-natural amino acid polypeptide described herein can be administered
for prophylactic, enhancing, and/or therapeutic treatments.
[172] The terms "enhance" or "enhancing" means to increase or prolong either in potency
or duration a desired effect Thus, in regard to enhancing the effect of therapeutic agents, the term
"enhancing" refers to the ability to increase or prolong, either in potency or duration, the effect of
other therapeutic agents on a system. An "enhancing-effective amount," as used herein, refers to
an amount adequate to enhance the effect of another therapeutic agent in a desired system. When
used in a patient, amounts effective for this use will depend on the severity and course of the
disease, disorder or condition, previous therapy, the patient's health status and response to the
drugs, and the judgment of the treating physician.
[173] The term "modified," as used herein refers to any changes made to a given
polypeptide, such as changes to the length of the polypeptide, the amino acid sequence, chemical
structure, co-translational modification, or post-translational modification of a polypeptide. The

form "(modified)" term means that the polypeptides being discussed are optionally modified, that is, the polypeptides under discussion can be modified or unmodified.
[174] The term "post-translationally modified" refers to any modification of a natural or
non-natural amino acid that occurs to such an amino acid after it has been incorporated into a
polypeptide chain. The term encompasses, by way of example only, co-translational in vivo
modifications, co-translational in vitro modifications (such as in a cell-free translation system),
post-translational in vivo modifications, and post-translational in vitro modifications.
[175] In prophylactic applications, compositions containing the modified non-natural
amino acid polypeptide are administered to a patient susceptible to or otherwise at risk of a particular disease, disorder or condition. Such an amount is defined to be a "prophylactically effective amount." In this use, the precise amounts also depend on the patient's state of health, weight, and the like. It is considered well within the skill of the art for one to determine such prophylactically effective amounts by routine experimentation (e.g., a dose escalation clinical trial).
[176] The term "protected" refers to the presence of a "protecting group" or moiety thai
prevents reaction of the chemically reactive functional group under certain reaction conditions
The protecting group will vary depending on the type of chemically reactive group being
protected. For example, if the chemically reactive group is an amine or a hydrazide, the protecting
group can be selected from the group of tert-butyloxycarbonyl (t-Boc) and 9-
fluorenylmethoxycarbonyl (Fmoc). If the chemically reactive group is a thiol, the protecting group
can be orthopyridyldisulfide. If the chemically reactive group is a carboxylic acid, such as
butanoic or propionic acid, or a hydroxyl group, the protecting group can be benzyl or an alkyl
group such as methyl, ethyl, or tart-butyl. Other protecting groups known in the art may also be
used in or with the methods and compositions described herein, including photolabile groups such
as Nvoc and MeNvoc. Other protecting groups known in the art may also be used in or with the
methods and compositions described herein.
[177] By way of example only, blocking/protecting groups may be selected from:


[178] Other protecting groups are described in Greene and Wuts, Protective Groups in
Organic Synthesis, 3rd Ed., John Wiley & Sons, New York, NY, 1999, which is incorporated
herein by reference in its entirety.
[179] In therapeutic applications, compositions containing the modified non-natural .;
amino acid polypeptide are administered to a patient already suffering from a disease, condition or
disorder, in an amount sufficient to cure or at least partially arrest the symptoms of the disease,
disorder or condition. Such an amount is defined to be a 'therapeutically effective amount," and
will depend on the severity and course of the disease, disorder or condition, previous therapy, the
patient's health status and response to the drugs, and the judgment of the treating physician. It is
considered well within the skill of the art for one to determine such therapeutically effective
amounts by routine experimentation (e.g., a dose escalation clinical trial).
[180] The term "treating" is used to refer to either prophylactic and/or therapeutic
treatments.
[181] Non-naturally encoded amino acid polypeptides presented herein may include
isotopically-labelled compounds with one or more atoms replaced by an atom having an atomic
mass or mass number different from the atomic mass or mass number usually found in nature.
Examples of isotopes that can be incorporated into the present compounds include isotopes of
hydrogen, carbon, nitrogen, oxygen, fluorine and chlorine, such as 2H, 3H, 13C, 14C, l5N, ,80, 170,
S, F, CI, respectively. Certain isotopicallv-labelled conrnnunds described herein frvr evamnle

those into which radioactive isotopes such as 3H and I4C are incorporated, may be useful in drug and/or substrate tissue distribution assays. Further, substitution with isotopes such as deuterium, i.e., 2H, can afford certain therapeutic advantages resulting from greater metabolic stability, for example increased in vivo half-life or reduced dosage requirements.
[182] All isomers including but not limited to diastereomers, enantiomers, and mixtures
thereof are considered as part of the compositions described herein. In additional or further embodiments, the non-naturally encoded amino acid polypeptides are metabolized upon administration to an organism in need to produce a metabolite that is then used to produce a desired effect, including a desired therapeutic effect. In further or additional embodiments are active metabolites of non-naturally encoded amino acid polypeptides.
[183] In some situations, non-naturally encoded amino acid polypeptides may exist as
tautomers. In addition, the non-naturally encoded amino acid polypeptides described herein can exist in unsolvated as well as solvated forms with pharmaceutically acceptable solvents such as water, ethanol, and the like. The solvated forms are also considered to be disclosed herein. Those of ordinary skill in the art will recognize that some of the compounds herein can exist in several tautomeric forms. All such tautomeric forms are considered as part of the compositions described herein.
[184] Unless otherwise indicated, conventional methods of mass spectroscopy, NMR,
HPLC, protein chemistry, biochemistry, recombinant DNA techniques and pharmacology, within the skill of the art are employed.
DETAILED DESCRIPTION
L Introduction
[185] GH, e.g., hGH molecules comprising at least one unnatural amino acid are provided
in the invention. In certain embodiments of the invention, the GH, e.g., hGH polypeptide with at least one unnatural amino acid includes at least one post-translational modification. In one embodiment, the at least one post-translational modification comprises attachment of a molecule including but not limited to, a label, a dye, a polymer, a water-soluble polymer, a derivative of polyethylene glycol, a photocrosslinker, a radionuclide, a cytotoxic compound, a drug, an affinity label, a photoaffinity label, a reactive compound, a resin, a second protein or polypeptide or polypeptide analog, an antibody or antibody fragment, a metal chelator, a cofactor, a fatty acid, a

carbohydrate, a polynucleotide, a DNA, a RNA, an antisense polynucleotide, a saccharide, water-soluble dendrimer, a cyclodextrin, an inhibitory ribonucleic acid, a biomaterial, a nanoparticle, a spin label, a fluorophore, a metal-containing moiety, a radioactive moiety, a novel functional group, a group that covalently or noncovalently interacts with other molecules, a photocaged moiety, an actinic radiation excitable moiety, a photoisomerizable moiety, toothy a derivative of biotin, a biotin analogue, a moiety incorporating a heavy atom, a chemically cleavable group, a photocleavable group, an elongated side chain, a carbon-linked sugar, a redox-active agent, an amino thioacid, a toxic moiety, an isotopically labeled moiety, a biophysical probe, a phosphorescent group, a chemiluminescent group, an electron dense group, a magnetic group, an intercalating group, a chromophore, an energy transfer agent, a biologically active agent, a detectable label, a small molecule, a quantum dot, a nanotransmitter, a radionucleotide, a radiotransmitter, a neutron-capture agent, or any combination of the above or any other "desirable compound or substance, comprising a second reactive group to at least one unnatural amino acid comprising a first reactive group utilizing chemistry methodology that is known to one of ordinary skill in the art to be suitable for the particular reactive groups. For example, the first reactive group is an alkynyl moiety (including but not limited to, in the unnatural amino acid p-propargyloxyphenylalanine, where the propargyl group is also sometimes referred to as an acetylene moiety) and the second reactive group is an azido moiety, and [3+2] cycloaddition chemistry methodologies are utilized. In another example, the first reactive group is the azido moiety (including but not limited to, in the unnatural amino acidp-azido-L-phenylalanine) and the second reactive group is the alkynyl moiety. In certain embodiments of the modified GH, e.g., hGH polypeptide of the present invention, at least one unnatural amino acid (including but not limited to, unnatural amino acid containing a keto functional group) comprising at least one post-translational modification, is used where the at least one post-translational modification comprises a saccharide moiety, hi certain embodiments, the post-translational modification is made in vivo in a eukaryotic cell or in a non-eukaryotic cell.
[186] In certain embodiments, the protein includes at least one post-translational
modification that is made in vivo by one host cell, where the post-translational modification is not normally made by another host cell type. In certain embodiments, the protein includes at least one post-translational modification that is made in vivo by a eukaryotic cell, where the post-translational modification is not normally made by a non-eukaryotic cell. Examples of post-

translational modifications include, but are not limited to, glycosylation, acetylation, acylation, lipid-modification, palmitoylation, palmitate addition, phosphorylation, glycolipid-linkage modification, and the like. In one embodiment, the post-translational modification comprises attachment of an oligosaccharide to an asparagine by a GlcNAc-asparagine linkage (including but not limited to, where the oligosaccharide comprises (GlcNAc-Man)2-Man-GlcNAc-GlcNAc, and the like). In another embodiment, the post-translational modification comprises attachment of an oligosaccharide (including but not limited to, Gal-GalNAc, Gal-GlcNAc, etc.) to a serine or threonine by a GalNAc-serine, a GalNAc-threonine, a GlcNAc-serine, or a GlcNAc-threonine linkage. In certain embodiments, a protein or polypeptide of the invention can comprise a secretion or localization sequence, an epitope tag, a FLAG tag, a polyhistidine tag, a GST fusion, and/or the like. Examples of secretion signal sequences include, but are not limited to, a prokaryotic secretion signal sequence, a eukaryotic secretion signal sequence, a eukaryotic secretion signal sequence 5'-optimized for bacterial expression, a novel secretion signal sequence, pectate lyase secretion signal sequence, Omp A secretion signal sequence, and a phage secretion signal sequence. Examples of secretion signal sequences, include, but are not limited to, STTt (prokaryotic), Fd Gin and Ml 3 (phage), Bgl2: (yeast), and the signal sequence bla derived from a transposon.
[187] The protein or polypeptide of interest can contain at least one, at least two, at least
three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or ten or more unnatural amino acids. The unnatural amino acids can be the same or different, for example, there can be 1,2, 3,4, 5, 6, 7, 8, 9,10 or more different sites in the protein that comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more different unnatural amino acids. In certain embodiments, at least one, but fewer than all, of a particular amino acid present in a naturally occurring version of the protein is substituted with an unnatural amino acid.
[188] The present invention provides methods and compositions based on members of the
GH supergene family, in particular hGH, comprising at least one non-naturally encoded amino acid. Introduction of at least one non-naturally encoded amino acid into a GH supergene family member can allow for the application of conjugation chemistries that involve specific chemical reactions, including, but not limited to, with one or more non-naturally encoded amino acids while not reacting with the commonly occurring 20 amino acids. In some embodiments, fee GH

supergene family member comprising the non-naturally encoded amino acid is linked to a water soluble polymer, such as polyethylene glycol (PEG), via the side chain of the non-naturally encoded amino acid. This invention provides a highly efficient method for the selective modification of proteins with PEG derivatives, which involves the selective incorporation of non-genetically encoded amino acids, including but not limited to, those amino acids containing functional groups or substituents not found in the 20 naturally incorporated amino acids, including but not limited to a ketone, an azide or acetylene moiety, into proteins in response to a selector codon and the subsequent modification of those amino acids with a suitably reactive PEG derivative. Once incorporated, the amino acid side chains can then be modified by utilizing chemistry methodologies known to those of ordinary skill in the art to be suitable for the particular functional groups or substituents present in the non-naturally encoded amino acid. Known chemistry methodologies of a wide variety are suitable for use in the present invention to incorporate a water soluble polymer into the protein. Such methodologies include but are not limited to a Huisgen [3+2] cycloaddition reaction (see, e.g., Padwa, A. in Comprehensive Organic Synthesis, Vol. 4, (1991) Ed. Trost, B. M., Pergamon, Oxford, p. 1069-1109; and, Huisgen, R. in 1.3-Dipolar Cycloaddition Chemistry. (1984) Ed. Padwa, A., Wiley, New York, p. 1-176) with, including but not limited to, acetylene or azide derivatives, respectively.
[189] Because the Huisgen [3+2] cycloaddition method involves a cycloaddition rather
than a nucleophilic substitution reaction, proteins can be modified with extremely high selectivity. The reaction can be carried out at room temperature in aqueous conditions with excellent regioselectivity (1,4 > 1,5) by the addition of catalytic amounts of Cu(T) salts to the reaction mixture. See, e.g., Tornoe, et aL, (2002) J. Org. Chem. 67:3057-3064; and, Rostovtsev, et al., (2002) Angew. Chem. Int Ed. 41:2596-2599; and WO 03/101972. A molecule that can be added to a protein of the invention through a [3+2] cycloaddition includes virtually any molecule with a suitable functional group or substituent including but not limited to an azido or acetylene derivative. These molecules can be added to an unnatural amino acid with an acetylene group, including but not limited to, p-propargyloxyphenylalanine, or azido group, including but not limited to p-azido-phenylalanine, respectively.
[190J The five-membered ring that results from the Huisgen [3+2] cycloaddition is not
generally reversible in reducing environments and is stable against hydrolysis for extended periods

in aqueous environments. Consequently, the physical and chemical characteristics of a wide variety of substances can be modified under demanding aqueous conditions with the active PEG derivatives of the present invention. Even more important, because the azide and acetylene moieties are specific for one another (and do not, for example, react with any of the 20 common, genetically-encoded amino acids), proteins can be modified in one or more specific sites with extremely high selectivity.
[191] The invention also provides water soluble and hydrolytically stable derivatives of
PEG derivatives and related hydrophilic polymers having one or more acetylene or azide moieties. The PEG polymer derivatives that contain acetylene moieties are highly selective for coupling with azide moieties that have been introduced selectively into proteins in response to a selector codon. Similarly, PEG polymer derivatives that contain azide moieties are highly selective for coupling with acetylene moieties that have been introduced selectively into proteins in response to a selector codon.
[192] More specifically, the azide moieties comprise, but are not limited to, alkyl azides,
aryl azides and derivatives of these azides. The derivatives of the alkyl and aryl azides can include other substituents so long as the acetylene-specific reactivity is maintained. The acetylene ; moieties comprise alkyl and aryl acetylenes and derivatives of each. The derivatives of the alkyl and aryl acetylenes can include other substituents so long as the azide-specific reactivity is maintained.
[193] The present invention provides conjugates of substances having a wide variety of
functional groups, substituents or moieties, with other substances including but not limited to a label; a dye; a polymer, a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker, a radionuclide; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide; a water-soluble dendrimer; a cyclodextrin; an inhibitory ribonucleic acid; a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; an actinic radiation excitable moiety; a photoisomerizable moiety; biotin; a derivative of biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a

photocleavable group; an elongated side chain; a carbon-linked sugar; a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety, a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; a small molecule; a quantum dot; a nanotransmitter; a radionucleotide; a radiotransmitter; a neutron-capture agent; or any combination of the above, or any other desirable compound or substance. The present invention also includes conjugates of substances having azide or acetylene moieties with PEG polymer derivatives having the corresponding acetylene or azide moieties. For example, a PEG polymer containing an azide moiety can be coupled to a biologically active molecule at a position in the protein that contains a non-genetically encoded amino acid bearing an acetylene functionality. The linkage by which the PEG and the biologically active molecule are coupled includes but is not limited to the Huisgen [3+2] cycloaddition product.
[194] It is well established in the art that PEG can be used to modify the surfaces of
biomaterials (see, e.g., U.S. Patent 6,610,281; Mehvar, R., J. Pharm Pharm Sci., 3(1):125-136 ; (2000) which are incorporated by reference herein). The invention also includes biomaterials comprising a surface having one or more reactive azide or acetylene sites and one or more of the azide- or acetylene-containing polymers of the invention coupled to the surface via the Huisgen [3+2] cycloaddition linkage. Biomaterials and other substances can also be coupled to the azide-or acetylene-activated polymer derivatives through a linkage other than the azide or acetylene linkage, such as through a linkage comprising a carboxylic acid, amine, alcohol or thiol moiety, to leave the azide or acetylene moiety available for subsequent reactions.
[195] The invention, includes a method of synthesizing the azide- and acetylene-
containing polymers of the invention. In the case of the azi de-containing PEG derivative, the azide can be bonded directly to a carbon atom of the polymer. Alternatively, the azide-containing PEG derivative can be prepared by attaching a linking agent that has the azide moiety at one terminus to a conventional activated polymer so that the resulting polymer has the azide moiety at its terminus. In the case of the acetylene-containing PEG derivative, the acetylene can be bonded directly to a carbon atom of the polymer. Alternatively, the acetylene-containing PEG derivative can be prepared by attaching a linking agent that has the acetylene moiety at one terminus to a

conventional activated polymer so that the resulting polymer has the acetylene moiety at its terminus.
[196] More specifically, in the case of the azide-containing PEG derivative, a water
soluble polymer having at least one active hydroxyl moiety undergoes a reaction to produce a substituted polymer having a more reactive moiety, such as a mesylate, tresylate, tosylate or halogen leaving group, thereon. The preparation and use of PEG derivatives containing sulfonyl acid halides, halogen atoms and other leaving groups are known to those of ordinary skill in the art. The resulting substituted polymer then undergoes a reaction to substitute for the morereactive moiety an azide moiety at the terminus of the polymer. Alternatively, a water soluble polymer having at least one active nucleophilic or electrophilic moiety undergoes a reaction with a linking agent that has an azide at one terminus so that a covalent bond is formed between the PEG polymer and the linking agent and the azide moiety is positioned at the terminus of the polymer. Nucleophilic and electrophilic moieties, including amines, thiols, hydrazides, hydrazines, alcohols, carboxylates, aldehydes, ketones, thioesters and the like, are known to those of ordinary skill in the art.
[197] More specifically, in the case of the acetylene-containing PEG derivative, a water
soluble polymer having at least one active hydroxyl moiety undergoes a reaction to displace a . halogen or other activated leaving group from a precursor that contains an acetylene moiety. . Alternatively, a water soluble polymer having at least one active nucleophilic or electrophilic moiety undergoes a reaction with a linking agent that has an acetylene at one terminus so that a covalent bond is formed between the PEG polymer and the linking agent and the acetylene moiety is positioned at the terminus of the polymer. The use of halogen moieties, activated leaving group, nucleophilic and electrophilic moieties in the context of organic synthesis and the preparation and use of PEG derivatives is well established to practitioners in the art.
[198] The invention also provides a method for the selective modification of proteins to
add other substances to the modified protein, including but not limited to water soluble polymers such as PEG and PEG derivatives containing an azide or acetylene moiety. The azide- and acetylene-containing PEG derivatives can be used to modify the properties of surfaces and molecules where biocompatibility, stability, solubility and lack of immunogenicity are important, while at the same time providing a more selective means of attaching the PEG derivatives to proteins than was previously known in the art.

IL Growth Hormone Supergene Family
{199] The following proteins include those encoded by genes of the growth hormone (GH)
supergene family (Bazan, F., Immunology Today 11: 350-354 (1990); Bazan, J. F. Science 257: 410-413 (1992); Mott, H. R. and Campbell, L D., Current Opinion in Structural Biology 5: 114-121 (1995); Silvennoinen, O. and Ihle, J. N., SIGNALLING BY THE HEMATOPOIETIC CYTOKINE RECEPTORS (1996)): growth hormone, prolactin, placental lactogen, erythropoietin (EPO), thrombopoietin (TPO), interleukin-2 (IL-2), IL-3, IL-4, IL-5, IL-6, IL-7, IL-9, EL-10, IL-11, IL-12 (p35 subunit), IL-13, IL-15, oncostatin M, ciliary neurotrophic factor (CNTF)5 leukemia inhibitory factor (LIF), alpha interferon, beta interferon, epsilon interferon, gamma interferon, omega interferon, tau interferon, granulocyte-colony stimulating factor (G-CSF), granulocyte-macrophage colony stimulating factor (GM-CSF), macrophage colony stimulating factor (M-CSF) and cardiotrophin-1 (CT-1) ("the GH supergene family"). It is anticipated that additional members of this gene family will be identified in the future through gene cloning and sequencing. Members of the GH supergene family have similar secondary and tertiary structures, despite the fact that " they generally have limited amino acid or DNA sequence identity. The shared structural features allow, new members of the gene family to be readily identified and the non-natural amino acid methods and compositions described herein similarly applied. Given the extent of structural homology among the members of the GH supergene family, non-naturally encoded amino acids may be incorporated into any members of the GH supergene family using the present invention. Each member of this family of proteins comprises a four helical bundle, the general structure of which is shown in Figure 1. The general structures of family members hGH, EPO, IFNct-2, and G-CSF are shown in Figures 2, 3,4, and 5, respectively.
[2001 Structures of a number of cytokines, including G-CSF (Zink et al., FEBS Lett.
314:435 (1992); Zink et al., Biochemistry 33:8453 (1994); Hill et al, Proc. Natl. Acad. Sci.USA 90:5167 (1993), GM-CSF (Diederichs, K., et al Science 154: 1779-1782 (1991); Walter et al, J. Mol Biol 224:1075-1085 (1992)), IL-2 (Bazan, J. F. and McKay, D. B. Science 1ST. 410-413 (1992), IL-4 (Redfield et al., Biochemistry 30: 11029-11035 (1991); Powers et al, Science 256:1673-1677 (1992)), and IL-5 (Milburn et al., Nature 363: 172-176 (1993)) have been determined by X-ray diffraction and NMR studies and show striking conservation with the GH structure, despite a lack of significant primary sequence homology. IFN is considered to be a member of this family based upon modeling and other studies (Lee et al., J. Interferon Cytokine

Res. 15:341 (1995); Murgolo et aL, Proteins 17:62 (1993); Radhakrishnan et ah, Structure 4:1453 (1996); Klaus et aL, J. Mol. BioL 274:661 (1997)). EPO is considered to be a member of this family based upon modeling and mutagenesis studies (Boissel et aL, X BioL Chem. 268: 15983-15993 (1993); Wen et aL, J. BioL Cbem. 269: 22839-22846 (1994)). All of the above cytokines and growth factors are now considered to comprise one large gene family.
[201] In addition to sharing similar secondary and tertiary structures, members of this
family share the property that they must oligomerize cell surface receptors to activate intracellular signaling pathways. Some GH family members, including but not limited to; GH and EPO, bind a single type of receptor and cause it to form homodimers. Other family members, including but not limited to, IL-2, IL-4, and BL-6, bind more than one type of receptor and cause the receptors to form heterodimers or higher order aggregates (Davis et aL, (1993), Science 260: 1805-1808; Paonessa et aL, (1995), EMBO J. 14: 1942-1951; Mott and Campbell, Current Opinion in Structural Biology 5: 114-121 (1995)). Mutagenesis studies have shown that, like GH, these other cytokines and growth factors contain multiple receptor binding sites, typically two, and bind their ?: cognate receptors sequentially (Mott and Campbell, Current Opinion in Structural Biology 5: 114- '* 121 (1995); Matthews et aL, (1996) Proc. Natl. Acad Sci. USA 93: 9471-9476). Like'GH, the [202] A general conclusion reached from mutational studies of various members of the
GH supergene family is that the loops joining the alpha helices generally tend to not be involved in receptor binding. In particular the short B-C loop appears to be non-essential for receptor binding in most, if not all, family members. For this reason, the B-C loop may be substituted with non-naturally encoded amino acids as described herein in members of the GH supergene family. The A-B loop, the C-D loop (and D-E loop of interferon/ EL-10-like members of the GH superfamily) may also be substituted with a non-naturally-occurring amino acid. Amino acids proximal to helix A and distal to the final helix also tend not to be involved in receptor binding and also may be sites for introducing non-naturally-occurring amino acids. In some embodiments,

a non-naturally encoded amino acid is substituted at any position within a loop structure, including
but not limited to, the first 1, 2, 3, 4, 5, 6, 7, or more amino acids of the A-B, B-C, C-D or D-E
loop. In some embodiments, one or more non-naturally encoded amino acids are substituted
within the last 1,2, 3, 4, 5, 6,7, or more amino acids of the A-B, B-C, C-D or D-E loop.
[203] Certain members of the GH family, including but not limited to, EPO, IL-2, EL-3,
EL-4, IL-6, G-CSF, GM-CSF, TPO, IL-10, EL-12 p35, EL-13, IL-15 and beta interferon contain N-linked and/or O-linked sugars. The glycosylation sites in the proteins occur almost exclusively in the loop regions and not in the alpha helical bundles. Because the loop regions generally are not involved in receptor binding and because they are sites for the covalent attachment of sugar groups, they may be useful sites for introducing non-naturally-occurring amino acid substitutions into the proteins. Amino acids that comprise the N- and O-linked glycosylation sites in the proteins may be sites for non-naturally-occurring amino acid substitutions because these amino acids are surface-exposed. Therefore, the natural protein can tolerate bulky sugar groups attached to the proteins at these sites and the glycosylation sites tend to be located away from the receptor binding sites.
[204] Additional members of the GH supergene family are likely to be discovered in the
future. New members of the GH supergene family can be identified through computer-aided
secondary and tertiary structure analyses of the predicted protein sequences, and by selection
techniques designed to identify molecules that bind to a particular target. Members of the GH
supergene family typically possess four or five amphipathic helices joined by non-helical amino
acids (the loop regions). The proteins may contain a hydrophobic signal sequence at their N-
terminus to promote secretion from the cell. Such later discovered members of the GH supergene
family also are included within this invention. A related application is International Patent
Application entitled 'Modified Four Helical Bundle Polypeptides and Their Uses" published as
WO 05/074650 on August 18, 2005, which is incorporated by reference herein.
[205] Thus, the description of the growth hormone supergene family is provided for
illustrative purposes and by way of example only and not as a limit on the scope of the methods, compositions, strategies and techniques described herein. Further, reference to GH polypeptides in this application is intended to use the generic term as an example of any member of the GH supergene family. Thus, it is understood that the modifications and chemistries described herein

with reference to hGH polypeptides or protein can be equally applied to any member of the GH supergene family, including those specifically listed herein.
IIL General Recombinant Nucleic Acid Methods For Use With The Invention
[206] In numerous embodiments of the present invention, nucleic acids encoding a GH,
e.g., hGH polypeptide of interest will be isolated, cloned and often altered using recombinant
methods. Such embodiments are used, including but not limited to, for protein expression or
during the generation of variants, derivatives, expression cassettes, or other sequences derived
from a GH, e.g., hGH polypeptide. In some embodiments, the sequences encoding the
polypeptides of the invention are operably linked to a heterologous promoter. Isolation of hGH
and production of GH in host cells are described in, e.g., U.S. Patent Nos. 4,601,980, 4,604,359,
4,634,677, 4,658,021, 4,898,830, 5,424,199, 5,795,745, 5,854,026, 5,849,535; 6,004,931;
6,022,711; 6,143,523 and 6,608,183, which are incorporated by reference herein.
[207] A nucleotide sequence encoding a hGH polypeptide comprising a non-naturally .
encoded amino acid may be synthesized on the basis of the amino acid sequence of the parent polypeptide, including but not limited to, having the amino acid sequence shown in SEQ ID NO: 2 (hGH) and then changing the nucleotide sequence so as to effect introduction (i.e., incorporation or substitution) or removal (i.e., deletion or substitution) of the relevant amino acid residue(s). The nucleotide sequence may be conveniently modified by site-directed mutagenesis in accordance with conventional methods. Alternatively, the nucleotide sequence may be prepared by chemical synthesis, including but not limited to, by using an oligonucleotide synthesizer, wherein oligonucleotides are designed based on the amino acid sequence of the desired polypeptide, and preferably selecting those codons that are favored in the host cell in which the recombinant polypeptide will be produced. For example, several small oligonucleotides coding for portions of the desired polypeptide may be synthesized and assembled by PCR, ligation or ligation chain reaction. See, e.g., Barany, et ah, Proa Natl Acad. Set 88: 189-193 (1991); U.S. Patent 6,521,427 which are incoiporated by reference herein.
[208] This invention utilizes routine techniques in the field of recombinant genetics.
Basic texts disclosing the general methods of use in this invention include Sambrook et aL, Molecular Cloning, A Laboratory Manual (3rd ed. 2001); Kriegler, Gene Transfer and

Expression: A Laboratory Manual (1990); and Current Protocols in Molecular Biology (Ausubel etal, eds., 1994)).
{209] General texts which describe molecular biological techniques include Berger and
Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzvmology volume 152 Academic Press, Inc., San Diego, CA (Berger); Sambrook et aL, Molecular Clnninp; - A Laboratory Manual (2nd Ed.\ Vol. 1-3. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1989 ("Sambrook") and Current Protocols in Molecular Biology, F.M. Ausubel et aL, eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (supplemented through 1999) ("Ausubel")). These texts describe mutagenesis, the use of vectors, promoters and many other relevant topics related to, including but not limited to, the generation of genes or polynucleotides that include selector codons for production of proteins that include unnatural amino acids, orthogonal tRNAs, orthogonal synthetases, and pairs thereof.
[210] Various types of mutagenesis are used in the invention for a variety of purposes,
including but not limited to, to produce novel synthetases or tRNAs, to mutate tRNA molecules, to mutate polynucleotides encoding synthetases, to produce libraries of tRNAs, to produce libraries of synthetases, to produce selector codons, to insert selector codons that encode unnatural amino acids in a protein or polypeptide of interest They include but are not limited to site-directed, random point mutagenesis, homologous recombination, DNA shuffling or other recursive mutagenesis methods, chimeric construction, mutagenesis using uracil containing templates, oligonucleotide-directed mutagenesis, phosphorothioate-modified DNA mutagenesis, mutagenesis using gapped duplex DNA or the like, or any combination thereof. Additional suitable methods include point mismatch repair, mutagenesis using repair-deficient host strains, restriction-selection and restriction-purification, deletion mutagenesis, mutagenesis by total gene synthesis, double-strand break repair, and the like. Mutagenesis, including but not limited to, involving chimeric constructs, are also included in the present invention. In one embodiment, mutagenesis can be guided by known information of the naturally occurring molecule or altered or mutated naturally occurring molecule, including but not limited to, sequence, sequence comparisons, physical properties, secondary, tertiary, or quaternary structure, crystal structure or the like.

[211] The texts and examples found herein describe these procedures. Additional
information is found in the following publications and references cited within: Ling et al., Approaches to DNA mutagenesis: an overview, Anal Biochem. 254(2): 157-178 (1997); Dale et al., Oligonucleotide-directed random mutagenesis using the phosphorothioate method, Methods Mol Biol. 57:369-374 (1996); Smith, In vitro mutagenesis, Ann. Rev. Genet 19:423-462 (1985); Botstein & Shorfle, Strategies and applications of in vitro mutagenesis, Science 229:1193-1201 (1985); Carter, Site-directed mutagenesis, Biochem. J. 237:1-7 (1986); Kunkel, The efficiency of oligonucleotide directed mutagenesis, in Nucleic Acids & Molecular Biology (Eckstein, F. and Lilley, D.M.J. eds., Springer Veriag, Berlin) (1987); Kunkel, Rapid and efficient site-specific mutagenesis withoutphenotypic selection, Proc. Natl. Acad. Sci. USA 82:488-492 (1985); Kunkel et al., Rapid and efficient site-specific mutagenesis without phenotypic selection, Methods in Enzvmol. 154, 367-382 (1987); Bass et al., Mutant Trp repressors with new DNA-binding specificities, Science 242:240-245 (1988); Zoller & Smith, Oligonucleotide-directed mutagenesis using M13-derived vectors: an efficient and general procedure for the production of point mutations in any DNA fragment, Nucleic Acids Res. 10:6487-6500 (1982); Zoller & Smith, i Oligonucleotide-directed mutagenesis of DNA fragments cloned into Ml 3 vectors, Methods in Enzvmol. 100:468-500 (1983); Zoller & Smith, Oligonucleotide-directed mutagenesis: a simple method using two oligonucleotide primers and a single-stranded DNA template, Methods in Enzvmol. 154:329-350 (1987); Taylor et al., The use of phosphorothioate-modified DNA in restriction enzyme reactions to prepare nicked DNA, Nucl. Acids Res. 13: 8749-8764 (1985); Taylor et al., The rapid generation of oligonucleotide-directed mutations at high frequency using phosphorothioate-modified DNA. Nucl. Acids Res. 13: 8765-8785 (1985); Nakamaye & Eckstein, Inhibition of restriction endonuclease Nci I cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis, Nucl. Acids Res. 14: 9679-9698 (1986); Sayers et al., 5 '-3 ' * Exonucleases in phosphorothioate-based oligonucleotide-directed mutagenesis, Nucl. Acids Res. 16:791-802 (1988); Sayers et al., Strand specific cleavage of phosphorothioate-containing DNA by reaction with restriction endonucleases in the presence of ethidium bromide, (1988) Nucl. Acids Res. 16: 803-814; Kramer et al., The gapped duplex DNA approach to oligonucleotide-directed mutation construction, Nucl. Acids Res. 12: 9441-9456 (1984); Kramer & Fritz Oligonucleotide-directed construction of mutations via gapped duplex DNA, Methods in Enzvmol. 154:350-367 (1987); Kramer et al., Improved enzymatic in vitro reactions in the gapped

duplex DNA approach to oligonucleotide-directed construction of mutations, Nucl. Acids Res. 16: 7207 (1988); Fritz et al., Oligonucleotide-directed construction of mutations: a gapped duplex DNA procedure without enzymatic reactions in vitro, Nucl. Acids Res. 16: 6987-6999 (1988); Kramer et al., Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of E. coli, Cell 38:879-887 (1984); Carter et al., Improved oligonucleotide site-directed mutagenesis using Ml 3 vectors, Nucl. Acids Res. 13: 4431-4443 (1985); Carter, Improved oligonucleotide-directed mutagenesis using Ml 3 vectors, Methods in Bnzvmol. 154: 382-403 (1987); Eghtedarzadeh & Henikoff, Use of oligonucleotides to generate large deletions, Nucl. Acids Res. 14: 5115 (1986); Wells et al., Importance of hydrogen-bond formation in stabilizing the transition state ofsubtilisin, Phil. Trains. R. Soc. Lond. A 317: 415-423 (1986); Nambiar et al., Total synthesis and cloning of a gene coding for the ribonuclease Sprotein, Science 223: 1299-1301 (1984); Sakmar and Khorana, Total synthesis and expression of a gene for the alpha-subunit of bovine rod outer segment guanine nucleotide-binding protein (trafisducin), Nucl. Acids Res. 14: 6361-6372 (1988); Wells et al., Cassette mutagenesis: an :; efficient method for generation of multiple mutations at defined sites, Gene 34:315-323 (1985); » Grundstrom et al., Oligonucleotide-directed mutagenesis by microscale 'shot-gun'gene synthesis, ■•; Nucl. Acids Res. 13: 3305-3316 (1985); Mandecki, Oligonucleotide-directed double-strand break '\ repair in plasmids of Escherichia coli: a method for site-specific mutagenesis, Proc. Natl. Acad. -' Sci. USA. 83:7177-7181 (1986); Arnold, Protein engineering for unusual environments, Current, > Opinion in Biotechnology 4:450-455 (1993); Sieber, et al., Nature Biotechnology, 19:456-460 (2001); W- P. C. Stemmer, Nature 370, 389-91 (1994); and, I. A. Lorimer, I. Pastan, Nucleic Acids Res. 23, 3067-8 (1995). Additional details on many of the above methods can be found in Methods in Enzvmology Volume 154, which also describes useful controls for trouble-shooting problems with various mutagenesis methods.
[212] Oligonucleotides, e.g., for use in mutagenesis of the present invention, e.g.,
mutating libraries of synthetases, or altering tRNAs, are typically synthesized chemically according to the solid phase phosphoramidite triester method described by Beaucage and Caruthers, Tetrahedron Letts. 22(20): 1859-1862, (1981) e.g., using an automated synthesizer, as described in Needham-VanDevanter et al., Nucleic Acids Res., 12:6159-6168 (1984).

[213] The invention also relates to eukaryotic host cells, non-eukaryotic host cells, and
organisms for the in vivo incorporation of an unnatural amino acid via orthogonal tRNA/RS pairs. Host cells are genetically engineered (including but not limited to, transformed, transduced or transfected) with the polynucleotides of the invention or constructs which include a polynucleotide of the invention, including but not limited to, a vector of the invention, which can be, for example, a cloning vector or an expression vector. For example, the coding regions for the orthogonal tRNA, the orthogonal tRNA synthetase, and the protein to be derivatized are operably linked to gene expression control elements that are functional in the desired host cell. The vector can be, for example, in the form of a plasmid, a cosmid, a phage, a bacterium, a virus, a naked polynucleotide, or a conjugated polynucleotide. The vectors are introduced into cells and/or microorganisms by standard methods including electroporation (Fromm et al., Proc. Natl. Acad. Sci. USA 82, 5824 (1985)), infection by viral vectors, high velocity ballistic penetration by small particles with the nucleic acid either within the matrix of small beads or particles, or on the surfac (Klein et al., Nature 327, 70-73 (1987), and/or the like.
[214] The engineered host cells can be cultured in conventional nutrient media modifie
as appropriate for such activities as, for example, screening steps, activating promoters or selectin transformants. These cells can optionally be cultured into transgenic organisms. ■ Other useft references, including but not limited to for cell isolation and culture (e.g., for subsequent nuclei acid isolation) include Freshney (1994) Culture of Animal Cells, a Manual of Basic Technique third edition, Wiley- Liss, New York and the references cited therein; Payne et al (1992) Plar Cell and Tissue Culture in Liquid Systems John Wiley & Sons, Inc. New York, NY; Gamborg an Phillips (eds.) (1995) Plant Cell. Tissue and Organ Culture: Fundamental Methods Springer Lab Manual, Springer-Verlag (Berlin Heidelberg New York) and Atlas and Parks (eds.) The Handbook of Microbiological Media (1993) CRC Press, Boca Raton, FL.
[215] Several well-known methods of introducing target nucleic acids into cells are
available, any of which can be used in the invention. These include: fusion of the recipient cells with bacterial protoplasts containing the DNA, electroporation, projectile bombardment, and infection with viral vectors (discussed further, below), etc. Bacterial cells can be used to amplify the number of plasmids containing DNA constructs of this invention. The bacteria are grown to log phase and the plasmids within the bacteria can be isolated by a variety of methods known in

the art {see, for instance, Sambrook). In addition, kits are commercially available for the purification of plasmids from bacteria, (see, e.g., EasyPrep™, FlexiPrep™, both from Pharmacia Biotech; StrataCIean™ from Stratagene; and, QIAprep™ from Qiagen). The isolated and purified plasmids are then further manipulated to produce other plasmids, used to transfect cells or incorporated into related vectors to infect organisms. Typical vectors contain transcription and translation terminators, transcription and translation initiation sequences, and promoters useful for regulation of the expression of the particular target nucleic acid. The vectors optionally comprise generic expression cassettes containing at least one independent terminator sequence, sequences permitting replication of the cassette in eukaryotes, or prokaryotes, or both, (including; but not limited to, shuttle vectors) and selection markers for both prokaryotic and eukaryotic systems. Vectors are suitable for replication and integration in prokaryotes, eukaryotes, or both. See, Gillam & Smith, Gene 8:81 (1979); Roberts, et aly Nature, 328:731 (1987); Schneider, R, et at, . Protein Expr. Purif. 6(1): 10-14 (1995); Ausubel, Sambrook, Berger {all supra), A catalogue of bacteria and bacteriophages useful for cloning is provided, e.g., by the ATCC, e.g., The ATCC •= Catalogue of Bacteria and Bacteriophage (1992) Ghema et ah (eds) published by the ATCC. Additional basic procedures for sequencing, cloning and other aspects of molecular biology and underlying theoretical considerations are also found in Watson et ah (1992) Recombinant DNA v Second Edition Scientific American Books, NY. In addition, essentially any nucleic acid (and virtually any labeled nucleic acid, whether standard or non-standard) can be custom or standard ordered from any of a variety of commercial sources, such as the Midland Certified Reagent Company (Midland, TX available on the World Wide Web at mcrc.com), The Great American Gene Company (Ramona, CA available on the World Wide Web at genco.com), ExpressGen Inc. (Chicago, EL available on the World Wide Web at expressgen.com), Operon Technologies Inc. (Alameda, CA) and many others.
(a) Selector Codons
[216] Selector codons of the invention expand the genetic codon framework of protein
biosynthetic machinery. For example, a selector codon includes, but is not limited to, a unique
three base codon, a nonsense codon, such as a stop codon, including but not limited to, an amber
codon (UAG), an ochre codon, or an opal codon (UGA), an unnatural codon, a four or more base
codon, a rare codon, or the like. It is readily apparent to those of ordinary skill in the art that there
is a wide range in the number of selector codons that can be introduced into a desired gene or

polynucleotide, including but not limited to, one or more, two or more, three or more, 4, 5, 6, 7, 8, 9, 10 or more in a single polynucleotide encoding at least a portion of the hGH polypeptide.
[217] In one embodiment, the methods involve the use of a selector codon that is a stop
codon for the incorporation of one or more unnatural amino acids in vivo in a cell. For example, an O-tRNA is produced that recognizes the stop codon, including but not limited to, UAG, and is aminoacylated by an O-RS with a desired unnatural amino acid. This O-tRNA is not recognized by the naturally occurring host's aminoacyl-tRNA synthetases. Conventional site-directed mutagenesis can be used to introduce the stop codon, including but not limited to, TAG, at the site of interest in a polypeptide of interest. See, e.g, Sayers, J.R., et al. (1988), 5'~39 Exonucleases in phosphorothioaie-based oligonucleotide-directed mutagenesis. Nucleic Acids Res, 16:791-802. When the O-RS, O-tRNA and the nucleic acid that encodes the polypeptide of interest are combined in vivo, the unnatural amino acid is incorporated in response to the UAG codon to give a polypeptide containing the unnatural amino acid at the specified position.
[218] The incorporation of unnatural amino acids in vivo can be done without significant
perturbation of the eukaryotic host cell. For example, because the suppression efficiency for the UAG codon depends upon the competition between the O-tRNA, including but not limited to, the amber suppressor tRNA, and a eukaryotic release factor (including but not limited to, eRF) (which binds to a stop codon and initiates release of the growing peptide from the ribosome), the suppression efficiency can be modulated by, including but not limited to, increasing the expression level of O-tRNA, and/or the suppressor tRNA.
[219] Unnatural amino acids can also be encoded with rare codons. For example, when
the arginine concentration in an in vitro protein synthesis reaction is reduced, the rare arginine codon, AGG, has proven to be efficient for insertion of Ala by a synthetic tRNA acylated with alanine. See, e.g., Ma et al., Biochemistry. 32:7939 (1993). In this case, the synthetic tRNA competes with the naturally occurring tRNAArg, which exists as a minor species in Escherichia coli. Some organisms do not use all triplet codons. An unassigned codon AGA in Micrococcus luteus has been utilized for insertion of amino acids in an in vitro transcription/translation extract. See, e.g., Kowal and Oliver, Nucl. Acid. Res., 25:4685 (1997). Components of the present invention can be generated to use these rare codons in vivo.

[220] Selector codons also comprise extended codons, including but not limited to, four
or more base codons, such as, four, five, six or more base codons. Examples of four base codons include, but are not limited to, AGGA, CUAG, UAGA, CCCU and the like. Examples of five base codons include, but are not limited to, AGGAC, CCCCU, CCCUC, CUAGA, CUACU, UAGGC and the like. A feature of the invention includes using extended codons based on frameshift suppression. Four or more base codons can insert, including but not limited to, one or multiple unnatural amino acids into the same protein. For example, in the presence of mutated O-tRNAs, including but not limited to, a special frameshift suppressor tRNAs, with anticodon loops, for example, with at least 8-10 nt anticodon loops, the four or more base codon is read as single amino acid. In other embodiments, the anticodon loops can decode, including but not limited to, at least a four-base codon, at least a five-base codon, or at least a six-base codon or more. Since there are 256 possible four-base codons, multiple unnatural amino acids can be encoded in the same cell using a four or more base codon. See, Anderson et al., (2002) Exploring the Limits of Codon and Anticodon Size, Chemistry and Biology, 9:237-244; Magliery, (2001) Expanding the Genetic Code: Selection of Efficient Suppressors of Four-base Codons and Identification of "Shifty' Four-base Codons with a Library Approach in Escherichia coli9 J. Mol. Biol. 307: 755-769.
[221] For example, four-base codons have been used to incorporate unnatural amino
acids into proteins using in vitro biosynthetic methods. See, e.g., Ma et al., (1993) Biochemistry, 32:7939; and Hohsaka et al., (1999) J. Am. Chem. Soc, 121:34. CGGG and AGGU were used to simultaneously incorporate 2-naphthylalanine and an NBD derivative of lysine into streptavidin in vitro with two chemically acylated frameshift suppressor tRNAs. See, e.g., Hohsaka et al., (1999) J. Am. Chem. Soc. 121:12194. In an in vivo study, Moore et al. examined the ability of tRNALeu derivatives with NCUA anticodons to suppress UAGN codons (N can be U, A,- G, or C), and found that the quadruplet UAGA can be decoded by a tRNALeu with a UCUA anticodon with an efficiency of 13 to 26% with little decoding in the 0 or-1 frame. See, Moore et al., (2000) J. MoL Biol.. 298:195. In one embodiment, extended codons based on rare codons or nonsense codons can be used in the present invention, which can reduce missense readthrough and frameshift suppression at other unwanted sites.

[222] For a given system, a selector codon can also include one of the natural three base
codons, where the endogenous system does not use (or rarely uses) the natural base codon. For example, this includes a system that is lacking a tRNA that recognizes the natural three base codon, and/or a system where the three base codon is a rare codon.
[223] Selector codons optionally include unnatural base pairs. These unnatural base pairs
further expand the existing genetic alphabet. One extra base pair increases the number of triplet
codons from 64 to 125. Properties of third base pairs include stable and selective base pairing,
efficient enzymatic incorporation into DNA with high fidelity by a polymerase, and the efficient
continued primer extension after synthesis of the nascent unnatural base pair. Descriptions of
unnatural base pairs which can be adapted for methods and compositions include, e.g., Hirao, et
al., (2002) An unnatural base pair for incorporating amino acid analogues into protein, Nature
Biotechnology, 20:177-182. See, also, Wu, Y., et al., (2002) J. Am. Chem. Soc. 124:14626-
14630. Other relevant publications are listed below. '
[224] For in vivo usage, the unnatural nucleoside is membrane permeable and is
phosphorylated to form the corresponding triphosphate. In addition, the increased genetic information is stable and not destroyed by cellular enzymes. Previous efforts by Benner and others took advantage of hydrogen bonding patterns that are different from those in canonical Watson-Crick pairs, the most noteworthy example of which is the iso-C:iso-G pair. See, e.g., Switzer et al., (1989) J. Am. Chem. Soc, 111:8322; and Piccirilli et al., (1990) Nature. 343:33; Kool, (2000) Curr. Opin. Chem. Biol., 4:602. These bases in general mispair to some degree with natural bases and cannot be enzymatically replicated. Kool and co-workers demonstrated that hydrophobic packing interactions between bases can replace hydrogen bonding to drive the formation of base pair. See, Kool, (2000) Curr. Opin. Chem. Biol., 4:602; and Guckian and Kool, (1998) Angew. Chem. Int. Ed. Engl.. 36, 2825. In an effort to develop an unnatural base pair satisfying all the above requirements, Schultz, Romesberg and co-workers have systematically synthesized and studied a series of unnatural hydrophobic bases. A PICS:PICS self-pair is found to be more stable than natural base pairs, and can be efficiently incorporated into DNA by Klenow fragment of Escherichia coli DNA polymerase I (KF). See, e.g., McMinn et al., (1999) J. Am. Chem. Soc. 121:11585-6; and Ogawa et al., (2000) J. Am. Chem. Soc. 122:3274. A 3MN:3MN self-pair can be synthesized by KF with efficiency and selectivity sufficient for biological

function. See, e.g., Ogawa et al., (2000) J. Am. Chem. Soc, 122:8803. However, both bases act as a chain terminator for further replication. A mutant DNA polymerase has been recently evolved that can be used to replicate the PICS self pair. In addition, a 7AI self pair can be replicated. See, e.g., Tae et al., (2001) J. Am. Chem. Soc.% 123:7439. A novel metallobase pair, DipicrPy, has also been developed, which forms a stable pair upon binding Cu(H). See, Meggers et al., (2000) J. Am. Chem. Soc, 122:10714. Because extended codons and unnatural codons are intrinsically orthogonal to natural codons, the methods of the invention can take advantage of this property to generate orthogonal tRNAs for them.
[225] A translational bypassing system can also be used to incorporate an unnatural
amino acid in a desired polypeptide. In a translational bypassing system, a large sequence is incorporated into a gene but is not translated into protein. The sequence contains a structure that serves as a cue to induce the ribosome to hop over the sequence and resume translation downstream of the insertion.
[226] - In certain embodiments, the protein or polypeptide of interest (or portion thereof) in
the methods and/or compositions of the invention is encoded by a .nucleic acid. Typically, the nucleic acid comprises at least one selector codon, at least two selector codons, at least three selector codons, at least four selector codons, at least five selector codons, at least six selector codons, at least seven selector codons, at least eight selector codons, at least nine selector codons, ten or more selector codons.
[227] Genes coding for proteins or polypeptides of interest can be mutagenized using
methods well-known to one of skill in the art and described herein to include, for example, one or more selector codon for the incorporation of an unnatural amino acid: For example, a nucleic acid for a protein of interest is mutagenized to include one or more selector codon, providing for the incorporation of one or more unnatural amino acids. The invention includes any such variant, including but not limited to, mutant, versions of any protein, for example, including at least one unnatural amino acid. Similarly, the invention also includes corresponding nucleic acids, i.e., any nucleic acid with one or more selector codon that encodes one or more unnatural amino acid.
[228] Nucleic acid molecules encoding a protein of interest such as a hGH polypeptide
may be readily mutated to introduce a cysteine at any desired position of the polypeptide. Cysteine is widely used to introduce reactive molecules, water soluble polymers, proteins, or a

wide variety of other molecules, onto a protein of interest. Methods suitable for the incorporation of cysteine into a desired position of a polypeptide are known to those of ordinary skill in the art, such as those described in U.S. Patent No. 6,608,183, which is incorporated by reference herein, and standard mutagenesis techniques.
IV. Non-Naturatty Encoded Amino Acids
[229] A very wide variety of non-naturally encoded amino acids are suitable for use in
the present invention. Any number of non-naturally encoded amino acids can be introduced into a
GH, e.g., hGH polypeptide. In general, the introduced non-naturally encoded amino acids are
substantially chemically inert toward the 20 common, genetically-encoded amino acids (i.e.,
alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine,
isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan,
tyrosine, and valine). In some embodiments, the non-naturally encoded amino acids include side
chain functional groups that react efficiently and selectively with functional groups not found in
the 20 common amino acids (including but not limited to, azido, ketone, aldehyde and aminooxy
groups) to form stable conjugates. For example, a GH, e.g., hGH polypeptide that includes a non-
naturally encoded amino acid containing an azido functional group can be reacted with a polymer
(including but not limited to, poly(ethylene glycol) or, alternatively, a second polypeptide
containing an alkyne moiety to form a stable conjugate resulting for the selective reaction of the
azide and the alkyne functional groups to form a Huisgen [34-2] cycloaddition product.
[2301 The generic structure of an alpha-amino acid is illustrated as follows (Formula I):
I

[231] A non-naturally encoded amino acid is typically any structure having the above-
listed formula wherein the R group is any substituent other than one used in the twenty natural amino acids, and may be suitable for use in the present invention. Because the non-naturally encoded amino acids of the invention typically differ from the natural amino acids only in the structure of the side chain, the non-naturally encoded amino acids form amide bonds with other amino acids, including but not limited to, natural or non-naturally encoded, in the same manner in

which they are formed in naturally occurring polypeptides. However, the non-naturally encoded amino acids have side chain groups that distinguish them from the natural amino acids. For example, R optionally comprises an alkyi-, aryl-, acyl-, keto-, azido-, hydroxyl-, hydrazine, cyano-, halo-, hydrazide, alkenyl, alkynl, ether, thiol, seleno-, sulfonyl-, borate, boronate, phospho, phosphono, phosphine, heterocyclic, enone, imine, aldehyde, ester, thioacid, hydroxylamine, amino group, or the like or any combination thereof. Other non-naturally occurring amino acids of interest that may be suitable for use in the present invention include, but are not limited to, amino acids comprising a photoactivatable cross-linker, spin-labeled amino acids, fluorescent amino acids, metal binding amino acids, metal-containing amino acids, radioactive amino acids, amino acids with novel functional groups, amino acids that covalently or noncovalently interact with other molecules, photocaged and/or photoisomerizable amino acids, amino acids comprising biotin or a biotin analogue, glycosylated amino acids such as a sugar substituted serine, other carbohydrate modified amino acids, keto-containing amino acids, amino acids comprising polyethylene glycol or polyether, heavy atom substituted amino acids, chemically cleavable and/or photocleavable amino acids, amino acids with an elongated side chains as compared to natural amino acids, including but not limited to, polyethers or long chain hydrocarbons, including but not limited to, greater than about 5 or greater than about 10 carbons, carbon-linked sugar-containing amino acids, redox-active amino acids, amino thioacid containing amino acids, and amino acids comprising one or more toxic moiety.
[232] Exemplary non-naturally encoded amino acids that may be suitable for use in the
present invention and that are useful for reactions with water soluble polymers include, but are not limited to, those with carbonyl, aminooxy, hydrazine, hydrazide, semicarbazide, azide and alkyne reactive groups. In some embodiments, non-naturally encoded amino acids comprise a saccharide moiety. Examples of such amino acids include 7\T-acetyl-L-glucosaminyl-L-serine, Af-acetyl-L-galactosammyl-L-serine, iV^acetyl-L-glucosaminyl-L-threonine, i^-acetyl-L-glucosaminyl-L-asparagine and O-maimosaminyl-L-serine. Examples of such amino acids also include examples where the naturally-occuring N- or O- linkage between the amino acid and the saccharide is replaced by a covalent linkage not commonly found in nature - including but not limited to, an alkene, an oxime, a thioether, an amide and the like. Examples of such amino acids also include saccharides that are not commonly found in naturally-occuring proteins such as 2-deoxy-glucose, 2-deoxygalactose and the like.

[233] Many of the non-naturally encoded amino acids provided herein are commercially
available, e.g., from Sigma-Aldrich (St. Louis, MO, USA), Novabiochem (a division of EMD Biosciences, Darmstadt, Germany), or Peptech (Burlington, MA, USA). Those that are not commercially available are optionally synthesized as provided herein or using standard methods known to those of ordinary skill in the art. For organic synthesis techniques, see, e.g., Organic Chemistry by Fessendon and Fessendon, (1982, Second Edition, Willard Grant Press, Boston Mass.); Advanced Organic Chemistry by March (Third Edition, 1985, Wiley and Sons, New York); and Advanced Organic Chemistry by Carey and Sundberg (Third Edition, Parts A and B, 1990, Plenum Press, New York). See, also, U.S. Patent Application Publications 2003/0082575 and 2003/0108885, which are incorporated by reference herein. In addition to unnatural amino acids that contain novel side chains, unnatural amino acids that may be suitable for use in the present invention also optionally comprise modified backbone structures, including but not limited to, as illustrated by the structures of Formula II and HI:

wherein Z typically comprises OH, NH2, SH, NH-R', or S~R'; X and Y, which can be the same or different, typically comprise S or O, and R and R, which are optionally the same or different, are typically selected from the same list of constituents for the R group described above for the unnatural amino acids having Formula I as well as hydrogen. For example, unnatural amino acids of the invention optionally comprise substitutions in the amino or cafboxyl group as illustrated by Formulas II and HL Unnatural amino acids of this type include, but are not limited to, a-hydroxy acids, a-thioacids, a-aminothiocarboxylates, including but not limited to, with side chains corresponding to the common twenty natural amino acids or unnatural side chains. In addition,

substitutions at the a-carbon optionally include, but are not limited to, L, D, or a-a-disubstituted amino acids such as D-glutamate, D-alanine, D-methyl-O-tyrosine, aminobutyric acid, and the like. Other structural alternatives include cyclic amino acids, such as proline analogues as well as 3, 4 ,6, 7, 8, and 9 membered ring proline analogues, {3 and y amino acids such as substituted p-alanine and y-amino butyric acid.
[234] Many unnatural amino acids are based on natural amino acids, such as tyrosine,
glutamine, phenylalanine, and the like, and are suitable for use in the present invention. Tyrosine analogs include, but are not limited to, para-substituted tyrosines, ortho-substituted tyrosines, and meta substituted tyrosines, where the substituted tyrosine comprises, including but not limited to, a keto group (including but not limited to, an acetyl group), a benzoyl group, an amino group, a hydrazine, an hydroxyamine, a thiol group, a carboxy group, an isopropyl group, a methyl group, a Ce - C20 straight chain or branched hydrocarbon, a saturated or unsaturated hydrocarbon, an O-methyl group, a polyether group, a nitro group, an alkynyl group or the like. In addition, multiply substituted aryl rings are also contemplated. Glutamine analogs that may be suitable for use in the present invention include, but are not limited to, a-hydroxy derivatives, y-substituted derivatives, cyclic derivatives, and amide substituted glutamine derivatives. Example phenylalanine analogs that may be suitable for use in the present invention include, but are not limited to, para-substituted phenylalanines, ortho-substituted phenyalanines, and meta-substituted phenylalanines, where the substituent comprises, including but not limited to, a hydroxy group, a methoxy group, a methyl group, an allyl group, an aldehyde, an azido, an iodo, a bromo, a keto group (including but not limited toy an acetyl group), a benzoyl, an alkynyl group, or the like. Specific examples of unnatural amino acids that may be suitable for use in the present invention include, but are not limited to, a/>-acetyl-L- phenylalanine, an O-methyl-L-tyrosine, an L-3-(2-naphthyl)alanine, a 3-methyl-phenylalanine, an O-4-aIlyl-L-tyrosine, a 4-propyl-L-tyrosme, a tri-O-acetyl-GlcNAcp-serine, an L-Dopa, a fluorinated phenylalanine, an isopropyl-L-phenylalanine, a 7?-azido-L-phenylalanine, a 77-acyl-L-phenylalanine, a /?-benzoyl-L-phenylalanine, an L-phosphoserine, a phosphonoserine, a phosphonotyrosine, a /?-iodo-phenylalanine, a j3-bromophenylalanine, a p-amino-L-phenylalanine, an isopropyl-L-phenylalanine, and a p-propargyloxy-phenylalanine, and the like. Examples of structures of a variety of unnatural amino acids that may be suitable for use in the present invention are provided in, for example, WO 2002/085923 entitled "In vivo

incorporation of unnatural amino acids." See also Kiick et al., (2002) Incorporation ofazides into recombinant proteins for chemoselective modification by the Staudinger ligation, PNAS 99:19-24, which is incorporated by reference herein, for additional methionine analogs.
[235] In one embodiment, compositions of a GH, e.g., hGH polypeptide that include an
unnatural amino acid (such as p-(propargyloxy)-phenyalanine) are provided. Various compositions comprising /?-(prapargyloxy)-phenyalanine and, including but not limited to, proteins and/or cells, are also provided. In one aspect, a composition that includes the p-(propargyloxy)-phenyalanine unnatural amino acid, further includes an orthogonal tRNA. The unnatural amino acid can be bonded (including but not limited to, covalently) to the orthogonal tRNA, including but not limited to, covalently bonded to the orthogonal tRNA though an amino-acyl bond, covalently bonded to a 3'OH or a 2'OH of a terminal ribose sugar of the orthogonal tRNA, etc.
[236} The chemical moieties via unnatural amino acids that can be incorporated into
proteins offer a variety of advantages and manipulations of the protein. For example, the unique reactivity of a keto functional group allows selective modification of proteins with any of a number of hydrazine- or hydroxylamine-containing reagents in vitro and in vivo. A heavy atom unnatural amino acid, for example, can be useful for phasing X-ray structure data. The site-specific introduction of heavy atoms using unnatural amino acids also provides selectivity and flexibility in choosing positions for heavy atoms. Photoreactive unnatural amino acids (including but not limited to, amino acids with benzophenone and arylazides (including but not limited to, phenylazide) side chains), for example, allow for efficient in vivo and in vitro photocrosslinking of protein. Examples of photoreactive unnatural amino acids include, but are not limited to, p-azido-phenylalanine and p-benzoyl-phenylalanine. The protein with the photoreactive unnatural amino acids can then be crosslinked at will by excitation*of the photoreactive group-providing temporal control. In one example, the methyl group of an unnatural amino can be substituted with an isotopically labeled, including but not limited to, methyl group, as a probe of local structure and dynamics, including but not limited to, with the use of nuclear magnetic resonance and vibrational spectroscopy. Alkynyl or azido functional groups, for example, allow the selective modification of proteins with molecules through a [3+2] cycloaddition reaction.

[237] A non-natural amino acid incorporated into a polypeptide at the amino terminus
can be composed of an R group that is any substituent other than one used in the twenty natural amino acids and a 2nd reactive group different from the NH2 group normally present in a-amino acids (see Formula I). A similar non-natural amino acid can be incorporated at the carboxyl terminus with a 2nd reactive group different from the COOH group normally present in a-amino acids (see Formula I).
[238] The unnatural amino acids of the invention may be selected or designed to provide
additional characteristics unavailable in the twenty natural amino acids. For example, unnatural amino acid may be optionally designed or selected to modify the biological properties of a protein into which they are incorporated. For example, the following properties may be optionally modified by inclusion of an unnatural amino acid into a protein: toxicity, biodistribution, solubility, stability, e.g., thermal, hydrolytic, oxidative, resistance to enzymatic degradation, and the like, facility of purification and processing, structural properties, spectroscopic properties, chemical and/or photochemical properties, catalytic activity,.redox potential, half-life, ability to react with other molecules, e.g., covalently or noncovalently, and the like.
STRUCTURE AND SYNTHESIS OF NON-NATURAL AMINO ACIDS: CARBONYL. CARBONYL-LIKE. MASKED CARBONYL. PROTECTED CARBONYL GROUPS, AND HYDROXYLAMINE GROUPS
[239] In some embodiments the present invention provides a GH, e.g., hGH, linked to a
water soluble polymer, e.g., a PEG, by an oxime bond.
[240] Many types of non-naturally encoded amino acids are suitable for formation of
oxime bonds. These include, but are not limited to, non-naturally encoded amino acids containing a carbonyl, dicarbonyl, or hydroxylamine group. Such amino acids are described in U.S. Patent Application Nos. 60/638,418; 60/638,527; and 60/639,195, entitled "Compositions containing, methods involving, and uses of non-natural amino acids and polypeptides," filed December 22, 2004, whiGh are incorporated herein by reference in their entirety. Such amino acids are also described in U.S. Patent Application Nos. 60/696,210; 60/696,302; and 60/696,068, entitled "Compositions containing, methods involving, and uses of non-natural amino acids and polypeptides," filed July 1, 2005, which are incorporated herein by reference in their entirety. Non-naturally encoded amino acids are also described in U.S. Patent Application No. 10/126,931

filed on 19 April 2002 and U.S. Patent Application No. 10/126,927, filed 19 Apr 2002, which are incorporated by reference herein in their entirety.
[241] Some embodiments of the invention utilize GH, e.g., hGH polypeptides that are
substituted at one or more positions with a para-acetylphenylalanine amino acid. The synthesis of p-acetyl-(+/-)-phenyManine and m-acetyl-(+/-)-phenylalanine are described in Zhang, Z., et al., Biochemistry 42: 6735-6746 (2003), incorporated by reference. Other carbonyl- or dicarbonyl-containing amino acids can be similarly prepared by one of ordinary skill in the art. Further, non-limiting examplary syntheses of non-natural amino acid that are included herein are presented in FIGS. 4, 24-34 and 36-39 of U.S. Patent Application No. 10/126,931, which is incorporated by reference herein in its entirety.
[242] Amino acids with an electrophilic reactive group allow for a variety of reactions to
link molecules via nucleophilic addition reactions among others. Such electrophilic reactive groups include a carbonyl group (including a keto group and a dicarbonyl group), a carbonyl-like group (which has reactivity similar to a carbonyl group (including a keto group and a dicarbonyl group) and is structurally similar to a carbonyl group), a masked carbonyl group (which can be readily converted into a carbonyl group (including a keto group and a dicarbonyl group)), or a protected carbonyl group (which has reactivity similar to a carbonyl group (including a keto group and a dicarbonyl group) upon deprotection). Such amino acids include amino acids having the structure of Formula (IV):

wherein:
A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted Iowa: alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower

heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;
B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -0-, -0-(alkyIene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(0)k- where k is 1, 2, or 3, -S(0)k(aIkylene or substituted alkylene)-, -C(O)-, -C(0)-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'-(alkylene or substituted alkylene)-, -C(0)N(R>, -CON(R>(alkylene or substituted alkylene)-, -CSN(R>, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, -N(R5)C(0)0-, -S(0)kN(R')-, -N(R')C(0)N(R')-5 -N(R')C(S)N(R>, -N(R')S(0)kN(R')-, -N(R>N=, -C(R>N-, -C(R')=N-N(R,)", -C(R»)=N-N=, -C(R5)2-N=N-, and -C(R,)2-N(R')-N(R5)-, where each R' is independently H, alkyl, or substituted alkyl;
Ji
R is H, alkyl, substituted alkyl, cycloaDcyl, or substituted cycloalkyl;
each R" is independently H, alkyl, substituted alkyl, or a protecting group, or when more than one R" group is present, two R" optionally form a heterocycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;
each of R3 and R4 is independently H, halogen, lower alkyl, or substituted lower alkyl, or R3 and R4 or two R3 groups optionally form a cycloalkyl or a heterocycloalkyl;
or the -A-B-J-R groups together form a bicyclic or tricyclic cycloalkyl or heterocycloalkyl comprising at least one carbonyl group, including a dicarbonyl group, protected carbonyl group,

including a protected dicarbonyl group, or masked carbonyl group, including a masked, dicarbonyl group;
or the -J-R group together forms a monocyclic or bicyclic cycloalkyl or heterocycloalkyl comprising at least one. carbonyl group, including a dicarbonyl group, protected carbonyl group, including a protected dicarbonyl group, or masked carbonyl group, including a masked dicarbonyl group;
with a proviso that when A is phenylene and each R3 is H, B is present; and that when A is -(CH2)4- and each R3 is H, B is not -NHC(0)(CH2CH2)S and that when A and B are absent and each R3 is H, R is not methyl.
[243] In addition, having the structure of Formula (V) are included:

wherein:
A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;
B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -0-, -0-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(0)k- where k is 1, 2, or 3, -S(0)k(alkylene or substituted alkylene)-, -C(O)-, -C(0)-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R>, -NR'-(alkylene or substituted alkylene)-, -C(0)N(R>, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R>, -CSN(R9)-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, -N(R')C(0)0-, -S(0)kN(R')-, -N(R0C(O)N(R')-, -N(R,)C(S)N(R')-, -NCR^SCOXNCRO-, -N(R>N=, -C(R')=N-, -CCR'^N-NCR')-, -C(R,)=N-N=

-C(R')2-N=N-, and -C(Rs)2-N(Ra)-N(R')-, where each R' is independently H, alkyl, or substituted alkyl;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;
with a proviso that when A is phenylene, B is present; and that when A is -(CHfe)-*-, B is not -NHC(0)(CH2CH2)-; and that when A and B axe absent, R is not methyl.
(244] In addition, amino acids having the structure of Formula (VI) are included:
R
wherein:
B is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -0-, -0-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(0)k- where k is 1, 2, or 3, -S(OX(alkylene or substituted alkylene)-, -C(O)-, -C(0> (alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NRXalkylene or substituted alkylene}-, -C(0)NCR')-, -CON(R>(alkylene or substituted alkylene)-, -CSN(R>, -CSN(R>(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, -N(RJ)C(0)0-, -S(OXN(R>, -N(R,)C(0)N(R')-, -N(R')C(S)N(R>, -N(R')S(0)kN(R>, -N(R')-N=% -C(R>N-, -C(R')=N-N(R,>, -C(R>N-N= -C(RJ)2-N=N-, and -C(R VNCRO-NtR')-, where each R* is independently H, alkyl, or substituted alkyl;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;

R] is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;
each Ra is independently selected from the group consisting of H, halogen, alkyl, substituted alkyl, -N(R% -C(0)kR' where k is 1, 2, or 3, -C(0)N(R% -OR', and -S(0)kR\ where each R' is independently H, alkyl, or substituted alkyl.
[245] In addition, the following amino acids are included;

compounds are optionally amino protected group, carboxyl protected or a salt thereof. Ir addition, any of the following non-natural amino acids may be incorporated into a non-natura amino acid polypeptide.
[246] In addition, the following amino acids having the structure of Formula (VH) are
included:

wherein
B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -0-, -0-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or

substituted alkylene)-, -S(0)k- where k is 1, 2, or 3, -S(OX(alkylene or substituted alkylene)-, -0(0)-, -C(0)-(aIkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'-(alkylene or substituted alkylene)-, -C(0)N(R>, -CON(R>(alkylene or substituted alkylene)-, -CSN(R')-, -CSN(R5)-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, -N(R')C(0)0-, -S(0)fcN(R>, -N(R>)C(0)N(R>, -N(R')C(S)N(R>, -N(R0S(O)kN(R0-, -N(R>N=, -C(RJ)=N-, -C(R>N-N(R>, -C(R>N-N=, -C(R,)2-N=N-, and -C(R')2-N(R>N(R')-, where each R' is independently H, alkyl, or substituted alkyl;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide or polynucleotide;
each Ra is independently selected from the group consisting of H, halogen, alkyl, substituted alky -N(R% -C(0)kR* where k is 1, 2, or 3, -C(0)N(R5)2, -OR', and -S(0)kR\ where each R' i independently H, alkyl, or substituted alkyl; and n is 0 to 8;
with a proviso that when A is -(CH2)4-, B is not -NHC(Q)(CH2CH2)-.
[247] In addition, the following amino acids are included:


, wherein such compounds are optionally amino protected, optionally carboxyl protected, optionally amino protected and carboxyl protected, or a salt thereof. In addition, these non-natural amino acids and any of the following non-natural amino acids may be incorporated into a non-natural amino acid polypeptide.
[248] In addition, the following amino acids having the structure of Formula (VH[) are
included:

wherein A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;
B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O-, -0-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(OV where k is 1, 2, or 3, -S(0)k(alkylene or substituted alkylene)-, -C(0)-> -C(0)-(alkyIene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-> -NR'-Calkylene or substituted alkylene)-, -C(0)N(R>, -CON(R>(alkylene or substituted alkylene)-, -CSN(R>, -CSN(R')-(alkylene or substituted alkylene)-, ~N(R.9)CO-(alkylene or substituted alkylene)-, -N(R')C(0)0-, -S(0)kN(R>, -N(R*)C(0)N(R>, ~N(R')C(S)N(R>, -N(R0S(O)kN(R% -N(R')-N=, -C(R')=N-, -C(R>N-N(R>, -C(R>N-N= -C(RJ)2-N=N-, and -C(RVN(R')-N(R>, where each R' is independently H, alkyl, or substituted alkyl;

Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide.
[249] In addition, the following amino acids having the structure of Formula (DQ are
included:
I
B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene. lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -0-, -0-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(0)k- where k is 1, 2, or 3, -S(0)ie(alkylene or substituted alkylene)-, -C(0>, -C(0)-(alkylene or substituted alkylene)-, -C(S>, -C(S)-(alkylene or substituted alkylene)-, -N(R>, -NR7-(alkylene or substituted alkylene)-, -C(0)N(R>, -CON(R>(alkylene or substituted alkylene)-, -CSN(R>, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, -N(R')C(0)0-, -S(0)kN(R>, -N(R')C(0)N(R>, -N(R*)C(S)N(R')-, -N(R')S(0)ieN(R>, -N(R')-N=, -C(R>N-, -C(R>N-N(R>, -C(R')=N-N=, -C(R,)2-N=N-, and -C(R')2-N(R')-N(R>, where each R' is independently H, alkyl, or substituted alkyl;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;

wherein each Ra is independently selected from the group consisting of H, halogen, alkyl, substituted alkyl, -N(R% -C(0)kR5 where k is 1, 2, or 3, -C(0)N(R')2, -OR', and -S(0)kR', where each R5 is independently H, alkyl, or substituted alkyl.
[250] In addition, the following amino acids are included:

compounds are optionally amino protected, optionally carboxyl protected, optionally amino protected and carboxyl protected, or a salt thereof. In addition, these non-natural amino acids and any of the following non-natural amino acids may be incorporated into a non-natural amino acid polypeptide.
[251] In addition, the following amino acids having the structure of Formula (X) are
included:

wherein B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -O, -0-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(0)k- where k is 1, 2, or 3, -S(0)k(alkylene or substituted alkylene)-, -C(O)-, -C(0)-(alkylene or substituted alkylene)-, -C(S>, -C(S)-(alkylene or substituted alkylene)-, -N(R>, -NR*-(alkylene or substituted alkylene)-, -C(0)N(R>, -CON(R> (alkylene or substituted alkylene)-, -CSN(R>, -CSN(R>(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, -N(R')C(0)0-, -S(0)kN(R>, -N(R')C(0)N(R'>,

-N(R')C(S)N(R')-, -N(R')S(0)kN(R')-, -N(R')-N=, -C(R>N-, -C(R>N-N(R>, -C(R')=N-N=, -C(RJ)2-N=N-5 and -C(R')2-N(R')-N(R5)-, where each R' is independently H, alkyl, or substituted alkyl;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;
each Ra is independently selected from the group consisting of H, halogen, alkyl, substituted alkyl, -N(R% -C(0)kR' where k is 1, 2, or 3, -C(0)N(R')2, -OR', and -S(0)kR\ where each R' is independently H, alkyl, or substituted alkyl; and n is 0 to 8.
[252] In addition, the following amino acids are included:
6 , wherein such compounds are optionally amino protected, optionally carboxyl
protected, optionally amino protected and carboxyl protected, or a salt thereof. In addition, these non-natural amino acids and any of the following non-natural amino acids may be incorporated into a non-natural amino acid polypeptide.
[253] In addition to monocaibonyl structures, the non-natural amino acids^ described
herein may include groups such as dicarbonyl, dicarbonyl like, masked dicarbonyl and protected dicarbonyl groups.
[254] For example, the following amino acids having the structure of Formula (XI) are
included:

F
wherein A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;
B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -0-, -0-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(0)k- where k is 1, 2, or 3, -S(0)k(alkylene or substituted alkylene)-, -C(O)-, »C(0>(alkylene or substituted alkylene)-, -C(S>, -C(S)-(alkylene or substituted alkylene)-, -N(R>, -NR'-(alkylene or substituted alkylene)-, -C(0)N(R>, -CON(R')-(alkylene oi substituted alkylene)-, -CSN(R5)-, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, -N(R')C(0)0-, -S(0)kN(R>, -N(R')C(O)N(R0--N(R9)C(S)N(R')-, -N(R0S(O)kN(R>, -N(R>N=, -C(R')=N-, -C(R>N-N(R'K -C(R5)=N-N=: -C(R')2-N=N-, and -C(R02-N(R>N(R'>, where each R' is independently H, alkyl, or substituted alkyl; .
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide.
[255] In addition, the following amino acids having the structure of Formula (XII) are
included:

F
B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -0-, ~0-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(0)k- where k is 1, 2, or 3, -S(0)k(aIkylene or substituted alkylene)-, -C(0)-, -C(0)-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -N(R')-, -NR'-(alkylene or substituted alkylene)-, -C(0)N(R>, -CON(R')-(alkylene or substituted alkylene)-, -CSN(R>, -CSN(R')-(alkylene or substituted alkylene)-, -N(R')CO-(alkylene or substituted alkylene)-, -N(R')C(0)0-, -S(0)kN(R>, -N(R0C(O)N(R>, -N(R')C(S)N(R>, -N(R')S(OXN(R>, -N(R')-N=, -C(R>N-, -C(R')=N-N(R>? -C(R,)=N-N=, -C(R')2-N=N-, and -C(R02-N(R>N(R>, where each Ra is independently H, alkyl, or substituted alkyl;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and whoa present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;
wherein each Ra is independently selected from the group consisting of H, halogen, alkyl, substituted alkyl, -N(R% -C(0)kR' where k is 1,2, or 3, -C(0)N(R')2, -OR\ and -S(0)kR\ where each R* is independently H, alkyl, or substituted alkyl.
[256] In addition, the following amino acids are included:

wherein such compounds are optionally amino protected, optionally carboxyl protected, optionally amino protected and carboxyl protected, or a salt thereof. In addition, these non-natural amino acids and any of the following non-natural amino acids may be incorporated into a non-natural amino acid polypeptide.
[257] I*1 addition, the following amino acids having the structure of Formula (XHI) are
included:

wherein B is optional, and when present is a linker selected from the group consisting of lower alkylene, substituted lower alkylene, lower alkenylene, substituted lower alkenylene, lower heteroalkylene, substituted lower heteroalkylene, -0-, -0-(alkylene or substituted alkylene)-, -S-, -S-(alkylene or substituted alkylene)-, -S(0)k- where k is 1, 2, or 3, -S(0)k(alkylene or substituted alkylene)-, -C(O)-, -C(0)-(alkylene or substituted alkylene)-, -C(S)-, -C(S)-(alkylene or substituted alkylene)-, -NCR')-, -NR'-(alkylene or substituted alkylene)-, -C(0)N(R>, ~CON(R> (alkylene or substituted alkylene)-, -CSN(R>, -CSN(R>(alkylene or substituted alkylene)-, ~N(R')CO-(alkylene or substituted alkylene)-, -N(R')C(0)0-, -S(0)kN(R>, -N(R')C(0)N(R')-, -N(R')C(S)N(R')-, -N(R0S(O)kN(R')~, -N(R>N=, -C(R>N-, -C(R')=N-N(R>, -C(R')=N-N=, -C(R')2-N=1SI-, and -CCR'^-NCRO-NCR')-, where each R' is independently H, alkyl, or substituted alkyl;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;

each Rais independently selected from the group consisting of H, halogen, alkyl, substituted alkyl, -N(R% -CCO^R' where k is 1, 2, or 3, -C(0)N(R')2, -OR', and -S(0)kR', where each R' is independently H, alkyl, or substituted alkyl; and n is 0 to 8.
[258] In addition, the following amino acids are included:

protected, optionally amino protected and carboxyl protected, or a salt thereof. In addition, these non-natural amino acids and any of the following non-natural amino acids may be incorporated into a non-natural amino acid polypeptide.
[259J In addition, the following amino acids having the structure of Formula (XIV) are
included:

wherein:
A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted Iowa: cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene,

lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;
Xi is C, S, or S(0); and L is alkylene, substituted alkylene, N(R')(alkylene) or N(RJ)(substituted alkylene), where R5 is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl.
[260] In addition, the following amino acids having the structure of Formula (XTV-A) are
included:

wherein:
A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;

L is alkylene, substituted alkylene, N(R')(alkylene) or N(R')(substituted alkylene), where R' is H, alkyl,. substituted alkyl, cycloalkyl, or substituted cycloalkyl.
[261] In addition, the following amino acids having the structure of Formula (XTV-B) are
included:
R
wherein:
A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted aryleue, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, . or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;
L is alkylene, substituted alkylene, N(R')(alkylene) or N(R')(substituted alkylene), where R* is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl.
[262] In addition, the following amino acids having the structure of Formula (XV) are
included:


wherein:
A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide,
or polynucleotide; and or polynucleotide; >:
Xi is C, S, or S(O); and n is 0, 1, 2, 3, 4, or 5; and each R8 and R9 on each CR8R9 group is .*. independently selected from the group consisting of H, alkoxy, alkylamine, halogen, alkyl, aryl, or ■ any R8 and R9 can together form =0 or a cycloalkyl, or any to adjacent R8 groups can together form a cycloalkyl.
[2631 In addition, the following amino acids having the structure of Formula (XV-A) are
included:


A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lo^er heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;
R 0 R Q
n is 0,1, 2, 3,4, or 5; and each R and R on each CR R group is independently selected from the group consisting of H, alkoxy, alkylamine, halogen, alkyl, aryl, or any R and R can together
Q
form =0 or a cycloalkyl, or any to adjacent R groups can*together form a cycloalkyl.
[264] In addition, the following amino acids having the structure of Formula (XV-B) are '
included:

wherein:
A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;

Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;
n is 0,1, 2, 3, 4, or 5; and each R8 and R9 on each CR*R9 group is independently selected from the group consisting of H, alkoxy, aDcylamine, halogen, alkyl, aryl, or any R and R can together form =0 or a cycloalkyl, or any to adjacent R8 groups can together form a cycloalkyl.
[265] In addition, the following amino acids having the structure of Formula (XVI) are
included:

A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;
Xi is C, S, or S(O); and L is alkylene, substituted alkylene, NOR-'Xalkylene) or N(R')(substituted alkylene), where R' is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl.

[266] In addition, the following amino acids having the structure of Formula (XVI-A) are
included:
n A
A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;
R is H, alky], substituted alkyl, cycloalkyl, or substituted cycloalkyl;
R] is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;
L is alkylene, substituted alkylene, N(R')(alkylene) or N(R')(substituted alkylene), where R' is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl.
[267] In addition, the following amino acids having the structure of Formula (XVI-B) are
included:


A is optional, and when present is lower alkylene,, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene., substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;
R is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;
L is alkylene, substituted alkylene, N(R')(a&ylene) or N(R')(substituted alkylene), where RJ is H, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl.
[268] In addition, amino acids having the structure of Formula (XVTT) are included:

wherein:
A is optional, and when present is lower alkylene, substituted lower alkylene, lower cycloalkylene, substituted lower cycloalkylene, lower alkenylene, substituted lower alkenylene, alkynylene, lower heteroalkylene, substituted heteroalkylene, lower heterocycloalkylene, substituted lower heterocycloalkylene, arylene, substituted arylene, heteroarylene, substituted heteroarylene, alkarylene, substituted alkarylene, aralkylene, or substituted aralkylene;


bonding to the A group and (b) indicates bonding to respective carbonyl groups, R3 and R4 are independently chosen from H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl, or R3 and R4 or two R3 groups or two R4 groups optionally form a cycloalkyl or a heterocycloalkyl;
R is H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
T3 is a bond, C(R)(R), O, or S, and R is H, halogen, alkyl, substituted alkyl, cycloalkyl, or ■ substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin, amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, * ■ or polynucleotide.
[269] In addition, amino acids having the structure of Formula (XVIII) are included:


bonding to the A group ana (U) maicates uouumg iu irapwvuvw vuiuviij* 6*v.*^, *^ ~~- *«, -re independently chosen from H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl, or R3 and R4 or two R3 groups or two R4 groups optionally form a cycloalkyl or a heterocycloalkyi;
R is H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
T3 is a bond, C(R)(R), O, or S, and R is H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl;
Ri is optional, and when present, is H, an amino protecting group, resin^ amino acid, polypeptide, or polynucleotide; and
R2 is optional, and when present, is OH, an ester protecting group, resin, amino acid, polypeptide, or polynucleotide;
each Ra is independently selected from the group consisting of H, halogen, alkyl, substituted alkyl, -N(R% -CCO^R' where k is 1, 2, or 3, -C(0)N(R% -OR9, and -S(0)kR\ where each R' is independently H, alkyl, or substituted alkyl.
[270] In addition, amino acids having the structure of Formula (XDQ are included:


R is H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl; and
T3 is O, or S.
[271] In addition, amino acids having the structure of Formula (XX) are included:

wherein:
R is H, halogen, alkyl, substituted alkyl, cycloalkyl, or substituted cycloalkyl.
[272] In addition, the following amino acids having structures of Formula (XXT) are
included:

[273] The synthesis of p-acetyl-(+/-)-phenylalanine and m-acetyl-(+/-)-phenylalanine is
described in Zhang, Z., et al., Biochemistry 42: 6735-6746 (2003), incorporated by reference. Other carbonyl- or dicarbonyl-containing amino acids can be similarly prepared by one of ordinary skill in the art Further, non-limiting exemplary syntheses of non-natural amino acid that are include herein are presented in FIGS. 4, 24-34 and 36-39.
[274] La some embodiments, a polypeptide comprising a non-natural amino acid is
chemically modified to generate a reactive carbonyl or dicarbonyl functional group. For instance, an aldehyde functionality useful for conjugation reactions can be generated from a functionality having adjacent amino and hydroxyl groups. Where the biologically active molecule is a polypeptide, for example, an N-terminal serine or threonine (which may be normally present or may be exposed via chemical or enzymatic digestion) can be used to generate an aldehyde

functionality under mild oxidative cleavage conditions using periodate. See, e.g., Gaertner, et. al., Bioconjug. Chem. 3: 262-268 (1992); Geoghegan, K. & Stroh, J., Bioconjug. Chem. 3:138-146 (1992); Gaertner et al., J. Biol. Chem. 269:7224-7230 (1994). However, methods known in the art are restricted to the amino acid at the N-terminus of the peptide or protein.
[275] In the present invention, a non-natural amino acid bearing adjacent hydroxyl and
amino groups can be incorporated into the polypeptide as a "masked" aldehyde functionality. For example, 5-hydroxylysine bears a hydroxyl group adjacent to the epsilon amine. Reaction conditions for generating the aldehyde typically involve addition of molar excess of sodium metaperiodate under mild conditions to avoid oxidation at other sites within the polypeptide. The pH of the oxidation reaction is typically about 7.0. A typical reaction involves the addition of about 1.5 molar excess of sodium meta periodate to a buffered solution of the polypeptide, followed by incubation for about 10 minutes in the dark. See, e.g. U.S. Patent No. 6,423,685.
[276] The carbonyi or dicarbbnyl functionality can be reacted selectively with a
hydroxylamjne-containing reagent under mild conditions in aqueous solution to form the corresponding oxime linkage that is stable under physiological conditions. See, e.g., Jencks, W. P., J. Am. Chem. Soc. 81, 475-481 (1959); Shao, J. and Tarn, J. P., J. Am. Chem. Soc. 117:3893-3899 (1995). Moreover, the unique reactivity of the carbonyi or dicarbonyl group allows for selective modification in the presence of the other amino acid side chains. See, e.g., Cornish, V. W., et al., J. Am. Chem. Soc. 118:8150-8151 (1996); Geoghegan, K. F. & Stroh, J. G., Bioconjug. Chem. 3:138-146 (1992); Mahal, L. K., et al., Science 276:1125-1128 (1997).
[277] Structure and Synthesis of Non-Natural Amino Acids: Hydroxylamine-
Containing Amino Acids
[278] U.S. Provisional Patent Application No. 60/638,418 is incorporated by reference in
its entirety. Thus, the disclosures provided in Section V (entitled teNon-natural Amino Acids"), Part B (entitled "Structure and Synthesis of Non-Natural Amino Acids: Hydroxylamine-Containing Amino Acids*'), in U.S. Provisional Patent Application No. 60/638,418 apply fully to the methods, compositions (including Formulas I-XXXV), techniques and strategies for making, purifying, characterizing, and using non-natural amino acids, non-natural amino acid polypeptides and modified non-natural amino acid polypeptides described herein to the same extent as if such disclosures were fully presented herein.

CHEMICAL SYNTHESIS OF UNNATURAL AMINO ACIDS
[279] Many of the unnatural amino acids suitable for use in the present invention are
commercially available, e.g., from Sigma (USA) or Aldrich (Milwaukee, WI, USA). Those that are not commercially available are optionally synthesized as provided herein or as provided in various publications or using standard methods known to those of ordinary skill in the art. For organic synthesis techniques, see, e.g., Organic Chemistry by Fessendon and Fessendon, (1982, Second Edition, Willard Grant Press, Boston Mass.); Advanced Organic Chemistry by March (Third Edition, 1985, Wiley and Sons, New York); and Advanced Organic Chemistry by Carey and Sundberg (Third Edition, Parts A and B, 1990, Plenum Press, New York). Additional publications describing the synthesis of unnatural amino acids include, e.g., WO 2002/085923 entitled "In vivo incorporation of Unnatural Amino Acids;" Matsoukas et al., (1995) J. Med. Chan., 38,4660-4669; King, F.E. & Kidd, D.A.A. (1949) A New Synthesis ofGlutamine and ofy-Dipeptides of Glutamic Acid from Phthylated Intermediates. J. Chem. Soc, 3315-3319; Friedman, O.M. & Chatterrji, R. (1959) Synthesis of Derivatives ofGlutamine as Model Substrates for Anti-Tumor Azents.~S. Am. Chem. Soc. 81, 3750-3752; Craig, J.C. et al. (19SS) Absolute Configuration of the Enantiomers of 7-Cliloro-4 [[4-(diethylamino)-l-methylbutyl] amino] quinoline (Chloroquine). J. Org. Chem. 53, 1167-1170; Azoulay, M., Vilmont, M. & Frappier, F. (1991) Glutamine analogues as Potential Antimalarials, Eur. J. Med. Chem. 26, 201-5; Koskinen, A.M.P. * & Rapoport, H. (1989) Synthesis of 4-Substituted Prolines as Conformationally Constrained Amino Acid Analogues. J. Org. Chem, 54, 1859-1866; Christie, B.D. & Rapoport, H. (1985) Synthesis of Optically Pure Pipecolates from L-Asparagine. Application to the Total Synthesis of (+)-Apovincamine through Amino Acid Decarbonylation and Iminium Ion Cyclization. J. Org. Chem. 50:1239-1246; Barton et al., (1987) Synthesis of Novel alpha-Amino-Acids and Derivatives Using Radical Chemistry: Synthesis of L- and D-alpha-Amino-Adipic Acids, L-alpha-aminopimelic Acid and Appropriate Unsaturated Derivatives. Tetrahedron 43:4297-4308; and, Subasinghe et al., (1992) Quisqualic acid analogues: synthesis of beta-heterocyclic 2-aminopropanoic acid derivatives and their activity at a novel quisqualate-sensitized site. J. Med. Chem. 35:4602-7. See also, U.S. Patent Publication No. US 2004/0198637 entitled "Protein Arrays," which is incorporated by reference herein.
A. Carbonyl reactive groups

[280] Amino acids with a carbonyl reactive group allow for a variety of reactions to link
molecules (including but not limited to, PEG or other water soluble molecules) via nucleophilic
addition or aldol condensation reactions among others.
[281] Exemplary carbonyl-containing amino acids can be represented as follows:
(CH2)nR1COR2 R3HN^^SSs"COR4
wherein n is 0-10; Ri is an alkyl, aryl, substituted alkyl, or substituted aryl; R2 is H, alkyl, aryl, substituted alkyl, and substituted aryl; and R3 is H, an amino acid, a polypeptide, or an amino terminus modification group, and R4 is H, an amino acid, a polypeptide, or a carboxy terminus modification group. In some embodiments, n is 1, Ri is phenyl and R2 is a simple alkyl (i.e., methyl, ethyl, or propyl) and the ketone moiety is positioned in the para position relative to the alkyl side chain. In some embodiments, n is 1, Ri is phenyl and R2 is a simple alkyl (i.e., methyl, ethyl, or propyl) and the ketone moiety is positioned in the meta position relative to the alkyl side chain.
[282] The synthesis of ^-acetyl-(+/-)-phenylalanine and 7H-acetyl-(+/-)-phenylalanine is
described in Zhang, Z., et al., Biochemistry 42: 6735-6746 (2003), which is incorporated by reference herein. Other carbonyl-containing amino acids can be similarly prepared by one of ordinary skill in the art.
[283] In some embodiments, a polypeptide comprising a non-naturally encoded amino
acid is chemically modified to generate a reactive carbonyl functional group. For instance, an aldehyde functionality useful for conjugation reactions can be* generated from a functionality having adjacent amino and hydroxyl groups. Where the biologically active molecule is a polypeptide, for example, an TV-terminal serine or threonine (which may be normally present or may be exposed via chemical or enzymatic digestion) can be used to generate an aldehyde functionality under mild oxidative cleavage conditions using periodate. See, e.g., Gaertner, et al, Bioconjug. Chem. 3: 262-268 (1992); Geoghegan, K. & Stroh, J., Bioconjug. Chem. 3:138-146 (1992); Gaertner et al, J. Biol Chem. 269:7224-7230 (1994). However, methods known in the art are restricted to the amino acid at the //-terminus of the peptide or protein.
[284] In the present invention, a non-naturally encoded amino acid bearing adjacent
hydroxyl and amino groups can be incorporated into the polypeptide as a "masked" aldehyde functionality. For example, 5-hydroxylysine bears a hydroxyl group adjacent to the epsilon

amine. Reaction conditions for generating the aldehyde typically involve addition of molar excess of sodium metaperiodate under mild conditions to avoid oxidation at other sites within the polypeptide. The pH of the oxidation reaction is typically about 7.0. A typical reaction involves the addition of about 1.5 molar excess of sodium meta periodate to a buffered solution of the polypeptide, followed by incubation for about 10 minutes in the dark. See, e.g. U.S. Patent No. 6,423,685, which is incorporated by reference herein.
[285] The caibonyl functionality can be reacted selectively with a hydrazine-, hydrazide-,
hydroxylamine-, or semicarbazide-containing reagent under mild conditions in aqueous solution to form the corresponding hydrazone, oxime, or semicarbazone linkages, respectively, that are stable under physiological conditions. See, e.g., Jencks, W. P., J. Am. Chem. Soc. 81, 475-481 (1959); Shao, J. and Tarn, J. P., J. Am. Chem. Soc. 117:3893-3899 (1995). Moreover, the unique reactivity of the carbonyl group allows for selective modification in the presence of the other amino acid side chains. See, e.g.9 Cornish, V. W., et al> J. Am. Chem. Soc. 118:8150-8151 (1996); Geoghegan, K. F. & Stroh, J. G., Bioconjug. Chem. 3:138-146 (1992); Mahal, L. K., et al.9 Science 276:1125-1128 (1997).
B. Hydrazine, hydrazide or semicarbazide reactive groups
[286] Non-naturaily encoded ammo acids containing a nucleophilic group, such as a
hydrazine, hydrazide or semicarbazide, allow for reaction with a variety of electrophilic groups to
form conjugates (including but not limited to, with PEG or other water soluble polymers).
[287] Exemplary hydrazine, hydrazide or semicarbazide -containing amino acids can be
represented as follows:
(CH2)nRiX-C(0)-NH-HN2
r JL
R2HN COR3
wherein n is 0-10; Ri is an alkyl, aryl, substituted alkyl, or substituted aryl or not present; X, is O,
N, or S or not present; R2 is H, an amino acid, a polypeptide, or an amino terminus modification
group, and R3 is H, an amino acid, a polypeptide, or a carboxy terminus modification group.
[288] In some embodiments, n is 4, Ri is not present, and X is N. In some embodiments,
n is 2, Rj is not present, and X is not present. In some embodiments, n is 1, Ri is phenyl, X is O, and the oxygen atom is positioned para to the alphatic group on the aryl ring.

[289] Hydrazide-, hydrazine-, and semicarbazide-containing amino acids are available
from commercial sources. For instance, L-glutamate-y-hydrazide is available from Sigma Chemical (St. Louis, MO). Other amino acids not available commercially can be prepared by one of ordinary skill in the art See, e.g., U.S. Pat No. 6,281,211, which is incorporated by reference herein.
[290J Polypeptides containing non-naturally encoded amino acids that bear hydrazide,
hydrazine or semicarbazide functionalities can be reacted efficiently and selectively with a variety
of molecules that contain aldehydes or other functional groups with similar chemical reactivity.
See, e.g., Shao, J. and Tarn, J., J. Am. Chem. Soc. 117:3893-3899 (1995). The unique reactivity of
hydrazide, hydrazine and semicarbazide functional groups makes them significantly more reactive
toward aldehydes, ketones and other electrophilic groups as compared to the nucleophilic groups
present on the 20 common amino acids (including but not limited to, the hydroxyl group of serine
or threonine or the amino groups of lysine and the N-terminus).
C. Aminooxy-containing amino acids
[291J Non-naturally encoded amino acids containing an aminooxy (also called a
hydroxylamine) group allow for reaction with a variety of electrophilic groups to form conjugates
(including but not limited to, with PEG or other water soluble polymers). Like hydrazines,
hydrazides and semicarbazides, the enhanced nucleophilicity of the aminooxy group peimits.it to
react efficiently and selectively with a variety of molecules that contain aldehydes or other
functional groups with similar chemical reactivity. See, e.g, Shao, J. and Tarn, J., J. Am. Chem.
Soc. 117:3893-3899 (1995); H. Hang and C. Bertozzi, Ace. Chem. Res. 34: 727-736 (2001).
Whereas the result of reaction with a hydrazine group is the corresponding hydrazone, however,
an oxime results generally from the reaction of an aminooxy group with a carbonyl-containing
group such as a ketone.
[292] Exemplary amino acids containing aminooxy groups can be represented as follows:
(CHzJnRrX-tCH^-Y-O-N^ RzHN^^feoRa
wherein n is 0-10; R] is an alkyl, aryl, substituted alkyl, or substituted aryl or not present; X is O, N, S or not present; m is 0-10; Y = C(O) or not present; R2 is H, an amino acid, a polypeptide, or an amino terminus modification group, and R3 is H, an amino acid, a polypeptide, or a carboxy

terminus modification group. In some embodiments, n is 1, Ri is phenyl, X is O, m is 1, and Y is
present. In some embodiments, n is 2, Ri and X are not present, m is 0, and Y is not present.
[293J Aminooxy-containing amino acids can be prepared from readily available amino
acid precursors (homoserine, serine and threonine). See, e.g., M. Carrasco and R. Brown, J. Org. Chem. 68: 8853-8858 (2003). Certain aminooxy-containing amino acids, such as L-2-amino-4-(aminooxy)butyric acid), have been isolated from natural sources (Rosenthal, G, Life Sci. 60: 1635-1641 (1997). Other aminooxy-containing amino acids can be prepared by one of ordinary skill in the art.
D. Azide and alkyne reactive groups
[294) The unique reactivity of azide and alkyne functional groups makes them extremely
useful for the selective modification of polypeptides and other biological molecules. Organic azides, particularly alphatic azides, and alkynes are generally stable toward common reactive chemical conditions. In particular, both the azide and the alkyne functional groups are inert toward the side chains (i.e., R groups) of the 20 common amino acids found in naturally-occuring polypeptides. When brought into close proximity, however, the "spring-loaded" nature of the azide and alkyne groups is revealed and they react selectively and efficiently via Huisgen [3+2] cycloaddition reaction to generate the corresponding triazole. See, e.g., Chin J., et al9 Science 301:964-7 (2003); Wang, Q., et al, J. Am. Chem. Soc. 125, 3192-3193 (2003); Chin, J. W., et al9 J. Am. Chem. Soc. 124:9026-9027 (2002).
[295J Because the Huisgen cycloaddition reaction involves a selective cycloaddition
reaction (see, e.g., Padwa, A., in COMPREHENSIVE ORGANIC SYNTHESIS, Vol. 4, (ed. Trost, B. M., 1991), p. 1069-1109; Huisgen, R. in 1,3-DlPOLAR CYCLOADDITION CHEMISTRY, (ed. Padwa, A., 1984) , p. 1-176 ) rather than a nucleophilic substitution, the incorporation of non-naturally encoded amino acids bearing azide and alkyne-containing side chains permits the resultant polypeptides to be modified selectively at the position of the non-naturally encoded amino acid, Cycloaddition reaction involving azide or alkyne-containing GH, e.g., hGH polypeptide can be carried out at room temperature under aqueous conditions by the addition of Cu(II) (including but not limited to, in the form of a catalytic amount of Q1SO4) in the presence of a reducing agent for reducing Cu(II) to Cu(I), in situ, in catalytic amount. See, e.g., Wang, Q., et al9 J. Am. Chem. Soc. 125, 3192-3193 (2003); Tornoe, C. W., et al9 J. Org. Chem. 67:3057-3064 (2002); Rostovtsev, et al., Angew. Chem. Int. Ed. 41:2596-2599 (2002). Exemplary reducing agents include, including

but not limited to, ascorbate, metallic copper, quinine, hydroquinone, vitamin K, glutathione, cysteine, Fe , Co , and an applied electric potential.
[296] Li some cases, where a Huisgen [3+2] cycloaddition reaction between an azide and
an alkyne is desired, the GH, e.g., hGH polypeptide comprises a non-naturally encoded amino acid
comprising an alkyne moiety and the water soluble polymer to be attached to the amino acid
comprises an azide moiety. Alternatively, the converse reaction (i.e., with the azide moiety on the
amino acid and the alkyne moiety present on the water soluble polymer) can also be performed.
[297] The azide functional group can also be reacted selectively with a water soluble
polymer containing an aryl ester and appropriately functionalized with an aryl phosphine moiety to generate an amide linkage. The aryl phosphine group reduces the azide in situ and the resulting amine then reacts efficiently with a proximal ester linkage to generate the corresponding amide. See, e.g., E. Saxon and C. Bertozzi, Science 287, 2007-2010 (2000). The azide-containing amino acid can be either an alkyl azide (including but not limited to, 2-amino-6-azido-l-hexanoic acid) or an aryl azide (p-azido-phenylalanine).
[298] Exemplary water soluble polymers containing an aryl ester and a phosphine moiety •
can be represented as follows:
wherein X can be O, N, S or not present, Ph is phenyl, W is a water soluble polymer and R can be H, alkyl, aryl, substituted alkyl and substituted aryl groups. Exemplary R groups include but are not limited to -CH2, -C(CH3) 3, -OR5, -NR'R", -SR', -halogen, -C(0)R', -CONR'R", -S(0)2R\ -S(0)2NR'R", -CN and -N02. R\ R", Rm and R"" each independently refer to hydrogen, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, including but not limited to, aryl substituted with 1-3 halogens, substituted or unsubstituted alkyl, alkoxy or thioalkoxy groups, or arylalkyl groups. When a compound of the invention includes more than one R group, for example, each of the R groups is independently selected as are each R\ R", R'" and R"" groups when more than one of these groups is present When R* and R" are attached to the same nitrogen atom, they can be combined with the nitrogen atom to form a 5-, 6-, or 7-membered ring. For example, -NR'R" is meant to include, but not be limited to, 1-pyrrolidinyl and 4-morpholinyl. From the above discussion of substituents, one of skill in the art will understand that the term "alkyl" is meant to include groups including carbon atoms bound to groups other than hydrogen

groups, such as haloalkyl (including but not limited to, -CF3 and -CH2CF3) and acyl (including but not limited to, -C(0)CH3, -C(0)CF3, -C(0)CH2OCH3, and the like).
[299] The azide functional group can also be reacted selectively with a water soluble
polymer containing a thioester and appropriately functionalized with an aryl phosphine moiety to generate an amide linkage. The aryl phosphine group reduces the azide in situ and the resulting amine then reacts efficiently with the thioester linkage to generate the corresponding amide. Exemplary water soluble polymers containing a thioester and a phosphine moiety can be represented as follows:
Ph2P(H2C)n/SYX^w O
wherein n is 1-10; X can be O, N, S or not present, Ph is phenyl, and W is a water soluble
polymer.
[300] Exemplary alkyne-containing amino acids can be represented as follows:
(CH^XfCH^CCH
R2HN COR3
wherein n is 0-10; Ri is an alkyl, aryl, substituted alkyl, or substituted aryl or not present; X is O, N, S or not present; m is 0-10, R2 is H, an amino acid, a polypeptide, or an amino terminus modification group, and R3 is H, an amino acid, a polypeptide, or a carboxy terminus modification group. In some embodiments, n is 1, Ri is phenyl, X is not present, m is 0 and the acetylene -* moiety is positioned in the para position relative to the alkyl side chain. In some embodiments, n is 1, Ri is phenyl, X is O, m is 1 and the propargyloxy group is positioned in Qiepara position relative to the alkyl side chain (i.e., O-propargyl-tyrosine). In some embodiments, n is 1, Ri and X are not present and m is 0 (i.e., proparylglycine).
[301] Alkyne-containing amino acids are commercially available. For example,
propargylglycine is commercially available from Peptech (Burlington, MA). Alternatively, alkyne-containing amino acids can be prepared according to standard methods. For instance, p-propargyloxyphenylalanine can be synthesized, for example, as described in Deiters, A., et al, J. Am. Chem. Soc. 125: 11782-11783 (2003), and 4-alkynyl-L-phenylalanine can be synthesized as described in Kayser, B., et at., Tetrahedron 53(7): 2475-2484 (1997). Other alkyne-containing amino acids can be prepared by one of ordinary skill in the art

[302] Exemplary azide-containing amino acids can be represented as follows:
(QH^RiXtCHaJmNa
R2HN ^COR3
wherein ri is 0-10; Ri is an alkyl, aryl, substituted alkyl, substituted aryl or not present; X is O, N,
S or not present; m is 0-10; Ri is H, an amino acid, a polypeptide, or an amino terminus
modification group, and R3 is H, an amino acid, a polypeptide, or a carboxy terminus modification
group. In some embodiments, n is 1, Ri is phenyl, X is not present, m is 0 and the azide moiety is
positioned para to the alkyl side chain. In some embodiments, n is 0-4 and Ri and X are not
present, and m=0. In some embodiments, n is 1, R\ is phenyl, X is O, m is 2 and the f5-
azidoethoxy moiety is positioned in ihopara position relative to the alkyl side chain.
[303] Azide-containing amino acids are available from commercial sources. For
instance, 4-azidophenylalanine can be obtained from Chem-Impex International, Inc. (Wood Dale, IL). For those azide-containing amino acids that are not commercially available, the azide group can be prepared relatively readily using standard methods known to those of ordinary skill in the art, including but not limited to, via displacement of a suitable leaving group (including but not limited to, halide, mesylate, tosylate) or via opening of a suitably protected lactone. See, e.g., Advanced Organic Chemistry by March (Third Edition, 1985, Wiley and Sons, New York).
E. Aminothiol reactive groups
[304] The unique reactivity of beta-substituted aminothiol functional groups makes them
extremely useful for the selective modification of polypeptides and other biological molecules that ■ contain aldehyde groups via formation of the thiazolidine. See, e.g., J. Shao and J. Tarn, /. Am. Chem. Soc. 1995, 117 (14) 3893-3899. In some embodiments, beta-substituted aminothiol amino acids can be incorporated into GH, e.g., hGH polypeptides and then reacted with water soluble polymers comprising an aldehyde functionality. In some embodiments, a water soluble polymer, drug conjugate or other payload can be coupled to a GH, e.g., hGH polypeptide comprising a beta-substituted aminothiol amino acid via formation of the thiazolidine. CELLULAR UPTAKE OF UNNATURAL AMINO ACIDS
[305] Unnatural amino acid uptake by a cell is one issue that is typically considered when
designing and selecting unnatural amino acids, including but not limited to, for incorporation into a protein. For example, the high charge density of a-amino acids suggests that these compounds

are unlikely to be cell permeable. Natural amino acids are taken up into the eukaryotic cell via a
collection of protein-based transport systems. A rapid screen can be done which assesses which
unnatural amino acids, if any, are taken up by cells. See, e.g., the toxicity assays in, e.g., U.S.
Patent Publication No. US 2004/0198637 entitled "Protein Arrays" which is incorporated by
reference herein; and Liu, D.R. & Schultz, P.G. (1999) Progress toward the evolution of an
organism with an expanded genetic code. PNAS United States 96:4780-4785. Although uptake is
easily analyzed with various assays, an alternative to designing unnatural amino acids that are
amenable to cellular uptake pathways is to provide biosynthetic pathways to create amino acids in
vivo.
(i) BIOSYNTHESIS OF UNNATURAL AMINO ACIDS
[306] Many biosynthetic pathways already exist in cells for the production of amino acids
and other compounds. While a biosynthetic method for a particular unnatural amino acid may not
exist in nature, including but not limited to, in a cell, the invention provides such methods. For
example, biosynthetic pathways for unnatural amino acids are optionally generated in host cell by
adding new enzymes or modifying existing host cell pathways. Additional new enzymes are
optionally naturally occurring enzymes or artificially evolved enzymes. For example, the
biosynthesis of/7-aminophenylalanine (as presented in an example in WO 2002/085923. entitled
"In vivo incorporation of unnatural amino acids") relies on the addition of a combination of
known enzymes from other organisms. The genes for these enzymes can be introduced into a
eukaryotic cell by transforming the cell with a plasmid comprising the genes. The genes, when
expressed in the cell, provide an enzymatic pathway to synthesize the desired compound.
Examples of the types of enzymes that are optionally added are provided in the examples below.
Additional enzymes sequences are found, for example, in Genbank. Artificially evolved enzymes
are also optionally added into a cell in the same manner. In this manner, the cellular machinery
and resources of a cell are manipulated to produce unnatural amino acids.
[307] A variety of methods are available for producing novel enzymes for use in
biosynthetic pathways or for evolution of existing pathways. For example, recursive recombination, including but not limited to, as developed by Maxygen, Inc. (available on the World Wide Web at maxygen.com), is optionally used to develop novel enzymes and pathways. See, e.g., Stemmer (1994), Rapid evolution of a protein in vitro by DNA shuffling, Nature 370(4):389-391; and, Stemmer, (1994), DNA shuffling by random fragmentation and reassembly:

In vitro recombination for molecular evolution, Proc. Natl. Acad. Sci. USA., 91:10747-10751. Similarly DesignPath™, developed by Genencor (available on the World Wide Web at genencor.com) is optionally used for metabolic pathway engineering, including but not limited to, to engineer a pathway to create O-methyl-L-tyrosine in a cell. This technology reconstructs existing pathways in host organisms using a combination of new genes, including but not limited to, those identified through functional genomics, and molecular evolution and design. Diversa Corporation (available on the World Wide Web at diversa.com) also provides technology for rapidly screening libraries of genes and gene pathways, including but not limited to, to create new pathways.
[308] Typically, the unnatural amino acid produced with an engineered biosynthetic
pathway of the invention is produced in a concentration sufficient for efficient protein biosynthesis, including but not limited to, a natural cellular amount, but not to such a degree as to affect the concentration of the other amino acids or exhaust, cellular resources. . Typical concentrations produced in vivo in this maimer are about 10 mM to about 0.05 mM. Once a cell is transformed with a plasmid comprising the genes used to produce enzymes desired for a specific pathway and an unnatural amino acid is generated, in vivo selections are optionally used to further optimize the production of the unnatural amino acid for both ribosomal protein synthesis and cell growth.
(b) Polypeptides with Unnatural Amino Acids
[309J The incorporation of an unnatural amino acid can be done for a variety of purposes,
including but not limited to, tailoring changes in protein structure and/or function, changing size,
acidity, nucleophilicity, hydrogen bonding, hydrophobicity, accessibility of protease target sites,
targeting to a moiety (including but not limited to, for a protein array), adding a biologically active
molecule, attaching a polymer, attaching a radionuclide, modulating serum half-life, modulating
tissue penetration (e.g. tumors), modulating active transport, modulating tissue, cell or organ
specificity or distribution, modulating immunogenicity, modulating protease resistance, etc.
Proteins that include an unnatural amino acid can have enhanced or even entirely new catalytic or
biophysical properties. For example, the following properties are optionally modified by inclusion
of an unnatural amino acid into a protein: toxicity, biodistribution, structural properties,
spectroscopic properties, chemical and/or photochemical properties, catalytic ability, half-life
(including but not limited to, serum half-life), ability to react with other molecules, including but

not limited to, covalently or noncovalently, and the like. The compositions including proteins that include at least one unnatural amino acid are useful for, including but not limited to, novel therapeutics, diagnostics, catalytic enzymes, industrial enzymes, binding proteins (including but not limited to, antibodies), and including but not limited to, the study of protein structure and function. See, e.g., Dougherty, (2000) Unnatural Amino Acids as Probes of Protein Structure and Function* Current Opinion in Chemical Biology. 4:645-652.
[310] In one aspect of the invention, a composition includes at least one protein with at
least one, including but not limited to, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least tea or more unnatural amino acids. The unnatural amino acids can be the same or different, including but not limited to, there can be 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more different sites in the protein that comprise 1, 2, 3,4, 5, 6, 7, 8, 9, or 10 or more different unnatural amino acids. In another aspect, a composition includes a protein with at least one, but fewer than all, of a particular amino acid present in the protein is substituted with the unnatural amino acid. For a given protein with more than one unnatural amino acids, the unnatural amino acids can be identical or different (including but not limited to, the protein can include two or more different types of unnatural amino acids, or can include two of the same unnatural amino acid). For a given protein with more than two unnatural amino acids, the . unnatural amino acids can be the same, different or a combination of a multiple unnatural amino acid of the same kind with at least one different unnatural amino acid.
[311] Proteins or polypeptides of interest with at least one unnatural amino acid are a
feature of the invention. The invention also includes polypeptides or proteins with at least one unnatural amino acid produced using the compositions and methods of the invention. An excipient (including but not limited to, a pharmaceutically acceptable excipient) can also be present with the protein.
[312] By producing proteins or polypeptides of interest with at least one unnatural amino
acid in eukaryotic cells, proteins or polypeptides will typically include eukaryotic post-translational modifications. In certain embodiments, a protein includes at least one unnatural amino acid and at least one post-translational modification that is made in vivo by a eukaryotic cell, where the post-translational modification is not made by a prokaryotic cell. For example, the post-translation modification includes, including but not limited to, glycosylation, acetylation,

acylation, lipid-modification, palmitoylation, palmitate addition, phosphorylation, glycolipid-linkage modification, glycosylation, and the like. In one aspect, the post-translational modification includes attachment of an oligosaccharide (including but not limited to, (GlcNAc-Man)2-Man-GlcNAc-GlcNAc)) to an asparagine by a GlcNAc-asparagine linkage. See Table 1 which lists some examples of N-linked oligosaccharides of eukaryotic proteins (additional residues can also be present, which are not shown). In another aspect, the post-translational modification includes attachment of an oligosaccharide (including but not limited to, Gal-GalNAc, Gal-GlcNAc, etc.) to a serine or threonine by a GalNAc-serine or GalNAc-threonine linkage, or a GlcNAc-serine or a GlcNAc-threonine linkage.

[313] La yet another aspect, the post-translation modification includes proteolytic
processing of precursors (including but not limited to, calcitonin precursor, calcitonin gene-related peptide precursor, preproparathyroid hormone, preproinsulin, proinsulin, prepro-opiomelanocortin, proopiomelanocortin and the like), assembly into a multisubunit protein or macromolecular assembly, translation to another site in the cell (including but not limited to, to organelles, such as the endoplasmic reticulum, the Golgi apparatus, the nucleus, lysosomes,

peroxisomes, mitochondria, chloroplasts, vacuoles, etc., or through the secretory pathway). In certain embodiments, the protein comprises a secretion or localization sequence, an epitope tag, a FLAG tag, a polyhistidine tag, a GST fusion, or the like. U.S. Patent Nos. 4,963,495 and 6,436,674, which are incorporated herein by reference, detail constructs designed to improve secretion of GH, e.g., hGH polypeptides.
1314] One advantage of an unnatural amino acid is that it presents additional chemical
moieties that can be used to add additional molecules. These modifications can be made in vivo in a eukaryotic or non-eukaryotic cell, or in vitro. Thus, in certain embodiments, the post-translational modification is through the unnatural amino acid. For example, the post-translational modification can be through a nucleophilic-electrophilic reaction. Most reactions currently used for the selective modification of proteins involve covalent bond formation between nucleophilic and electrophilic reaction partners, including but not limited to the reaction of a-haloketones with histidine or cysteine side chains. Selectivity in these cases is determined by the number and > accessibility of the nucleophilic residues in the protein. In proteins of the invention, other more selective reactions can be used such as the reaction of an unnatural keto-amino acid with v hydrazides or aminooxy compounds, in vitro and in vivo. See, e.g., Cornish, et al., (1996) J.Am. Chem. Soc 118:8150-8151; Mahal, et al., (1997) Science, 276:1125-1128; Wang, et al., (2001) : Science 292:498-500; Chin, et al, (2002) J. Am. Chem. Soc. 124:9026-9027; Chin, et al., (2002) ) Proc. Natl. Acad. Sci., 99:11020-11024; Wang, et al., (2003) Proc. Natl. Acad. Sci.. 100:56-61; .' Zhang, et al., (2003) Biochemistry 42:6735-6746; and, Chin, et al., (2003) Science. 301:964-7, all of which are incorporated by reference herein. This allows the selective labeling of virtually any protein with a host of reagents including fluorophores, crosslinking agents, saccharide derivatives and cytotoxic molecules. See also, U.S. Patent No. 6,927,042 entitled "Glycoprotein synthesis/'which is incorporated by reference herein. Post-translational modifications, including but not limited to, through an azido amino acid, can also made through the Staudinger ligation (including but not limited to, with triarylphosphine reagents). See, e.g., Kiick et al., (2002) Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation, PNAS 99:19-24.
[3151 This invention provides another highly efficient method for the selective
modification of proteins, which involves the genetic incorporation of unnatural amino acids,

including but not limited to, containing an azide or alkynyl moiety into proteins in response to a selector codon. These amino acid side chains can then be modified by, including but not limited to, a Huisgen [3+2] cycloaddition reaction (see, e.g., Padwa, A. in Comprehensive Organic Synthesis; Vol 4. (1991) Ed. Trost, B. M., Pergamon, Oxford, p. 1069-1109; and, Huisgen, R. in 1.3-Dipolar Cycloaddition Chemistry. (1984) EA Padwa, A., Wiley, New York, p. 1-176) with, including but not limited to, alkynyl or azide derivatives, respectively. Because this method involves a cycloaddition rather than a nucleophilic substitution, proteins can be modified with extremely high selectivity. This reaction can be carried out at room temperature in aqueous conditions with excellent regioselectivity (1,4 > 1,5) by the addition of catalytic amounts of Cu(I) salts to the reaction mixture. See, e.g., Tomoe, et aL, (2002) J. Org. Chem. 67:3057-3064; and, Rostovtsev, et aL, (2002) Angew. Chem. Int. Ed. 41:2596-2599. Another method that can be used is the ligand exchange on a bisarsenic compound with a tetracysteine motif, see, e.g., Griffin, et aL, (1998) Science 281:269-272.
[316] A molecule that can be added to a protein of the invention through a [3+2]
cycloaddition includes virtually any molecule with an azide or alkynyl derivative. Molecules include, but are not limited to, dyes, fluorophores, crosslinking agents, saccharide derivatives, polymers (including but not limited to, derivatives of polyethylene glycol), photocrosslinkers, cytotoxic compounds, affinity labels, derivatives of biotin, resins, beads, a second protein or polypeptide (or more), polynucleotide^) (including but not limited to, DNA, RNA, etc.), metal chelators, cofactors, fatty acids, carbohydrates, and the like. These molecules can be added to an unnatural amino acid with an alkynyl group, including but not limited to, p-propargyloxyphenylalanine, or azido group, including but not limited to, p-azido-phenylalanine, respectively.
V. In vivo generation of GH, e.g,, hGH polypeptides comprising non-genetically-
encoded amino acids
[317J The GH, e.g., hGH polypeptides of the invention can be generated in vivo using
modified tRNA and tRNA synthetases to add to or substitute amino acids that are not encoded in
naturally-occurring systems.
[318] Methods for generating tRNAs and tRNA synthetases which use amino acids that
are not encoded in naturally-occurring systems are described in, e.g., U.S. Patent Application
Publications 2003/0082575 (Serial No. 10/126,927) and 2003/0108885 (Serial No. 10/126,931)

which are incorporated by reference herein. These methods involve generating a translational machinery that functions independently of the synthetases and tRNAs endogenous to the translation system (and are therefore sometimes referred to as "orthogonal"). Typically, the translation system comprises an orthogonal tRNA (O-tRNA) and an orthogonal aminoacyl tRNA synthetase (O-RS). Typically, the O-RS preferentially aminoacylates the O-tRNA with at least one non-naturally occurring amino acid in the translation system and the O-tRNA recognizes at least one selector codon that is not recognized by other tRNAs in the system. The translation system thus inserts the non-naturally-encoded amino acid into a protein produced in the system, in response to an encoded selector codon, thereby "substituting" an amino acid into a position in the encoded polypeptide.
[319] A wide variety of orthogonal tRNAs and aminoacyl tRNA synthetases have been
described in the art for inserting particular synthetic amino acids into polypeptides, and are
generally suitable for use in the present invention. For example, keto-specific O-
tRNA/aminoacyl-tRNA synthetases are described in Wang, L., et al, Proa Natl Acad Sci. USA
100:56-61 (2003) and Zhang, Z. et al., Biochem. 42(22):6735-6746 (2003). Exemplary O-RS, or
portions thereof, are encoded by polynucleotide sequences and include amino acid sequences
disclosed in U.S. Patent Application Publications 2003/0082575 and 2003/0108885, each
incorporated herein by reference. Corresponding O-tRNA molecules for use with the O-RSs are
also described in U.S. Patent Application Publications 2003/0082575 (Serial No. 10/126,927) and
2003/0108885 (Serial No. 10/126,931) which are incorporated by reference herein.
[320] An example of an azide-specific O-tRNA/aminoacyl-tRNA synthetase system is
described in Chin, J. W., et al, 1 Am. Chem. Soc. 124:9026-9027 (2002). Exemplary O-RS sequences for p-azido-L-Phe include, but are not limited to, nucleotide sequences SEQ ID NOs: 14-16 and 29-32 and amino acid sequences SEQ ID NOs: 46-48 and 61-64 as disclosed in U.S. Patent Application Publication 2003/0108885 (Serial No. 10/126,931) which is incorporated by reference herein. Exemplary O-tRNA sequences suitable for use in the present invention include, but are not limited to, nucleotide sequences SEQ ID NOs: 1-3 as disclosed in U.S. Patent Application Publication 2003/0108885 (Serial No. 10/126,931) which is incorporated by reference herein. Other examples of O-tRNA/aminoacyl-tRNA synthetase pairs specific to particular non-naturally encoded amino acids are described in U.S. Patent Application Publication 2003/0082575 (Serial No. 10/126,927) which is incorporated by reference herein. O-RS and O-tRNA that

incorporate both keto- and azide-containing amino acids in & cerevisiae are described in Chin, J. W., etaU Science 301:964-967 (2003).
(321] Several other orthogonal pairs have been reported. Glutaminyl (see, e.g, Liu, D.
R., and Schultz, P. G. (1999) Proc. Natl. Acad. Sex. U. S. A. 96:4780-4785), aspartyl (see, e.g, Pastrnak, M-, et al., (2000) Helv. Chim. Acta 83:2277-2286), and tyrosyl (see, e.g, Ohno, S., et al., (1998) J. Biochem. (Tokyo. Jpn.) 124:1065-1068; and, Kowal, A. K., et al., (2001) Proc. Natl. Acad. Sci. U. S. A. 98:2268-2273) systems derived from & cerevisiae tRNA's and synthetases have been described for the potential incorporation of unnatural amino acids in E. colt Systems derived from the E. coli glutaminyl (see, e.g, Kowal, A. K., et al., (2001) Proc. Natl. Acad Sci. U. S.A. 98:2268-2273) and tyrosyl (see, e.g, Edwards, H., and Schimmel, P. (1990) Mol. Cell. Biol. 10:1633-1641) synthetases have been described for use in S. cerevisiae. The E. coli tyrosyl system has been used for the incorporation of 3-iodo-L-tyrosine in vivo, in mammalian cells. See, Sakamoto, K., et al., (2002) Nucleic Acids Res. 30:4692-4699.
[322] Use of O-tRNA/aminoacyl-tRNA synthetases involves selection of a specific codon
which encodes the non-naturally encoded amino acid. While any codon can be used, it is generally desirable to select a codon that is rarely or never used in the cell in which the O-tRNA/aminoacyl-tRNA synthetase is expressed. For example, exemplary codons include nonsense codon such as stop codons (amber, ochre, and opal), four or more base codons and other natural three-base codons that are rarely or unused.
[323] Specific selector codon(s) can be introduced into appropriate positions in the GH,
e.g., hGH polynucleotide coding sequence using mutagenesis methods known in the art (including but not limited to, site-specific mutagenesis, cassette mutagenesis, restriction selection mutagenesis, etc.).
[324] Methods for generating components of the protein biosynthetic machinery, such as
O-RSs, O-tRNAs, and orthogonal O-tRNA/O-RS pairs that can be used to incorporate a non-naturally encoded amino acid are described in Wang, L., et al, Science 292: 498-500 (2001); Chin, J. W., et al, J. Am. Chem. Soc. 124:9026-9027 (2002); Zhang, Z. et al, Biochemistry 42: 6735-6746 (2003). Methods and compositions for the in vivo incorporation of non-naturally encoded amino acids are described in U.S. Patent Application Publication 2003/0082575 (Serial No. 10/126,927) which is incorporated by reference herein. Methods for selecting an orthogonal tRNA-tRNA synthetase pair for use in in vivo translation system of an organism are also described

in U.S. Patent Application Publications 2UU3/UUb2^/^ (Serial INO. iu/izo,y;z/j ana ZUUS/UIUBSBD (Serial No. 10/126,931) which are incorporated by reference herein. PCT Publication No. WO 04/035743 entitled "Site Specific Incorporation of Keto Amino Acids into Proteins," which is incorporated by reference herein in its entirety, describes orthogonal RS and tRNA pairs for the incorporation of keto amino acids. PCT Publication No. WO 04/094593 entitled Expanding the Eukaryotic Genetic Code," which is incorporated by reference herein in its entirety, describes orthogonal RS and tRNA pairs for the incorporation of non-naturally encoded amino acids in eukaryotic host cells.
[325] Methods for producing at least one recombinant orthogonal aminoacyl-tRNA
synthetase (O-RS) comprise: (a) generating a library of (optionally mutant) RSs derived from at
least one aminoacyl-tRNA synthetase (RS) from a first organism, including but not limited to, a
prokaryotic organism, such as Methanococcus jannaschii, Methanobacterium
thermoautotrophicum, Hahbacterium, Escherichia coli, A.fulgidus, P.furiosus, P. horikoshii, A.
pernix, T. thermophilic, or the like, or a eukaryotic organism; (b) selecting (and/or screening) the
library of RSs (optionally mutant RSs) for members that aminoacylate an orthogonal tRNA (O-
tRNA) in the presence of a non-naturally encoded amino acid and a natural amino acid, thereby
providing a pool of active (optionally mutant) RSs; and/or, (c) selecting (optionally through
negative selection) the pool for active RSs (including but not limited to, mutant RSs) that
preferentially aminoacylate the O-tRNA in the absence of the non-naturally encoded amino acid,
thereby providing the at least one recombinant O-RS; wherein the at least one recombinant O-RS
preferentially aminoacylates the O-tRNA with the non-naturally encoded amino acid.
[326] In one embodiment, the RS is an inactive RS. The inactive RS can be generated by
mutating an active RS. For example, the inactive RS can be generated by mutating at least about
1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 6, or at least
about 10 or more amino acids to different amino acids, including but not limited to, alanine.
[327] Libraries of mutant RSs can be generated using various techniques known in the
art, including but not limited to rational design based on protein three dimensional RS structure, or mutagenesis of RS nucleotides in a random or rational design technique. For example, the mutant RSs can be generated by site-specific mutations, random mutations, diversity generating recombination mutations, chimeric constructs, rational design and by other methods described herein or known in the art

[328] In one embodiment, selecting (and/or screening) the library of RSs (optionally
mutant RSs) for members that are active, including but not limited to, that aminoacylate an orthogonal tRNA (O-tRNA) in the presence of a non-naturally encoded amino acid and a natural amino acid, includes: introducing a positive selection or screening marker, including but not limited to, an antibiotic resistance gene, or the like, and the library of (optionally mutant) RSs into a plurality of cells, wherein the positive selection and/or screening marker comprises at least one selector codon, including but not limited to, an amber, ochre, or opal codon; growing the plurality of cells in the presence of a selection agent; identifying cells that survive (or show a specific response) in the presence of the selection and/or screening agent by suppressing the at least one selector codon in the positive selection or screening marker, thereby providing a subset of positively selected cells that contains the pool of active (optionally mutant) RSs. Optionally, the selection and/or screening agent concentration can be varied.
[329] In one aspect, the positive selection marker is a chloramphenicol acetyltransferase
(CAT) gene and the selector codon is an amber stop codon in the CAT gene. Optionally, the positive selection marker is a ^-lactamase gene and the selector codon is an amber stop codon in the P-lactamase gene. In another aspect the positive screening marker comprises a fluorescent or luminescent screening marker or an affinity based screening marker (including but not limited to, a cell surface marker).
[330] In one embodiment, negatively selecting or screening the pool for active RSs
(optionally mutants) that preferentially aminoacylate the O-tRNA in the absence of the non-naturally encoded amino acid includes: introducing a negative selection or screening marker with the pool of active (optionally mutant) RSs from the positive selection or screening into a plurality of cells of a second organism, wherein the negative selection or screening marker comprises at least one selector codon (including but not limited to, an antibiotic resistance gene, including but not limited to, a chloramphenicol acetyltransferase (CAT) gene); and, identifying cells that survive or show a specific screening response in a first medium supplemented with the non-naturally encoded amino acid and a screening or selection agent, but fail to survive or to show the specific response in a second medium not supplemented with the non-naturally encoded amino acid and the selection or screening agent, thereby providing surviving cells or screened cells with the at least one recombinant O-RS. For example, a CAT identification protocol optionally acts as a positive selection and/or a negative screening in determination of appropriate O-RS recombinants.

For instance, a pool of clones is optionally replicated on growth plates containing CAT (which comprises at least one selector codon) either with or without one or more non-naturally encoded amino acid. Colonies growing exclusively on the plates containing non-naturally encoded amino acids are thus regarded as containing recombinant O-RS. In one aspect, the concentration of the selection (and/or screening) agent is varied. In some aspects the first and second organisms are different. Thus, the first and/or second organism optionally comprises: a prokaryote, a eukaryote, a mammal, an Escherichia coli, a fungi, a yeast, an archaebacterium, a eubacterium, a plant, an insect, a protist, etc. In other embodiments, the screening marker comprises a fluorescent or luminescent screening marker or an affinity based screening marker.
[331] In another embodiment, screening or selecting (including but not limited to,
negatively selecting) the pool for active (optionally mutant) RSs includes: isolating the pool of active mutant RSs from the positive selection step (b); introducing a negative selection or screening marker, wherein the negative selection or screening marker comprises at least one selector codon (including but not limited to, a toxic marker gene, including but not limited to, a ribonuclease bamase gene, comprising at least one selector codon), and the pool of active (optionally mutant) RSs into a plurality of cells of a second organism; and identifying cells that survive or show a specific screening response in a first medium not supplemented with the non-naturally encoded amino acid, but fail to survive or show a specific screening response in a second medium supplemented with the non-naturally encoded amino acid, thereby providing surviving or screened cells with the at least one recombinant O-RS, wherein the at least one recombinant O-RS is specific for the non-naturally encoded amino acid. In one aspect, the at least one selector codon comprises about two or more selector codons. Such embodiments optionally can include wherein the at least one selector codon comprises two or more selector codons, and wherein the first and second organism are different (including but not limited to, each organism is optionally, including but not limited to, a prokaryote, a eukaryote, a mammal, an Escherichia coli, a fungi, a yeast, an archaebacteria, a eubacteria, a plant, an insect, a protist, etc.). Also, some aspects include wherein the negative selection marker comprises a ribonuclease bamase gene (which comprises at least one selector codon). Other aspects include wherein the screening marker optionally comprises a fluorescent or luminescent screening marker or an affinity based screening marker. In the embodiments herein, the screenings and/or selections optionally include variation of the screening and/or selection stringency.

[332] In one embodiment, the methods for producing at least one recombinant orthogonal
aminoacyl-tRNA synthetase (O-RS) can further comprise: (d) isolating the at least one recombinant O-RS; (e) generating a second set of O-RS (optionally mutated) derived from the at least one recombinant O-RS; and, (f) repeating steps (b) and (c) until a mutated O-RS is obtained that comprises an ability to preferentially aminoacylate the O-tRNA. Optionally, steps (d)-(f) are repeated, including but not limited to, at least about two times* In one aspect, the second set of mutated O-RS derived from at least one recombinant O-RS can be generated by mutagenesis, including but not limited to, random mutagenesis, site-specific mutagenesis, recombination or a combination thereof.
[333] The stringency of the selection/screening steps, including but not limited to, the
positive selection/screening step (b), the negative selection/screening step (c) or both the positive and negative selection/screening steps (b) and (c), in the above-described methods, optionally includes varying the selection/screening stringency. In another embodiment, the positive selection/screening step (b), the negative selection/screening step (c) or both the positive and negative selection/screening steps (b) and (c) comprise using a,reporter, wherein the reporter is detected by fluorescence-activated cell sorting (FACS) or wherein the reporter is detected by luminescence. Optionally, the reporter is displayed on a cell surface, on a phage display or the like and selected based upon affinity or catalytic activity involving the non-naturally encoded amino acid or an analogue. In one embodiment, the mutated synthetase is displayed on a cell surface, on a phage display or the like.
[334] Methods for producing a recombinant orthogonal tRNA (O-tRNA) include: (a)
generating a library of mutant tRNAs derived from at least one tRNA, including but not limited to, a suppressor tRNA, from a first organism; (b) selecting (including but not limited to, negatively selecting) or screening the library for (optionally mutant) tRNAs that are aminoacylated by an aminoacyl-tRNA synthetase (RS) from a second organism in the absence of a RS from the first organism, thereby providing a pool of tRNAs (optionally mutant); and, (c) selecting or screening the pool of tRNAs (optionally mutant) for members that are aminoacylated by an introduced orthogonal RS (O-RS), thereby providing at least one recombinant O-tRNA; wherein the at least one recombinant O-tRNA recognizes a selector codon and is not efficiency recognized by the RS from the second organism and is preferentially aminoacylated by the O-RS. In some embodiments the at least one tRNA is a suppressor tRNA and/or comprises a unique three base codon of natural

and/or unnatural bases, or is a nonsense codon, a rare codon, an unnatural codon, a codon comprising at least 4 bases, an amber codon, an ochre codon, or an opal stop codon. In one embodiment, the recombinant O-tRNA possesses an improvement of orthogonality. It will be appreciated that in some embodiments, O-tRNA is optionally imported into a first organism from a second organism without the need for modification. In various embodiments, the first and second organisms are either the same or different and are optionally chosen from, including but not limited to, prokaryotes (including but not limited to, Methanococcus jannaschii, Methanobacterium thermoautotrophicwn, Escherichia coli, Halobacterium, etc.), eukaryotes, mammals, fimgi, yeasts, archaebacteria, eubacteria, plants, insects, protists, etc. Additionally, the recombinant tRNA is optionally aminoacylated by a non-naturally encoded amino acid, wherein the non-naturally encoded amino acid is biosynthesized in vivo either naturally or through genetic manipulation. The non-naturally encoded amino acid is optionally added to a growth medium for at least the first or second organism.
[335] In one aspect, selecting (including but not limited to, negatively selecting) or
screening the library for (optionally mutant) tRNAs that are aminoacylated by an aminoacyl-tRNA
synthetase (step (b)) includes: introducing a toxic marker gene, wherein the toxic, marker gene ;
comprises at least one of the selector codons (or a gene that leads to the production of a toxic or
static agent or a gene essential to the organism wherein such marker gene comprises at least one
selector codon) and the library of (optionally mutant) tRNAs into a plurality of cells from the *;
second organism; and, selecting surviving cells, wherein the surviving cells contain the pool of
(optionally mutant) tRNAs comprising at least one orthogonal tRNA or nonfunctional tRNA. For
example, surviving cells can be selected by using a comparison ratio cell density assay.
[336] In another aspect, the toxic marker gene can include two or more selector codons.
In another embodiment of the methods, the toxic marker gene is a ribonuclease barnase gene, where the ribonuclease barnase gene comprises at least one amber codon. Optionally, the ribonuclease barnase gene can include two or more amber codons.
[337] In one embodiment, selecting or screening the pool of (optionally mutant) tRNAs
for members that are aminoacylated by an introduced orthogonal RS (O-RS) can include: introducing a positive selection or screening marker gene, wherein the positive marker gene comprises a drug resistance gene (including but not limited to, P-lactamase gene, comprising at least one of the selector codons, such as at least one amber stop codon) or a gene essential to the

organism, or a gene that leads to detoxification of a toxic agent, along with the O-RS, and the pool of (optionally mutant) tRNAs into a plurality of cells from the second organism; and, identifying surviving or screened cells grown in the presence of a selection or screening agent, including but not limited to, an antibiotic, thereby providing a pool of cells possessing the at least one recombinant tRNA, where the at least one recombinant tRNA is aminoacylated by the O-RS and inserts an amino acid into a translation product encoded by the positive marker gene, in response to the at least one selector codons. In another embodiment, the concentration of the selection and/or screening agent is varied.
{338] Methods for generating specific O-tRNA/O-RS pairs are provided. Methods
include: (a) generating a library of mutant tRNAs derived from at least one tRNA from a first organism; (b) negatively selecting or screening the library for (optionally mutant) tRNAs that are aminoacylated by an aminoacyl-tRNA synthetase (RS) from a second organism in the absence of a RS from the first organism, thereby providing a pool of (optionally mutant) tRNAs; (c) selecting or screening the pool of (optionally mutant) tRNAs for members that are aminoacylated by an introduced orthogonal RS (O-RS), thereby providing at least one recombinant O-tRNA. The at least one recombinant O-tRNA recognizes a selector codon and is not efficiency recognized by the RS from the second organism and is preferentially aminoacylated by the O-RS. The method also includes (d) generating a library of (optionally mutant) RSs derived from at least one aminoacyl-tRNA synthetase (RS) from a third organism; (e) selecting or screening the library of mutant RSs for members that preferentially aminoacylate the at least one recombinant O-tRNA in the presence of a non-naturally encoded amino acid and a natural amino acid, thereby providing a pool of active (optionally mutant) RSs; and, (f) negatively selecting or screening the pool for active (optionally mutant) RSs that preferentially aminoacylate the at least one recombinant O-tRNA in the absence of the non-naturally encoded amino acid, thereby providing the at least one specific O-tRNA/O-RS pair, wherein the at least one specific O-tRNA/O-RS pair comprises at least one recombinant O-RS that is specific for the non-naturally encoded amino acid and the at least one recombinant O-tRNA. Specific O-tRNA/O-RS pairs produced by the methods are included. For example, the specific O-tRNA/O-RS pair can include, including but not limited to, a mutRNATyr-mutTyrRS pair, such as a mutRNATyr-SS12TyrRS pair, a mutRNALeu-mutLeuRS pair, a mutRNAThr-mutThrRS pair, a mutRNAGlu-mutGluRS pair, or the like. Additionally, such methods include

wherein the first and third organism are the same (including but not limited to, Methanococcus jannaschii).
[339] Methods for selecting an orthogonal tRNA-tRNA synthetase pair for use in an in
vivo translation system of a second organism are also included in the present invention. The methods include: introducing a marker gene, a tRNA and an aminoacyl-tRNA synthetase (RS) isolated or derived from a first organism into a first set of cells from the second organism; introducing the marker gene and the tRNA into a duplicate cell set from a second organism; and, selecting for surviving cells in the first set that fail to survive in the duplicate cell set or screening for cells showing a specific screening response that fail to give such response in the duplicate cell set, wherein the first set and the duplicate cell set are grown in the presence of a selection or screening agent, wherein the surviving or screened cells comprise the orthogonal tRNA-tRNA synthetase pair for use in the in the in vivo translation system of the second organism. In one embodiment, comparing and selecting or screening includes an in vivo complementation assay. The concentration of the selection or screening agent can be varied.
[340] The organisms of the present invention comprise a variety of organism and a
variety of combinations. For example, the first and the second organisms of the methods of the present invention can be the same or different In one embodiment, the organisms are optionally a prokaryotic organism, including but not limited to, Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Halobacterium, Escherichia coli, A. julgidus, P. juriosiis, P. horikoshii, A. pernix, T. thermophilus, or the like. Alternatively, the organisms optionally comprise a eukaryotic organism, including but not limited to, plants (including but not limited to, complex plants such as monocots, or dicots), algae, protists, fungi (including but not limited to, yeast, etc), animals (including but not limited to, mammals, insects, arthropods, etc.), or the like. In another embodiment, the second organism is a prokaryotic organism, including but not limited to, Methanococcus jannaschii, Methanobacterium thermoautotrophicumy Halobacterium, Escherichia coli, A. julgidus, Halobacterium, P. furiosus, P. horikoshii, A. pernix, T. thermophilus, or the like. Alternatively, the second organism can be a eukaryotic organism, including but not limited to, a yeast, a animal cell, a plant cell, a fungus, a mainmalian cell, or the like. In various embodiments the first and second organisms are different.

VI. Location of non-naturally-oecurring amino acids in GH, e.g., hGHpolypeptides
[34 J J The present invention contemplates incorporation of one or more non-naturally-
occurring amino acids into GH, e.g., hGH polypeptides. One or more non-naturally-occurring
amino acids may be incorporated at a particular position which does not disrupt activity of the
polypeptide. This can be achieved by making "conservative" substitutions, including but not
limited to, substituting hydrophobic amino acids with hydrophobic amino acids, bulky amino
acids for bulky amino acids, hydrophilic amino acids for hydrophilic amino acids and/or inserting
the non-naturally-oecurring amino acid in a location that is not required for activity.
[342] Regions of GH, e.g., hGH can be illustrated as follows, wherein the amino acid
positions in hGH are indicated in the middle row (SEQ ID NO: 2):
Helix A Helix B Helix C Helix D
[1-5]- [6-33]- [34-74]- [75-96]- [97-105] - [106-129]- [130-153] - [154-183]- [184-191]
N-term A-B loop B-C loop C-D loop C-term
[343] A variety of biochemical and structural approaches can be employed to select the
desired sites for substitution with a non-naturally encoded amino acid within the GH, e.g., hGH polypeptide. It is readily apparent to those of ordinary skill in the art that any position of the polypeptide chain is suitable for selection to incorporate a non-naturally encoded amino acid, and selection may be based on rational design or by random selection for any or no particular desired purpose. Selection of desired sites may be for producing a GH, e.g., hGH molecule having any desired property or activity, including but not limited to, agonists, super-agonists, inverse agonists, antagonists, receptor binding modulators, receptor activity modulators, dimer or multimer formation, no change to activity or property compared to the native molecule, or manipulating any physical or chemical property of the polypeptide such as solubility, aggregation, or stability. For example, locations in the polypeptide required for biological activity of GH, e.g., hGH polypeptides can be identified using point mutation analysis, alanine scanning or homolog scanning methods known in the art. See, e.g., Cunningham, B. and Wells, J., Science, 244:1081-1085 (1989) (identifying 14 residues that are critical for GH, e.g., hGH bioactivity) and Cunningham, B., et ah Science 243: 1330-1336 (1989) (identifying antibody and receptor epitopes using homolog scanning mutagenesis). U.S. Patent No. 5,580,723; 5,834,250; 6,013,478; 6,428,954; and 6,451,561, which are incorporated by reference herein, describe methods for the systematic analysis of the structure and function of polypeptides such as hGH by identifying

active domains which influence the activity of the polypeptide with a target substance. Residues other than those identified as critical to biological activity by alanine or homolog scanning mutagenesis may be good candidates for substitution with a non-naturally encoded amino acid depending on the desired activity sought for the polypeptide. Alternatively, the sites identified as critical to biological activity may also be good candidates for substitution with a non-naturally encoded amino acid, again depending on the desired activity sought for the polypeptide. Another alternative would be to simply make serial substitutions in each position on the polypeptide chain with a non-naturally encoded amino acid and observe the effect on the activities of the polypeptide. It is readily apparent to those of ordinary skill in the art that any means, technique, or method for selecting a position for substitution with a non-natural amino acid into any polypeptide is suitable for use in the present invention.
[344] The structure and activity of naturally-occurring mutants of hGH polypeptides that
contain deletions can also be examined to determine regions of the protein that are likely to be tolerant of substitution with a non-naturally encoded amino acid. See, e.g., Kostyo et al, Biochem. Biophys. Acta, 925: 314 (1987); Lewis, U., et al, J. Biol Chem., 253:2679-2687 (1978) for hGH. In a similar manner, protease digestion and monoclonal antibodies can be used to identify regions of hGH that are responsible for binding the hGH receptor. See, e.g., Cunningham, B., et al Science 243: 1330-1336 (1989); Mills, J., et al, Endocrinology, 107:391-399 (1980); Li, C, Mol Cell Biochem., 46:31-41 (1982) (indicating that amino acids between residues 134-149 can be deleted without a loss of activity). Once residues that are likely to be intolerant to substitution with non-natuially encoded amino acids have been eliminated, the impact of proposed substitutions at each of the remaining positions can be examined from the three-dimensional crystal structure of the hGH and its binding proteins. See de Vos, A., et al, Science, 255:306-312 (1992) for hGH; all crystal structures of hGH are available in the Protein Data Bank (including 3HHR, 1AXI, and 1HWG) (PDB, available on the World Wide Web at rcsb.org), a centralized database containing three-dimensional structural data of large molecules of proteins and nucleic acids. Models may be made investigating the secondary and tertiary structure of polypeptides, if three-dimensional structural data is not available. Thus, those of ordinary skill in the art can readily identify amino acid positions that can be substituted with non-naturally encoded amino acids.

[345] In some embodiments, the GH, e.g., hGH polypeptides of the invention comprise
one or more non-naturally occurring amino acids positioned in a region of the protein that does not disrupt the helices or beta sheet secondary structure of the polypeptide.
[346] Exemplary residues of incorporation of a non-naturally encoded amino acid may be
those that are excluded from potential receptor binding regions (including but not limited to, Site I
and Site II), may be fully or partially solvent exposed, have minimal or no hydrogen-bonding
interactions with nearby residues, may be minimally exposed to nearby reactive residues, and may
be in regions that are highly flexible (including but not limited to, C-D loop) or structurally rigid
(including but not limited to, B helix) as predicted by the three-dimensional, crystal structure,
secondary, tertiary, or quaternary structure of hGH, bound or unbound to its receptor.
[347] In some embodiments, one or more non-naturally encoded amino acids are
incorporated at any position in one or more of the following regions corresponding to secondary structures in hGH as follows: positions corresponding to 1-5 (N-terminus), 6-33 (A helix), 34-74 (region between A helix and B helix, the A-B loop), 75-96 (B helix), 97-105 (region between B helix and C helix, the B-C loop), 106-129 (C helix), 130-153 (region between C helix and D helix, the C-D loop), 154-183 (D helix), 184-191 (C-terminus) from SEQ ID NO: 2. In other embodiments, GH polypeptides, e.g., hGH polypeptides of the invention comprise at least one non-naturally-occurring amino acid substituted for at least one amino acid located in at least one region of GH, e.g., hGH selected from the group consisting regions corresponding to the N-terminus (1-5), the N-terminal end of the A-B loop (32-46); the B-C loop (97-105), the C-D loop (132-149), and the C-terminus (184-191) of SEQ ID NO: 2. In some embodiments, one or more non-naturally encoded amino acids are incorporated at one or more of the following positions of GH, e.g., hGH corresponding to: before position 1 (i.e. at the N-terminus), 1, 2, 3, 4, 5, 8, 9, 11, 12, 15, 16, 19, 22, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 55, 57, 59, 65,66, 69,70, 71, 74, 88,91, 92,94, 95, 97, 98, 99,100,101,102,103,104,105,106, 107, 108, 109, 111, 112, 113, 115, 116, 119, 120, 122, 123, 126, 127, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153,154,155,156,158,159,161,168,172,183,184, 185,186,187,188,189,190,191,192 (i.e., at the caiboxyl terminus of the protein) of SEQ ID NO: 2 or the corresponding amino acids of SEQIDNO:lor3.

[348] Exemplary sites of incorporation of one or more non-naturally encoded amino acids
include sites corresponding to 29, 30, 33, 34, 35, 37, 39, 40,49, 57, 59, 66, 69, 70, 71, 74, 88, 91,
92, 94, 95, 98, 99, 101, 103, 107,108, 111, 122, 126, 129,130, 131, 133, 134,135, 136, 137, 139,
140, 141,142, 143, 145, 147, 154, 155, 156, 159, 183, 186, and 187, or any combination thereof
from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3.
1349] A subset of exemplary sites for incorporation of one or more non-naturally encoded
amino acid include sites corresponding to 29, 33, 35, 37, 39, 49, 57, 69, 70, 71, 74, 88, 91, 92, 94,
95, 98, 99, 101, 103, 107, 108, 111, 129, 130, 131, 133, 134, 135, 136, 137, 139, 140, 141, 142,
143,145, 147,154,155, 156,186, and 187, or any combination thereof from SEQ ID NO: 2 or the
corresponding amino acids of SEQ ID NO: 1 or 3. An examination of the crystal structure of GH,
e.g., hGH and its interactions with the GH, e.g., hGH receptor indicates that the side chains of
these amino acid residues are fully or partially accessible to solvent and the side chain of a non-
naturally encoded amino acid may point away from the protein surface and out into the solvent.
[350] Exemplary positions for incorporation of one or more non-naturally encoded amino
acids include sites corresponding to 35, 88, 91, 92, 94, 95, 99, 101, 103, 111, 131, 133, 134, 135, . 136, 139, 140, 143, 145, and 155, or any combination thereof from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. An examination of the crystal structure of GH, e.g., hGH and its interactions with the GH, e.g., hGH receptor indicates that the side chains of these amino acid residues are fully exposed to the solvent and the side chain of the native residue points out into the solvent.
[351] A subset of exemplary sites for incorporation of one or more non-naturally encoded
amino acids include sites corresponding to 30, 74, 103, or any combination thereof, from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. Another subset of exemplary sites for incorporation of one or more non-naturally encoded amino acids include sites corresponding to 35, 92, 143, 145, or any combination thereof from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. A further subset of exemplary sites for incorporation of one or more non-naturally encoded amino acids include sites corresponding to 35, 92, 131, 134, 143, 145, or any combination thereof, from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. Still a further subset of exemplary sites for incorporation of one or more non-naturally encoded amino acids include sites corresponding to 30, 35, 74, 92, 103, 145, or any combination thereof, from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. Yet a

further subset of exemplary sites for incorporation of one or more non-naturally encoded amino
acids include sites corresponding to 35, 92, 143, 145, or any combination thereof, from SEQ ID
NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. In certain embodiments, sites for
incorporation of one or more non-naturally encoded amino acids include a site corresponding to 35
from SEQ ID NO: 2 orthe corresponding amino acids of SEQ ID NO: 1 or 3.
[352] In some embodiments, at least one of the non-naturally encoded amino acids
incorporated into the GH, e.g., hGH, contains a carbonyl group, e.g., a ketone group. In certain embodiments, at least one of the non-naturally encoded amino acids incorporated into the GH, e.g., hGH is para-acetylphenylalanine. In some embodiments in which the GH, e.g., hGH contains a plurality of non-naturally-encoded amino acids, more than one of the non-naturally-encoded amino acids incorporated into the GH, e.g., hGH is para-acetylphenylalanine. In some embodiments in which the GH, e.g., hGH contains a plurality of non-naturally-encoded amino acids, substantially all of the non-naturally-encoded amino acids incorporated into the GH, e.g., hGH are para-acetylphenylalanine.
[353] In some embodiments, the non-naturally occurring amino acid is linked to a water
soluble polymer at one or more positions, including but not limited to, positions corresponding to: . before position 1 (i.e. at the N-terminus), 1, 2, 3, 4, 5, 8, 9, 11, 12, 15, 16, 19, 22, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 52, 55, 57, 59, 65, 66, 69, 70, 71, 74, 88, 91, 92, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 111, 112, 113, 115, 116, 119, 120, 122, 123, 126, 127, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 159, • 161, 168, 172, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192 (i.e., at the carboxyl terminus of the protein) (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3). In some embodiments, the non-naturally occurring amino acid is linked to a water soluble polymer at positions including but not limited to, positions corresponding to one or more of these positions: 30, 35, 74, 92, 103, 143,145 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3). In some embodiments, the non-naturally occurring amino acid is linked to a water soluble polymer at positions including but not limited to, positions corresponding to one or more of these positions: 35, 92, 143, 145 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3). In some embodiments, the non-naturally occurring amino acid is linked to a water soluble polymer at positions including but not limited to, positions corresponding to one or more of these

positions: 35, 92, 131, 134, 143, 145, or any combination thereof, from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. In some embodiments, the non-naturally occurring amino acid is linked to a water soluble polymer at positions including but not limited to, positions corresponding to one or more of these positions: 30, 35, 74, 92, 103, 145, or any combination thereof, from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. In some embodiments, the non-naturally occurring amino acid is linked to a water soluble polymer at positions including but not limited to, positions corresponding to one or more of these positions: 35, 92, 143, 145, or any combination thereof, from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. In some embodiments, the non-naturally occurring amino acid is linked to a water-soluble polymer at a position corresponding to, but not limited to, position 35 from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3 is linked to a water-soluble polymer.
[354] In some embodiments the water-soluble polymer(s) linked to the GH, e.g., hGH,
include one or more polyethylene glycol molecules (PEGs). The polymer, e.g., PEG, may be linear or branched. Typically, linear polymers, e.g., PEGs, used in the invention can have a MW of about 0.1 to about 100 kDa, or about 1 to about 60 kDa, or about 20 to about 40 kDa, or about 30 kDa. Typically, branched polymers, e.g., PEGs, used in the invention can have a MW of about 1 to about 100 kDa, or about 30 to about 50 kDa, or about 40 kDa. Polymers such as PEGs are described further herein. In certain embodiments, the linkage between the GH, e.g., hGH and the water-soluble polymer, e.g., PEG, is an oxime bond.
[355] Certain embodiments of the invention encompass compositions that include a GH,
e.g., hGH, linked to at least one water-soluble polymer by a covalent bond, where the covalent bond is an oxime bond. In some embodiments, the water-soluble polymer is a PEG, e.g., a linear PEG. In some embodiments encompassing at least one linear PEG linked by an oxime bond to a . GH, e.g., hGH, the PEG can have a MW of about 0.1 to about 100 kDa, or about 1 to about 60 kDa, or about 20 to about 40 kDa, or about 30 kDa. In certain embodiments encompassing a linear PEG linked by an oxime bond to a GH, e.g., hGH, the PEG has a MW of about 30 kDa. In some embodiments encompassing at least one branched PEG linked by an oxime bond to a GH, e.g., hGH, the PEG can have a MW of about 1 to about 100 kDa or about 30 to about 50 kDa, or about 40 kDa. In certain embodiments encompassing a branched PEG linked by an oxime bond to a GH, e.g., hGH, the PEG has a MW of about 40 kDa. In some embodiments, the GH is a GH,

e.g., hGH and in certain of these embodiments, the GH, e.g., hGH has a sequence that is at least about 80% identical to SEQ ID NO: 2; in some embodiments the GH, e.g., hGH has a sequence that is the sequence of SEQ ID NO: 2. In some embodiments, the GH, e.g., hGH, contains at least one non-naturally-encoded amino acid; in some of these embodiments, at least one oxime bond is between the non-naturally-encoded amino acid and at least one water-soluble polymer. In some embodiments, the non-naturally-encoded amino acid contains a carbonyl group, such as a ketone group; in some embodiments, the non-naturally-encoded amino acid is para-acetylphenylalanine. In some embodiments, the para-acetylphenylalanine is substituted at a position corresponding to position 35 of SEQ ID NO: 2.
[356] Thus, in some embodiments, the invention provides a GH, e.g., hGH, linked to at
least one water-soluble polymer, e.g., a PEG, by a covalent bond, where the covalent bond is an
oxime bond. In certain embodiments, the water-soluble polymer is a PEG and the PEG is a linear
PEG. In these embodiments, the linear PEG has a MW of about 0.1 to about 100 kDa, or about 1
to about 60 kDa, or about 20 to about 40 kDa, or about 30 kDa. In certain embodiments
encompassing a linear PEG linked by an oxime bond to a GH, e.g., hGH, the PEG has a MW of
about 30 kDa. hi certain embodiments, the water-soluble polymer is a PEG that is a branched
PEG. In these embodiments, the branched PEG has a MW of aboutl to about 100 kDa, or about
30 to about 50 kDa, or about 40 kDa. In certain embodiments encompassing a branched PEG
linked by an oxime bond to a GH, e.g., hGH, the PEG has a MW of about 40 kDa.
[357] In some embodiments, the invention provides a GH, e.g., hGH, where the GH, e.g.,
hGH contains a non-naturally encoded amino acid, where the GH is linked to at least one water-soluble polymer, e.g., a PEG, by a covalent bond, and where the covalent bond is an oxime bond between the non-naturally encoded amino acid and the water-soluble polymer, e.g., PEG. In some embodiments, the non-naturally-encoded amino acid is incorporated into the GH, e.g., hGH, at a position corresponding to position 35 of SEQ ID NO: 2. In certain embodiments where the water-soluble polymer is a PEG, the PEG is a linear PEG. In these embodiments, the linear PEG has a MW of about 0.1 to about 100 kDa, or about 1 to about 60 kDa, or about 20 to about 40 kDa, or about 30 kDa. In certain embodiments encompassing a linear PEG linked by an oxime bond to a GH, e.g., hGH, the PEG has a MW of about 30 kDa. In certain embodiments where the water-soluble polymer is a PEG, the PEG is a branched PEG. In these embodiments, the branched PEG has a MW of about 1 to about 100 kDa, or about 30 to about 50 kDa, or about 40 kDa. In certain

embodiments encompassing a branched PEG linked by an oxime bond to a GH, e.g., hGH, the PEG has a MW of about 40 kDa.
[358] In some embodiments, the invention provides a GH, e.g., hGH, where the GH, e.g.,
hGH contains a non-naturally encoded amino acid that is a carbonyl-containing non-naturally encoded amino acid, where the GH is linked to at least one water-soluble polymer, e.g., a PEG, by a covalent bond, and where the covalent bond is an oxime bond between the non-naturally encoded carbonyl-containing amino acid and the water-soluble polymer, e.g., PEG. In some embodiments, the non-naturally-encoded carbonyl-containing amino acid is incorporated into the GH, e.g., hGH, at a position corresponding to position 35 of SEQ ID NO: 2. In certain embodiments where the water-soluble polymer is a PEG, the PEG is a linear PEG. In these embodiments, the linear PEG has a MW of about 0.1 to about 100 kDa, or about 1 to about 60 kDa, or about 20 to about 40 kDa, or about 30 kDa. In certain embodiments encompassing a linear PEG linked by an oxime bond to a GH, e.g., hGH, the PEG has a MW of about 30 kDa. In certain embodiments where the water-soluble polymer is a PEG, the PEG is a branched PEG. hi these embodiments, the branched PEG has a MW of about 1 to about 100 kDa, or about 30' to about 50 kDa, or about 40 kDa. In certain embodiments encompassing a branched PEG linked by an oxime bond to a GH, e.g., hGH, the PEG has a MW of about 40 kDa.
[359] In some embodiments, the invention provides a GH, e.g., hGH, that contains a non-
naturally encoded amino acid that includes a ketone group, where the GH is linked to at least one . water-soluble polymer, e.g., a PEG, by a covalent bond, and where the covalent bond is an oxime bond between the non-naturally encoded amino acid containing a ketone group and the water-soluble polymer, e.g., PEG. In some embodiments, the non-naturally-encoded amino acid containing a ketone group is incorporated into the GH, e.g., hGH, at a position corresponding to position 35 of SEQ ID NO: 2. In certain embodiments where the water-soluble polymer is a PEG, the PEG is a linear PEG. In these embodiments, the linear PEG has a MW of about 0.1 to about 100 kDa, or about 1 to about 60 kDa, or about 20 to about 40 kDa, or about 30 kDa. In certain embodiments encompassing a linear PEG linked by an oxime bond to a GH, e.g., hGH, the PEG has a MW of about 30 kDa. In certain embodiments where the water-soluble polymer is a PEG, the PEG is a branched PEG. In these embodiments, the branched PEG has a MW of about 1 to about 100 kDa, or about 30 to about 50 kDa, or about 40 kDa. In certain embodiments

encompassing a branched PEG linked by an oxime bond to a GH, e.g., hGH, the PEG has a MW of about 40 kDa.
[360] In some embodiments, the invention provides a GH, e.g., hGH, that contains a non-
naturally encoded amino acid that is a para-acetylphenylalanine, where the GH linked to at least one water-soluble polymer, e.g., a PEG, by a covalent bond, and where the covalent bond is an oxime bond between fee para-acetylphenylalanine and the water-soluble polymer, e.g., PEG. In some embodiments, the para-acetylphenylalanine is incorporated into the GH, e.g., hGH, at a position corresponding to position 35 of SEQ ID NO: 2. In certain embodiments where the water-soluble polymer is a PEG, the PEG is a linear PEG. In these embodiments, the linear PEG has a MW of about 0.1 to about 100 kDa, or about 1 to about 60 kDa, or about 20 to about 40 kDa, or about 30 kDa. In certain embodiments encompassing a linear PEG linked by an oxime bond to a GH, e.g., hGH, the PEG has a MW of about 30 kDa. In certain embodiments where the water-soluble polymer is a PEG, the PEG is a branched PEG. In these embodiments, the branched PEG has a MW of about 1 to about 100 kDa, or about 30 to about 50 kDa, or about 40 kDa. In certain embodiments encompassing a branched PEG linked by an oxime bond to a GH. e.g., hGH, the ' PEG has a MW of about 40 kDa.
[3611 In certain embodiments the invention provides a GH, e.g., hGH that includes SEQ
ID NO: 2, and where the GH, e.g., hGH is substituted at a position corresponding to position 35 of SEQ ID NO: 2 with a para-acetylphenylalanine that is linked by an oxime linkage to a linear PEG of MW of about 30 kDa.
[362] In some embodiments, the invention provides a hormone composition that includes
a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH comprises the amino acid sequence of SEQ ID NO: 2, and where the GH, e.g., hGH contains at least one non-naturally-encoded amino acid substituted at one or more positions including, but not limited to, positions corresponding to: before position 1 (i.e. at the N-terminus), 1, 2, 3, 4, 5, 8, 9, 11, 12, 15, 16, 19, 22, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 55, 57, 59, 65, 66, 69, 70, 71, 74, 88, 91, 92, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 111, 112, 113, 115, 116, 119, 120, 122, 123, 126, 127, 129, 130r 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 159, 161, 168, 172, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192 (i.e., at the carboxyl terminus of the protein) (SEQ ID NO: 2 or the

corresponding amino acids of SEQ ID NO: 1 or 3). In some embodiments, the invention provides a hormone composition that includes a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH comprises the amino acid sequence of SEQ ID NO: 2, and where the GH, e.g., hGH contains at least one non-naturally-encoded amino acid substituted at one or more positions including, but not limited to, positions corresponding to: 30, 35, 74, 92, 103, 143, 145 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3). In some embodiments, the invention provides a hormone composition that includes a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH comprises the amino acid sequence of SEQ ID NO: 2, and where the GH, e.g., hGH contains at least one non-naturally-encoded amino acid substituted at one or more positions including, but not limited to, positions corresponding to: 35, 92, 143, 145 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3). hi some embodiments, the invention provides a hormone composition that includes a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH comprises the amino acid sequence of SEQ ID NO: 2, and where the GH, e.g., hGH contains at least one non-naturally-encoded amino acid substituted at one or more positions including, but not limited to, positions corresponding to: 35, 92, 131, 134, 143, 145, or any combination thereof, from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. Li some embodiments, the invention provides a hormone composition that includes a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH comprises the amino acid sequence of SEQ ID NO: 2, and where the GH, e.g., hGH contains at least one non-naturally-encoded amino acid substituted at one or more positions including, but not limited to, positions corresponding to: 30, 35, 74, 92, 103, 145, or any combination thereof, from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. In some embodiments, the invention provides a hormone composition that includes a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH comprises the amino acid sequence of SEQ ED NO: 2, and where the GH, e.g., hGH contains at least one non-naturally-encoded amino acid substituted at one or more positions including, but not limited to, positions corresponding to: 35, 92, 143, 145, or any combination thereof, from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. In some embodiments, the invention provides a hormone composition that includes a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH comprises the amino acid

sequence of SEQ ID NO: 2, and where the GH, e.g., hGH contains at least one non-naturally-
encoded amino acid substituted at one or more positions including, but not limited to, positions
corresponding to position 35 from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID
NO: 1 or 3. In embodiments in which the PEG is a linear PEG, the PEG can have a MW of about
0.1 to about 100 kDa, or about 1 to about 60 kDa, or about 20 to about 40 kDa, or about 30 kDa.
[363] In some embodiments, the invention provides a hormone composition that includes
a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH includes the amino acid sequence of SEQ ID NO: 2, and where the GH, e.g., hGH contains at least one non-natuially-encoded amino acid that is a para-acetylphenylalanine substituted at one or more positions including, but not limited to, positions corresponding to: before position 1 (i.e. at the N-terminus), 1, 2, 3, 4, 5, 8, 9, 11, 12, 15, 16, 19, 22, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 55, 57, 59, 65, 66, 69, 70, 71, 74, 88, 91, 92, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 111, 112, 113, 115, 116, 119, 120, 122, 123, 126, 127, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149; 150, 151, 152, 153, 154, 155, 156, 158, 159, 161, 168, 172, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192 (i.e., at the carboxyl terminus of the protein) (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3).; In some embodiments, the invention provides a hormone composition that includes a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH comprises the amino acid sequence of SEQ ID NO: 2, and where the GH, e.g., hGH contains at least one non-naturally-encoded amino acid that is a para-acetylphenylalanine substituted at one or more positions including, but not limited to, positions corresponding to: 30, 35, 74, 92, 103, 143, 145 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3). In some embodiments, the invention provides a hormone composition that includes a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH comprises the amino acid sequence of SEQ ID NO: 2, and where the GH, e.g., hGH contains at least one non-naturally-encoded amino acid that is a para-acetylphenylalanine substituted at one or more positions including, but not limited to, positions corresponding to: 35, 92, 143, 145 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3). hi some embodiments, the invention provides a hormone composition that includes a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH comprises the amino acid

.sequence of SEQ ID NO: 2, and where the GH, e.g., hGH contains at least one non-naturally-encoded amino acid that is a para-acetylphenylalanine substituted at one or more positions including, but not limited to, positions corresponding to: 35, 92, 131, 134, 143, 145, or any combination thereof, from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. In some embodiments, the invention provides a hormone composition that includes a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH comprises the amino acid sequence of SEQ ID NO: 2, and where the GH, e.g., hGH contains at least one non-naturally-encoded amino acid that is a para-acetylphenylalanine substituted at one or more positions including, but not limited to, positions corresponding to: 30, 35, 74, 92, 103, 145, or any combination thereof, from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. In some embodiments, the invention provides a hormone composition that includes a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH comprises the amino acid sequence of SEQ ID NO: 2, and where the GH, e.g., hGH contains at least one non-naturally-encoded amino acid that is a para-acetylphenylalanine substituted at one or more positions including, but not limited to, positions corresponding to: 35, 92, 143, 145, or any combination thereof, from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. In some embodiments, the invention provides a hormone composition that includes a GH, e.g., hGH, linked via an oxime bond to at least one PEG, e.g., a linear PEG, where the GH, e.g., hGH comprises the amino acid sequence of SEQ ID NO: 2, and where the GH, e.g., hGH contains at least one non-naturally-encoded amino acid that is a para-acetylphenylalanine substituted at one or more positions including, but not limited to, positions corresponding to position 35 from SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3. In embodiments in which the PEG is a linear PEG, the PEG can have a MW of about 0.1 to about 100 kDa, or about 1 to about 60 kDa, or about 20 to about 40 kDa, or about 30 kDa.
[364] In some embodiments, the invention provides a GH, e.g., hGH, where the GH, e.g.,
hGH contains at least one non-naturally encoded amino acid, where the GH is linked to a plurality of water-soluble polymers, e.g., a plurality of PEGs, by covalent bonds, where one or more of the covalent bond is an oxime bond between at least one of the non-naturally encoded amino acid and the water-soluble polymer, e.g., PEG. The GH, e.g., hGH, may be linked to about 2-100 water-soluble polymers, e.g., PEGs, or about 2-50 water-soluble polymers, e.g., PEGs, or about 2-25 water-soluble polymers, e.g., PEGs, or about 2-10 water-soluble polymers, e.g., PEGs, or about 2-

5 water-soluble polymers, e.g., PEGs, or about 5-100 water-soluble polymers, e.g., PEGs, or about 5-50 water-soluble polymers, e.g., PEGs, or about 5-25 water-soluble polymers, e.g., PEGs, or about 5-10 water-soluble polymers, e.g., PEGs, or about 10-100 water-soluble polymers, e.g., PEGs, or about 10-50 water-soluble polymers, e.g., PEGs, or about 10-20 water-soluble polymers, e.g., PEGs, or about 20-100 water-soluble polymers, e.g., PEGs, or about 20-50 water-soluble polymers, e.g., PEGs, or about 50-100 water-soluble polymers, e.g., PEGs. The one or more non-naturally-encoded amino acids may be incorporated into the GH, e.g., hGH, at any position described herein. In some embodiments, at least one non-naturally-encoded amino acid is incorporated into the GH, e.g., hGH, at a position corresponding to position 35 of SEQ ID NO: 2. In some embodiments, the non-naturally encoded amino acids include at least one non-naturally encoded amino acid that is a carbonyl-containing non-naturally encoded amino acid, e.g., a ketone-containing non-naturally encoded amino acid such as a para-acetylphenylalanine. In some embodiments, the GH, e.g., hGH, includes a para-acetylphenylalanine. In some embodiments, the para-acetylphenylalanine is incorporated into the GH, e.g., hGH, at a position corresponding to position 35 of SEQ ID NO: 2, where the para-acetylphenylalanine is linked to one of the polymers, e.g., one of the PEGs, by an oxinie bond. In some embodiments, at least one of the water-soluble polymers, e.g., PEGs, is linked to the GH, e.g., hGH, by a covalent bond to at least one of the non-naturally-encoded amino acids. In some embodiments, the covalent bond is an oxime bond. In some embodiments, a plurality of the water-soluble polymers, e.g., PEGs, are linked to the GH, e.g., hGH, by covalent bonds to a plurality of the non-naturally-encoded amino acids. In some embodiments, at least one the covalent bonds is an oxime bond; in some embodiments, a plurality of the covalent bonds are oxime bonds; in some embodiments, substantially all of the bonds are oxime bonds. The plurality of water-soluble polymers, e.g., PEG, may be linear, branched, or any combination thereof. In embodiments that incorporate one or more linear PEGs, the linear PEGs have a MW of about 0.1 to about 100 kDa, or about 1 to about 60 kDa, or about 20 to about 40 kDa, or about 30 kDa. In embodiments that incorporate one or more branched PEGs, the branched PEGs have a MW of about 1 to about 100 kDa, or about 30 to about 50 kDa, or about 40 kDa. It will be appreciated that embodiments employing a plurality of water-soluble polymers, e.g., PEGs, will, in general, employ such polymers at lower MWs than embodiments in which a single PEG is used. Thus, in some embodiments, the overall MW of the plurality of PEGs is about 0.1-500 kDa, or about 0.1-200 kDa, or about 0.1-100 kDa, or about 1-

1000 kDa, or about 1-500 kDa, or about 1-200 kDa, or about 1-100 kDa, or about 10-1000 kDa, or about 10-500 kDa, or about 10-200 kDa, or about 10-100 kDa, or about 10-50 kDa, or about 20-1000 kDa, or about 20-500 kDa, or about 20-200 kDa, or about 20-100 kDa, or about 20-80 kDa, about 20-60 kDa, about 5-100kDa, about 5-50 kDa, or about 5-20 kDa.
[365] Human GH antagonists include, but are not limited to, those with substitutions at:
1, 2, 3, 4, 5, 8,9, 11, 12, 15, 16, 19, 22, 103, 109,112, 113, 115, 116, 119, 120, 123, and 127 or an
addition at position 1 (i.e., at the N-terminus), or any combination thereof (SEQ ID NO:2, or the
corresponding amino acid in SEQ ID NO: 1, 3, or any other GH sequence).
[366] A wide variety of non-naturally encoded amino acids can be substituted for, or
incorporated into, a given position in a GH, e.g., hGH polypeptide. In general, a particular non-
naturally encoded amino acid is selected for incorporation based on an examination of the three
dimensional crystal structure of a GH, e.g., hGH polypeptide with its receptor, a preference for
conservative substitutions (i.e., aryl-based non-naturally encoded amino acids, such as p-
acetylphenylalanine or O-propargyltyrosine substituting for Phe, Tyr or Trp), and the specific
conjugation chemistry that one desires to introduce into the GH, e.g., hGH polypeptide (e.g., the
introduction of 4-azidophenylalanine if one wants to effect a Huisgen [3+2] cycloaddition with a .
water soluble polymer bearing an alkyne moiety or a amide bond formation with a water soluble
polymer that bears an aryl ester that, in turn; incorporates a phosphine moiety).
[367] In one embodiment, the method further includes incorporating into the protein the
unnatural amino acid, where the unnatural amino acid comprises a first reactive group; and contacting the protein with a molecule (including but not limited to, a label, a dye, a polymer, a water-soluble polymer, a derivative of polyethylene glycol, a photocrosslinker, a radionuclide, a cytotoxic compound, a drug, an affinity label, a photoaffinity label, a reactive compound, a resin, a second protein or polypeptide or polypeptide analog, an antibody or antibody fragment, a metal chelator, a cofactor, a fatty acid, a carbohydrate, a polynucleotide, a DNA, a RNA, an antisense polynucleotide, a saccharide, water-soluble dendrimer, a cyclodextrin, an inhibitory ribonucleic acid, a biomaterial, a nanoparticle, a spin label, a fluorophore, a metal-containing moiety, a radioactive moiety, a novel functional group, a group that covalently or noncovalently interacts with other molecules, a photocaged moiety, an actinic radiation excitable moiety, a photoisomerizable moiety, biotin, a derivative of biotin, a biotin analogue, a moiety incorporating a heavy atom, a chemically cleavable group, a photocleavable group, an elongated side chain, a

carbon-linked sugar, a redox-active agent, an amino thioacid, a toxic moiety, an isotopically labeled moiety, a biophysical probe, a phosphorescent group, a chemiluminescent group, an electron dense group, a magnetic group, an intercalating group, a chromophore, an energy transfer agent, a biologically active agent, a detectable label, a small molecule, a quantum dot, a nanotransmitter, a radionucleotide, a radiotransmitter, a neutron-capture agent, or any combination of the above, or any other desirable compound or substance) that comprises a second reactive group. The first reactive group reacts with the second reactive group to attach the molecule to the unnatural amino acid through a [3+2] cycloaddition. In one embodiment, the first reactive group is an alkynyl or azido moiety and the second reactive group is an azido or alkynyl moiety. For example, the first reactive group is the alkynyl moiety (including but not limited to, in unnatural amino acid p-propargyloxyphenylalanine) and the second reactive group is the azido moiety. In another example, the first reactive group is the'azido moiety (including but not limited to, in the unnatural amino acid p-azido-L-phenylalanine) and the second reactive group is the alkynyl . moiety.
[368] In some cases, the non-naturally encoded amino acid substitution(s) will be
combined with other additions, substitutions or deletions within the GH, e.g., hGH polypeptide to .-; affect other biological traits of the GH, e.g., hGH polypeptide. In some cases, the other additions, ■; substitutions or deletions may increase the stability (including but not limited to, resistance to ; proteolytic degradation) of the GH, e.g., hGH polypeptide or increase affinity of the GH, e.g., i hGH polypeptide for its receptor. In some embodiments, the GH, e.g., hGH polypeptide comprises an amino acid substitution selected from the group consisting of F10A, F10H, F10I; M14W, M14Q, M14G; H18D; H21N; G120A; R167N; D171S; E174S; F176Y, I179T or any combination thereof in SEQ ID NO: 2. In some cases, the other additions, substitutions or deletions may increase the solubility (including but not limited to, when expressed in E. coli or other host cells) of the GH, e.g., hGH polypeptide. In some embodiments additions, substitutions or deletions may increase the polypeptide solubility following expression in E. coli or other recombinant host cells. In some embodiments sites are selected for substitution with a naturally encoded or non-natural amino acid in addition to another site for incorporation of a non-natural amino acid that results in increasing the polypeptide solubility following expression in R coli or other recombinant host cells, hi some embodiments, the GH, e.g., hGH polypeptides comprise another addition, substitution or deletion that modulates affinity for the GH, e.g., hGH polypeptide

receptor, modulates (including but not limited to, increases or decreases) receptor dimerization, stabilizes receptor dimers, modulates circulating half-life, modulates release or bio-availability, facilitates purification, or improves or alters a particular route of administration. For instance, in addition to introducing one or more non-naturally encoded amino acids as set forth herein, one or more of the following substitutions are introduced: F10A, FlOH or F10I; M14W, M14Q, or M14G; H18D; H21N; R167N; D171S; E174S; F176Y and I179T to increase the affinity of the GH, e.g., hGH variant for its receptor. Similarly, GH, e.g., hGH polypeptides can comprise chemical or enzyme cleavage sequences, protease cleavage sequences, reactive groups, antibody-binding domains (including but not limited to, FLAG or poly-His) or other affinity based sequences (including, but not limited to, FLAG, poly-His, GST, etc.) or linked molecules (including, but not limited to, biotin) that improve detection (including, but not limited to, GFP), purification, transport through tissues or cell membranes, prodrug release or activation, hGH size reduction, or other traits of the polypeptide.
[369] In some embodiments, the substitution of a non-naturally encoded amino acid
generates an GH, e.g., hGH antagonist A subset of exemplary sites for incorporation of one or more non-naturally encoded amino acid include; 1, 2, 3,4, 5, 8, 9, 11, 12, 15, 16, 19,22, 103, 109, 112, 113, 115, 116, 119, 120, 123, 127, or an addition before position 1 (SEQ ID NO: 2, or the corresponding amino acid in SEQ ID NO: 1, 3, or any other GH sequence). In some embodiments, GH, e.g., hGH antagonists comprise at least one substitution in the regions 1-5 (N-terminus), 6-33 (A helix), 34-74 (region between A helix and B helix, the A-B loop), 75-96 (B helix), 97-105 (region between B helix and C helix, the B-C loop), 106-129 (C helix), 130-153 (region between C helix and D helix, the C-D loop), 154-183 (D helix), 184-191 (C-terminus) that cause GH to act as an antagonist. In other embodiments, the exemplary sites of incorporation of a non-naturally encoded amino acid include residues within the amino terminal region of helix A and a portion of helix C. In another embodiment, substitution of G120 with a non-naturally encoded amino acid such as p-azido-L-phenyalanine or O-propargyl-L-tyrosine. In other embodiments, the above-listed substitutions are combined with additional substitutions that cause the GH, e.g., hGH polypeptide to be an GH, e.g., hGH antagonist. For instance, a non-naturally encoded amino acid is substituted at one of the positions identified herein and a simultaneous substitution is introduced at G120 (e.g., G120R, G120K, G120W, G120Y, G120F, or G120E). In some embodiments, the GH, e.g., hGH antagonist comprises a non-naturally encoded amino acid

linked to a water soluble polymer that is present in a receptor binding region of the GH, e.g., hGH molecule.
[370] In some cases, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more amino acids are substituted with
one or more non-naturally-encoded amino acids. In some cases, the GH, e.g., hGH polypeptide
further includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more substitutions of one or more non-naturally
encoded amino acids for naturally-occurring amino acids. For example, in some embodiments,
one or more residues in the following regions of GH, e.g., hGH are substituted with one or more
non-naturally encoded amino acids: 1-5 (N-terminus); 32-46 (N-terminal end of the A-B loop);
97-105 (B-C loop); and 132-149 (C-D loop); and 184-191 (C-terminus). In some embodiments,
one or more residues in the following regions of GH, e.g., hGH are substituted with one or more
non-naturally encoded amino acids: 1-5 (N-terminus), 6-33 (A helix), 34-74 (region between A
helix and B helix, the A-B loop), 75-96 (B helix), 97-105 (region between B helix and C helix, the
B-C loop), 106-129 (C helix), 130-153 (region between C helix and D helix, the C-D loop), 154-
183 (D helix), 184-191 (C-terminus). In some cases, the one or more non-naturally encoded
residues are linked to one or more lower molecular weight linear or branched PEGs
(approximately ~ 5-20 kDa in mass or less), thereby enhancing binding affinity and comparable
serum half-life relative to the species attached to a single, higher molecular weight PEG.
[371] In some embodiments, up to two of the following residues of GH, e.g., hGH are
substituted with one or more non-naturally-encoded amino acids at position: 29, 30, 33, 34,35, 37, 39, 40, 49, 57, 59, 66, 69, 70, 71,74, 88, 91, 92, 94, 95, 98, 99, 101, 103,107,108, 111, 122, 126, 129, 130, 131, 133, 134, 135, 136, 137, 139, 140, 141, 142, 143, 145, 147, 154, 155, 156, 159, 183,186, and 187. In some cases, any of the following pairs of substitutions are made: K38X* and K140X*; K41X* and K145X*; Y35X* and E88X*; Y35X* and F92X*; Y35X* and Y143X*; F92X* and Y143X* wherein X* represents a non-naturally encoded amino acid. Preferred sites for incorporation of two or more non-naturally encoded amino acids include combinations of the following residues: 29, 33, 35, 37, 39, 49, 57, 69, 70,71, 74, 88, 91, 92, 94, 95, 98, 99, 101, 103, 107, 108, 111, 129, 130, 131, 133, 134, 135, 136, 137, 139, 140, 141, 142, 143, 145, 147, 154, 155,156, 186, and 187. Particularly preferred sites for incorporation of two or more non-naturally encoded amino acids include combinations of the following residues: 35, 88, 91, 92, 94, 95, 999 101,103, 111, 131,133,134,135,136,139,140,143,145, and 155.

[372] Preferred sites for incorporation in GH, e.g., hGH of two or more non-naturally
encoded amino acids include combinations of the following residues: before position 1 (i.e. at the N-terminus), 1, 2, 3, 4, 5, 8, 9, 11, 12, 15, 16, 19, 22,29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44,45, 46, 47, 48, 49, 52, 55, 57, 59, 65, 66, 69, 70, 71, 74, 88, 91, 92, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 111, 112, 113, 115, 116, 119, 120, 122, 123, 126, 127, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 159, 161, 168, 172, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192 (i.e. at the carboxyl terminus of the protein) or any combination thereof from SEQ ID NO: 2.
VII. Expression in Non~eukaryotes and Eukaryotes
[373] To obtain high level expression of a cloned GH, e.g., hGH polynucleotide, one
typically subclones polynucleotides encoding a GH, e.g., hGH polypeptide of the invention into an
expression vector that contains a strong promoter to direct transcription, a transcription/translatiori
terminator, and if for a nucleic acid encoding a protein, a ribosome binding site for translational
initiation. Suitable bacterial promoters are known to those of ordinary skill in the art and
described, e.g., in Sambrook et al. and Ausubel et ah . i
[374J Bacterial expression systems for expressing GH, e.g., hGH polypeptides of the;
invention are available in, including but not limited to, E. coli, Bacillus sp., Pseudomonas, fluorescens, Pseudomonas aeruginosa, Pseudomonas putida, and Salmonella (Palva et aL> Gene} 22:229-235 (1983); Mosbach et al, Nature 302:543-545 (1983)). Kits for such expression systems are commercially available. Eukaryotic expression systems for mammalian cells, yeast, and insect cells are known to those of ordinary skill in the art and are also commercially available. In cases where orthogonal tRNAs and aminoacyl tRNA synthetases (described above) are used to express the GH, e.g., hGH polypeptides of the invention, host cells for expression are selected based on their ability to use the orthogonal components. Exemplary host cells include Gram-positive bacteria (including but not limited to B. brevis, B. subtilis, or Streptomyces) and Gram-negative bacteria (E. coli, Pseudomonas fluorescens, Pseudomonas aeruginosa, Pseudomonas putida)9 as well as yeast and other eukaryotic cells. Cells comprising O-tRNA/O-RS pairs can be used as described herein.
[375] A eukaryotic host cell or non-eukaTyotic host cell of the present invention provides
the ability to synthesize proteins that comprise unnatural amino acids in large useful quantities. In

one aspect, the composition optionally includes, including but not limited to, at least 10 micrograms, at least 50 micrograms, at least 75 micrograms, at least 100 micrograms, at least 200 micrograms, at least 250 micrograms, at least 500 micrograms, at least 1 milligram, at least 10 milligrams, at least 100 milligrams, at least one gram, or more of the protein that comprises an unnatural amino acid, or an amount that can be achieved with in vivo protein production methods (details on recombinant protein production and purification are provided herein). In another aspect, the protein is optionally present in the composition at a concentration o£ including but not limited to, at least 10 micrograms of protein per liter, at least 50 micrograms of protein per liter, at least 75 micrograms of protein per liter, at least 100 micrograms of protein per liter, at least 200 micrograms of protein per liter, at least 250 micrograms of protein per liter, at least 500 micrograms of protein per liter, at least 1 milligram of protein per liter, or at least 10 milligrams of protein per liter or more, in, including but not limited to, a cell lysate, a buffer, a pharmaceutical buffer, or other liquid suspension (including but not limited to, in a volume of, including but not limited to, anywhere from about 1 nl to about 100 L). The production of large quantities (including but not limited to, greater that that typically possible with other methods, including but not limited to, in vitro translation) of a protein in a eukaryotic cell including at least one unnatural amino acid is a feature of the invention.
[376] A eukaryotic host cell or non-eukaryotic host cell of the present invention provides
the ability to biosynthesize proteins that comprise unnatural amino acids in large useful quantities.
For example, proteins comprising an unnatural amino acid can be produced at a concentration of,
including but not limited to, at least 10 fig/liter, at least 50 ng/liter, at least 75 pg/liter, at least 100
^g/liter, at least 200 jig/liter, at least 250 p,g/liter, or at least 500 ^g/liter, at least Img/liter, at least
2mg/liter, at least 3 mg/liter, at least 4 mg/liter, at least 5 mg/liter, at least 6 mg/liter, at least 7
mg/liter, at least 8 mg/liter, at least 9 mg/liter, at least 10 mg/liter, at least 20, 30, 40, 50, 60, 70,
80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900 mg/liter, 1 g/liter, 5 g/liter, 10 g/liter or more
of protein in a cell extract, cell lysate, culture medium, a buffer, and/or the like.
I. Expression Systems, Culture, and Isolation
{377] GH, e.g., hGH polypeptides may be expressed in any number of suitable expression
systems including, for example, yeast, insect cells, mammalian cells, and bacteria. A description of exemplary expression systems is provided below.

i,
[378] Yeast As used herein, the term "yeast" includes any of the various yeasts capable
of expressing a gene encoding a GH, e.g., hGH polypeptide. Such yeasts include, but are not limited to, ascosporogenous yeasts (Endomycetales), basidiosporogenous yeasts and yeasts belonging to the Fungi imperfecti (Blastomycetes) group. The ascosporogenous yeasts are divided into two families, Spermophthoraceae and Saccharomycetaceae. The latter is comprised of four subfamilies, Schizosaccharomycoideae (e.g., genus Schizosaccharomyces), Nadsonioideae, Lipomycoideae and Saccharomycoideae (e.g., genera Pichia, Kluyveromyces and Saccharomyces). The basidiosporogenous yeasts include the genera Leucosporidium, Rhodosporidium, Sporidiobolus, Filobasidium, and Filobasidiella. Yeasts belonging to the Fungi Imperfecti {Blastomycetes) group are divided into two families, Sporobolomycetaceae (e.g., genera Sporobolomyces and Bullerd) and Cryptococcaceae (e.g., genus Candida).
[379] Of particular interest for use with the present invention are species within the
genera Pichia, Kluyveromyces, Saccharomyces, Schizosaccharomyces, Hansenula, Torulopsis, and Candida, including, but not limited to, P. pastoris, P. guillerimondii, S. cerevisiae, S. carlsbergensis, S. diastaticus, S. douglasii, S. Huyveri, S, norbensis, S. oviformis, K. lactis, K. fragilis, C albicans, C maltosa, and H. polytnorpha.
[380] The selection of suitable yeast for expression of GH, e.g., hGH polypeptides is
within the skill of one of ordinary skill in the art In selecting yeast hosts for expression, suitable
hosts may include those shown to have, for example, good secretion capacity, low proteolytic,
activity, good secretion capacity, good soluble protein production, and overall robustness. Yeast
are generally available from a variety of sources including, but not limited to, the Yeast Genetic
Stock Center, Department of Biophysics and Medical Physics, University of California (Berkeley,
CA), and the American Type Culture Collection ("ATCC") (Manassas, VA).
[381] The term "yeast host" or "yeast host cell" includes yeast that can be, or has been,
used as a recipient for recombinant vectors or other transfer DNA. The term includes the progeny of the original yeast host cell that has received the recombinant vectors or other transfer DNA. It is understood that the progeny of a single parental cell may not necessarily be completely identical in morphology or in genomic or total DNA complement to the original parent, due to accidental or deliberate mutation. Progeny of the parental cell that are sufficiently similar to the parent to be characterized by the relevant property, such as the presence of a nucleotide sequence encoding a GH, e.g., hGH polypeptide, are included in the progeny intended by this definition.

[382] Expression and transformation vectors, including extrachromosomal replicons or
integrating vectors, have been developed for transformation into many yeast hosts. For example,
expression vectors have been developed for S. cerevisiae (Sikorski et aL, GENETICS (1989) 122:19;
Ito et aL, J. BACTERIOL. (1983) 153:163; Hinnen et aL, PROC. NATL. ACAD. SCL USA (1978)
75:1929); G albicans (Kurtz etaL,MOL. CELL. BlOL. (1986) 6:142); C maltosa (Kunze et aL, J.
BASIC MICROBIOL. (1985) 25:141); K polymorpha (Gleeson et aL, J. GEN. MICROBIOL. (1986)
132:3459; Roggenkamp et aL, MOL. GENETICS AND GENOMICS (1986) 202:302); K.Jragilis (Das et
aL, J. BACTERIOL. (1984) 158:1165); K. lactis (De Louvencourt et aL, J. BACTERIOL. (1983)
154:737; Van den Berg etal., BIOTECHNOLOGY (NY) (1990) 8:135); P. guillerimondii (Kunze et
aL, J. BASIC MICROBIOL. (1985) 25:141); P. pastoris (U.S. Patent Nos. 5,324,639; 4,929,555; and
4,837,148; Cregg et aL, MOL. CELL. BlOL. (1985) 5:3376); Schizosaccharomycespombe (Beach et
aL, NATURE (1982) 300:706); and 7. lipolytics; A. nidulans (Ballance et aL, BlOCHEM. BlOPHYS.
RES. COMMUN. (1983) 112:284-89; Tilburn et aL, GENE (1983) 26:205-221; and Yelton et aL,
PROC. NATL. ACAD. SCL USA (1984) 81:1470-74); A. niger (Kelly and Hynes, EMBO J. (1985) ;
4:475-479); J. reesia (EP 0 244 234); and filamentous fungi such as, e.g., Neurospora,
Penicillium, Tolypocladium (WO 91/00357), each incorporated by reference herein.
[383] Control sequences for yeast vectors are known to those of ordinary skill in the art
and include, but are not limited to, promoter regions from genes such as alcohol > dehydrogenase (ADH) (EP 0 284 044); enolase; glucokinase; glucose-6-phosphate isomerase;' glyceraldehyde-3-phosphate-dehydrogenase (GAP or GAPDH); hexokinase; phosphofructokinase; 3-phosphoglycerate mutase; and pyruvate kinase (PyK) (EP 0 329 203). The yeast PH05 gene, encoding acid phosphatase, also may provide useful promoter sequences (Miyanohara et aL, PROC. NATL. ACAD. SCL USA (1983) 80:1). Other suitable promoter sequences for use with yeast hosts may include the promoters for 3-phosphoglycerate kinase (Hitzeman et aL, J. BlOL. CHEM. (1980) 255:12073); and other glycolytic enzymes, such as pyruvate decarboxylase, triosephosphate isomerase, and phosphoglucose isomerase (Holland et aL, BIOCHEMISTRY (1978) 17:4900; Hess et aL, J. ADV. ENZYME REG. (1969) 7:149), Inducible yeast promoters having the additional advantage of transcription controlled by growth conditions may include the promoter regions for alcohol dehydrogenase 2; isocytochrome C; acid phosphatase; metallothionein; glyceraldehyde-3-phosphate dehydrogenase; degradative enzymes associated with nitrogen metabolism; and

enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further described in EP 0 073 657.
[384] Yeast enhancers also may be used with yeast promoters. In addition, synthetic
promoters'may also function as yeast promoters. For example, the upstream activating sequences (UAS) of a yeast promoter may be joined with the transcription activation region of another yeast promoter, creating a synthetic hybrid promoter. Examples of such hybrid promoters include the ADH regulatory sequence linked to the GAP transcription activation region. See U.S. Patent Nos. 4,880,734 and 4,876,197, which are incorporated by reference herein. Other examples of hybrid promoters include promoters that consist of the regulatory sequences of the ADH2, GAL4, GAL10, or PH05 genes, combined with the transcriptional activation region of a glycolytic enzyme gene such as GAP or PyK. See EP 0 164 556. Furthermore, a yeast promoter may include naturally occurring promoters of non-yeast origin that have the ability to bind yeast RNA polymerase and initiate transcription.
[385] Other control elements that may comprise part of the yeast expression vectors
include terminators, for example, from GAPDH or the enolase genes (Holland et al., J. BlOL. CHEM. (1981) 256:1385). In addition, the origin of replication from the 2fi plasmid origin is ;'■ suitable for yeast A suitable selection gene for use in yeast is the trpl gene present in the yeast , plasmid. See Tschumper et al., GENE (1980) 10:157; Kingsman et al., GENE (1979) 7:141. The ; trpl gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in t tryptophan. Similarly, Leu2-deficient yeast strains (ATCC 20,622 or 38,626) are complemented by known plasmids bearing the Leu2 gene.
[386] Methods of introducing exogenous DNA into yeast hosts are known to those of
ordinary skill in the art, and typically include, but are not limited to, either the transformation of spheroplasts or of intact yeast host cells treated with alkali cations. For example, transformation of yeast can be carried out according to the method described in Hsiao et al., PROC. NATL. ACAD. SCI. USA (1979) 76:3829 and Van Solingen et al., J. BACT. (1977) 130:946. However, other methods for introducing DNA into cells such as by nuclear injection, electroporation, or protoplast fusion may also be used as described generally in SAMBROOK ET AL., MOLECULAR CLONING: A LAB. MANUAL (2001). Yeast host cells may then be cultured using standard techniques known to those of ordinary skill in the art.

[387] Other methods for expressing heterologous proteins in yeast host cells are known to
those of ordinary skill in the art. See generally U.S. Patent Publication No. 20020055169, U.S. Patent Nos. 6,361,969; 6,312,923; 6,183,985; 6,083,723; 6,017,731; 5,674,706; 5,629,203; 5,602,034; ■ and 5,089,398; U.S. Reexamined Patent Nos. RE37,343 and RE35,749; PCT Published Patent Applications WO 99/07862; WO 98/37208; and WO 98/26080; European Patent Applications EP 0 946 736; EP 0 732 403; EP 0 480 480; WO 90/10277; EP 0 340 986; EP 0 329 203; EP 0 324 274; and EP 0 164 556. See also Gellissen et al., ANTONIE VAN LEEUWENHOEK (1992) 62(l-2):79-93; Romanos et al., YEAST (1992) 8(6):423-488; Goeddel, METHODS IN ENZYMOLOGY (1990) 185:3-7, each incorporated by reference herein.
[388J The yeast host strains may be grown in fermentors during the amplification stage
using standard feed batch fermentation methods known to those of ordinary skill in the art. The fermentation methods may be adapted to account for differences in a particular yeast host's carbon utilization pathway or mode of expression control. For example, fermentation of a Saccharomyces yeast host may require a single glucose feed, complex nitrogen source (e.g., casein hydrolysates), and multiple vitamin supplementation. In contrast, the methylotrophic yeast P.. pastoris may require glycerol, methanol, and trace mineral feeds, but only simple ammonium, (nitrogen) salts for optimal growth and expression. See, e.g., U.S. Patent No. 5,324,639; Elliott et al., J. PROTEIN CHEM. (1990) 9:95; and Fieschko et al., BIOTECH. BIOENG. (1987) 29:1113/ incorporated by reference herein.
[389] Such fermentation methods, however, may have certain common features
independent of the yeast host strain employed. For example, a growth limiting nutrient, typically carbon, may be added to the fermentor during the amplification phase to allow maximal growth. In addition, fermentation methods generally employ a fermentation medium designed to contain adequate amounts of carbon, nitrogen, basal salts, phosphorus, and other minor nutrients (vitamins, trace minerals and salts, etc.). Examples of fermentation media suitable for use with Pichia are described in U.S. Patent Nos. 5,324,639 and 5,231,178, which are incorporated by reference herein.
[390] Baculovirus-Mected Insect Cells The term "insect host" or "insect host cell" refers
to a insect that can be, or has been, used as a recipient for recombinant vectors or other transfer DNA. The term includes the progeny of the original insect host cell that has been transfected. It is understood that the progeny of a single parental cell may not necessarily be completely identical

in morphology or in genomic or total DNA complement to the original parent, due to accidental or
deliberate mutation. Progeny of the parental cell that are sufficiently similar to the parent to be
characterized by the relevant property, such as the presence of a nucleotide sequence encoding a
GH, e.g., hGH polypeptide, are included in the progeny intended by this definition.
[391] The selection of suitable insect cells for expression of GH, e.g., hGH polypeptides
is known to those of ordinary skill in the art Several insect species are well described in the art and are commercially available including Aedes aegypti, Bombyx mori, Drosophila melanogaster, Spodoptera frugiperda, and Trichoplusia nL In selecting insect hosts for expression, suitable hosts may include those shown to have, inter alia, good secretion capacity, low proteolytic activity, and overall robustness. Insect are generally available from a variety of sources including, but not limited to, the Insect Genetic Stock Center, Department of Biophysics and Medical Physics, University of California (Berkeley, CA); and the American Type Culture Collection ("ATCC") (Manassas, VA).
[392] Generally, the components of a baculovirus-infected insect expression system
include a transfer vector, usually a bacterial plasmid, which contains both a fragment of the baculovirus genome, and a convenient restriction site for insertion of the heterologous gene to be . expressed; a wild type baculovirus with sequences homologous to the baculovirus-specific fragment in the transfer vector (this allows for the homologous recombination of the heterologous.* gene in to the baculovirus genome); and appropriate insect host cells and growth media. The,; materials, methods and techniques used in constructing vectors, transfecting cells, picking plaques, growing cells in culture, and the like are known in the art and manuals are available describing these techniques.
[393] After inserting the heterologous gene into the transfer vector, the vector and the
wild type viral genome are transfected into an insect host cell where the vector and viral genome recombine. The packaged recombinant virus is expressed and recombinant plaques are identified and purified. Materials and methods for baculovirus/insect cell expression systems are commercially available in kit form from, for example, Invitrogen Corp. (Carlsbad, CA). These techniques are generally known to those of ordinary skill in the art and fully described in
SUMMERS AND SMITH, TEXAS AGRICULTURAL EXPERIMENT STATION BULLETIN NO. 1555 (1987),
herein incorporated by reference. See also, RICHARDSON, 39 METHODS IN MOLECULAR BIOLOGY:
BACULOVIRUS EXPRESSION PROTOCOLS (1995); AUSUBEL ET AL., CURRENT PROTOCOLS IN

MOLECULAR BIOLOGY 16.9-16.11 (1994); KING AND POSSEE, THE BACULOVIRUS SYSTEM: A LABORATORY GUIDE (1992); and O'REILLY ET AL., BACULOVIRUS EXPRESSION VECTORS: A LABORATORY MANUAL (1992).
[394] Indeed, the production of various heterologous proteins using baculovirus/insect
cell expression systems is known to those of ordinary skill in the art. See, e.g., U.S. Patent Nos. 6,368,825; 6342,216; 6,338,846; 6,261,805; 6,245,528, 6,225,060; 6,183,987; 6,168,932; 6,126,944; 6,096,304; 6,013,433; 5,965,393; 5,939,285; 5,891,676; 5,871,986; 5,861,279; 5,858,368; 5,843,733; 5,762,939; 5,753,220; 5,605,827; 5,583,023; 5,571,709; 5,516,657; 5,290,686; WO 02/06305; WO 01/90390; WO 01/27301; WO 01/05956; WO 00/55345; WO 00/20032; WO 99/51721; WO 99/45130; WO 99/31257; WO 99/10515; WO 99/09193; WO 97/26332; WO 96/29400; WO 96/25496; WO 96/06161; WO 95/20672; WO 93/03173; WO 92/16619; WO 92/02628; WO 92/01801; WO 90/14428; WO 90/10078; WO 90/02566; WO 90/02186; WO 90/01556; WO 89/01038; WO 89/01037; WO 88/07082, which are; incorporated by reference herein.
[395] Vectors that are useful in baculovirus/insect cell expression systems are known in .';
the art and include, for example, insect expression and transfer vectors derived from the '•■ baculovirus Autographacalifomica nuclear polyhedrosis virus (AcNPV), which is a helper- ! independent, viral expression vector. Viral expression vectors derived from this system usually i use the strong viral polyhedrin gene promoter to drive expression of heterologous genes. See-1-: generally, O'Reilly ET AL., BACULOVIRUS EXPRESSION VECTORS: A LABORATORY MANUAL (1992).
[396] Prior to inserting the foreign gene into the baculovirus genome, the above-
described components, comprising a promoter, leader (if desired), coding sequence of interest, and transcription termination sequence, are typically assembled into an intermediate transplacement construct (transfer vector). Intermediate transplacement constructs are often maintained in a replicon, such as an extra chromosomal element (e.g., plasmids) capable of stable maintenance in a host, such as bacteria. The replicon will have a replication system, thus allowing it to be maintained in a suitable host for cloning and amplification. More specifically, the plasmid may contain the polyhedrin polyadenylation signal (Miller, ANN. REV. MICROBIOL. (1988) 42:177) and a prokaryotic ampicillin-resistance (amp) gene and origin of replication for selection and propagation in E. colt

[397] One commonly used transfer vector for introducing foreign genes into AcNPV is
pAc373. Many other vectors, known to those of skill in the art, have also been designed including, for example, pVL985, which alters the polyhedrin start codon from ATG to ATT, and which introduces a BamHI cloning site 32 base pairs downstream from fhe ATT. See Luckow and Summers, VIROLOGY 170:31 (1989). Other commercially available vectors include, for example, PBlueBac4.5/V5-His; pBlueBacHis2; pMelBac; pBlueBac4.5 (Invitrogen Corp., Carlsbad, CA).
[398] After insertion of the heterologous gene, the transfer vector and wild type
)aculoviral genome are co-transfected into an insect cell host. Methods for introducing leterologous DNA into the desired site in the baculovirus virus are known in the art. See SUMMERS AND SMITH, TEXAS AGRICULTURAL EXPERIMENT STATION BULLETIN NO. 1555 (1987); Smith et al., MOL. CELL. BIOL. (1983) 3:2156; Luckow and Summers, VIROLOGY (1989) 170:31. ?or example, the insertion can be into a gene such as the polyhedrin gene, by homologous double crossover recombination; insertion can also be into a restriction enzyme site engineered into the lesired baculovirus gene. See Miller et al., BlOESSAYS (1989) 11(4):91.
399] Transfection may be accomplished by electroporation. See TROTTER AND WOOD,
59 METHODS IN MOLECULAR BIOLOGY (1995); Mann and King, J. GEN. VIROL. (1989) 70:3501. -. Mternatively, liposomes may be used to transfect the insect cells with the recombinant expression .■, sector and the baculovirus. See, e.g., Liebman et al., BlOTECHNlQUES (1999) 26(1):36; Graves et il, BIOCHEMISTRY (1998) 37:6050; Nomura et al., J. BIOL. CHEM. (1998) 273(22): 13570; Schmidt ?t al., PROTEIN EXPRESSION AND PURIFICATION (1998) 12:323; Siflfert et al., NATURE GENETICS 1998) 18:45; TILKINS ET AL., CELL BIOLOGY: A LABORATORY HANDBOOK 145-154 (1998); Cai et d., PROTEIN EXPRESSION AND PURIFICATION (1997) 10:263; Dolphin et al., NATURE GENETICS 1997) 17:491; Kost et al., GENE (1997) 190:139; Jakobsson et al., J. BIOL. CHEM. (1996) £71:22203; Rowles et al., J. BIOL. CHEM. (1996) 271(37):22376; Reverey et al., J. BlOL. CHEM. 1996) 271(39):23607-10; Stanley et al, J. BlOL. CHEM. (1995) 270:4121; Sisk et al., J. VIROL. 1994) 68(2):766; and Peng et al., BlOTECHNlQUES (1993) 14(2):274. Commercially available iposomes include, for example, Cellfectin® and Lipofectin® (Invitrogen, Corp., Carlsbad, CA). !n addition, calcium phosphate transfection may be used. See TROTTER AND WOOD, 39 METHODS N MOLECULAR BIOLOGY (1995); Kitts, NAR (1990) 18(19):5667; and Mann and King, J. GEN. WROL. (1989) 70:3501.

[400] Baculovirus expression vectors usually contain a baculovirus promoter. A
baculovirus promoter is any DNA sequence capable of binding a baculovirus RNA polymerase and initiating the downstream (3') transcription of a coding sequence (e.g., structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5' end of the coding sequence. This transcription initiation region typically includes an RNA polymerase binding site and a transcription initiation site. A baculovirus promoter may also have a second domain called an enhancer, which, if present, is usually distal to the structural gene. Moreover, expression may be either regulated or constitutive.
[401] Structural genes, abundantly transcribed at late times in the infection cycle, provide
particularly useful promoter sequences. Examples include sequences derived from the gene
encoding the viral polyhedron protein (FR1ESEN FT AL., The Regulation of Baculovirus Gene
Expression in THE MOLECULAR BIOLOGY OF BACULOVIRUSES (1986); EP 0 127 839 and 0 155
476) and the gene encoding the plO protein (Vlak et al, J. GEN. VIROL. (1988) 69:765).
[402] The newly formed baculovirus expression vector is packaged into an infectious
recombinant baculovirus and subsequently grown plaques may be purified by techniques known to -
those of ordinary skill in the art. See Miller et al., BlOESSAYS (1989) 11(4):91; SUMMERS AND :
SMITH, TEXAS AGRICULTURAL EXPERIMENT STATION BULLETIN No. 1555 (1987). .'•
{403] Recombinant baculovirus expression vectors have been developed for infection into *
several insect cells. For example, recombinant baculoviruses have been developed for, inter alia, « Aedes aegypti (ATCC No. CCL-125), Bombyx mori (ATCC No. CRL-8910), Drosophila melanogaster (ATCC No. 1963), Spodoptera frugiperda, and Trichoplusia ni. See Wright, NATURE (1986) 321:718; Cafbonell et al., J. VIROL. (1985) 56:153; Smith et al., MOL. CELL. BlOL. (1983) 3:2156. See generally, Fraser et al., IN VITRO CELL. DEV. BlOL. (1989) 25:225. More specifically, the cell lines used for baculovirus expression vector systems commonly include, but are not limited to, S© (Spodoptera frugiperda) (ATCC No. CRL-1711), S£21 (Spodoptera frugiperda) (Invitrogen Corp., Cat No. 11497-013 (Carlsbad, CA)), Tri-368 (Trichopulsia ni), and High-Five™ BTI-TN-5B1-4 (Trichopulsia ni).
[404] Cells and culture media are commercially available for both direct and fusion
expression of heterologous polypeptides in a baculovirus/expression, and cell culture technology is generally known to those of ordinary skill in the art.

[405] E. Coli, Pseudomonas species, and other Prokarvotes Bacterial expression
techniques are known to those of ordinary skill in the art. A wide variety of vectors are available for use in bacterial hosts. The vectors may be single copy or low or high multicopy vectors. Vectors may serve for cloning and/or expression. In view of the ample literature concerning vectors, commercial availability of many vectors, and even manuals describing vectors and their restriction maps and characteristics, no extensive discussion is required here. As is well-known, the vectors normally involve markers allowing for selection, which markers may provide for cytotoxic agent resistance, prototrophy or immunity. Frequently, a plurality of markers is present, which provide for different characteristics.
[406] A bacterial promoter is any DNA sequence capable of binding bacterial RNA
polymerase and initiating the downstream (3*) transcription of a coding sequence (e.g. structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5? end of the coding sequence. This transcription initiation region typically : includes an RNA polymerase binding site and a transcription initiation site. A bacterial promoter may also have a second domain called an operator, that may overlap an adjacent RNA polymerase binding site at which RNA synthesis begins. The operator permits negative regulated (inducible) transcription, as a gene repressor protein may bind the operator and thereby inhibit transcription of a specific gene. Constitutive expression may occur in the absence of negative regulatory elements, such as the operator. In addition, positive regulation may be achieved by a gene activator protein « binding sequence, which, if present is usually proximal (5!) to the RNA polymerase binding sequence. An example of a gene activator protein is the catabolite activator protein (CAP), which helps initiate transcription of the lac operon in Escherichia coli (E. coli) [Raibaud et al., ANNU, REV. GENET. (1984) 18:173]. Regulated expression may therefore be either positive or negative, thereby either enhancing or reducing transcription.
[407] Sequences encoding metabolic pathway enzymes provide particularly useful
promoter sequences. Examples include promoter sequences derived from sugar metabolizing enzymes, such as galactose, lactose (lac) [Chang et al., NATURE (1977) 198:1056], and maltose. Additional examples include promoter sequences derived from biosynthetic enzymes such as tryptophan (trp) [Goeddel et al., NUC. ACIDS RES. (1980) 8:4057; Yelverton et al., NUCL. ACIDS RES. (1981) 9:731; U.S. Pat. No. 4,738,921; EP Pub. Nos. 036 776 and 121 775, which are incorporated by reference herein]. The j3-galactosidase (bla) promoter system [Weissmann (1981)

"The cloning of interferon and other mistakes." In Interferon 3 (Ed. I. Gresser)], bacteriophage
lambda PL [Shimatake et al., NATURE (1981) 292:128] and T5 [U.S. Pat. No. 4,689,406, which are
incorporated by reference herein] promoter systems also provide useful promoter sequences.
Preferred methods of the present invention utilize strong promoters, such as the T7 promoter to
induce GH, e.g., hGH polypeptides at high levels. Examples of such vectors are known to those
of ordinary skill in the art and include the pET29 series from Novagen, and the pPOP vectors
described in WO99/05297, which is incorporated by reference herein. Such expression systems
produce high levels of GH, e.g., hGH polypeptides in the host without compromising host cell
viability or growth parameters. pET19 (Novagen) is another vector known in the art.
[408] In addition, synthetic promoters which do not occur in nature also function as
bacterial promoters. For example, transcription activation sequences of one bacterial or bacteriophage promoter may be joined with the operon sequences of another bacterial or bacteriophage promoter, creating a synthetic hybrid promoter [U.S. Pat. No. 4,551,433, which is incorporated by reference herein]. For example, the tac promoter is a hybrid trp-lac promoter comprised of both trp promoter and lac operon sequences that is regulated by the lac repressor [Amann et al., GENE (1983) 25:167; de Boer et al., PROC. NATL. ACAD. Sci. (1983) 80:21]. Furthermore, a bacterial promoter can include naturally occurring promoters of non-bacterial origin that have the ability to bind bacterial RNA polymerase and initiate transcription. A naturally occurring promoter of non-bacterial origin can also be coupled with a compatible* RNA polymerase to produce high levels of expression of some genes in prokaryotes. The bacteriophage T7 RNA polymerase/promoter system is an example of a coupled promoter system [Studier et al., J. MOL. BlOL. (1986) 189:113; Tabor et al., Proc Natl. Acad. Sci. (1985) 82:1074]. In addition, a hybrid promoter can also be comprised of a bacteriophage promoter and an E. coli operator region (EP Pub. No. 267 851).
[409] In addition to a functioning promoter sequence, an efficient ribosome binding site
is also useful for the expression of foreign genes in prokaryotes. In E. coli, the ribosome binding site is called the Shine-Dalgarno (SD) sequence and includes an initiation codon (ATG) and a sequence 3-9 nucleotides in length located 3-11 nucleotides upstream of the initiation codon [Shine et al., NATURE (1975) 254:34]. The SD sequence is thought to promote binding of mRNA to the ribosome by the pairing of bases between the SD sequence and the 31 and of E. coli 16S rRNA [Steitz et al. "Genetic signals and nucleotide sequences in messenger RNA", In Biological

Regulation and Development: Gene Expression (Ed. R. F. Goldberger, 1979)]. To express eukaryotic genes and prokaryotic genes with weak ribosome-binding site [Sambrook et al. "Expression of cloned genes in Escherichia coli", Molecular Cloning: A Laboratory Manual,
1989].
[410] The term "bacterial host" or "bacterial host cell" refers to a bacterial that can be, or
has been, used as a recipient for recombinant vectors or other transfer DNA. The term includes the progeny of the original bacterial host cell that has been transfected. It is understood that the progeny of a single parental cell may not necessarily be completely identical in morphology or in genomic or total DNA complement to the original parent, due to accidental or deliberate mutation. Progeny of the parental cell that are sufficiently similar to the parent to be characterized by the relevant property, such as the presence of a nucleotide sequence encoding a GH, e.g., hGH polypeptide, are included in the progeny intended by this definition.
[411] The selection of suitable host bacteria for expression of GH, e.g., hGH
polypeptides is known to those of ordinary skill in the art In selecting bacterial hosts for -expression, suitable hosts may include those shown to have, inter alia, good inclusion body
dow.com). U.S. Patent Nos. 4,755,465 and 4,859,600, which are incorporated by reference herein,
describe the use of Pseudomonas strains as a host cell for GH, e.g., hGH production.
[412] Once a recombinant host cell strain has been established (i.e., the expression
construct has been introduced into the host cell and host cells with the proper expression construct are isolated), the recombinant host cell strain is cultured under conditions appropriate for production of GH, e.g., hGH polypeptides. As will be apparent to one of skill in the art, the method of culture of the recombinant host cell strain will be dependent on the nature of the expression construct utilized and the identity of the host cell. Recombinant host strains axe normally cultured using methods that are known to those of ordinary skill in the art Recombinant host cells are typically cultured in liquid medium containing assimilatable sources of carbon, nitrogen, and inorganic salts and, optionally, containing vitamins, amino acids, growth factors, and other proteinaceous culture supplements known to those of ordinary skill in the art. Liquid media for culture of host cells may optionally contain antibiotics or anti-fungals to prevent the growth of undesirable microorganisms and/or compounds including, but not limited to, antibiotics to select for host cells containing the expression vector.
[413] Recombinant host cells may be cultured in batch or continuous formats, with either
cell harvesting (in the case where the GH, e.g., hGH polypeptide accumulates intracellularly) or harvesting of culture supernatant in either batch or continuous formats. For production in prokaryotic host cells, batch culture and cell harvest are preferred.
[414] The GH, e.g., hGH polypeptides of the present invention are normally purified after
expression in recombinant systems. The GH, e.g., hGH polypeptide may be purified from host cells or culture medium by a variety of methods known to the art. GH, e.g., hGH polypeptides produced in bacterial host cells may be poorly soluble or insoluble (in the form of inclusion bodies). In one embodiment of the present invention, amino acid substitutions may readily be made in the GH, e.g., hGH polypeptide that are selected for the purpose of increasing the solubility of the recombinantly produced protein utilizing the methods disclosed herein as well as those known in the art In the case of insoluble protein, the protein may be collected from host cell lysates by centrifugation and may further be followed by homogenization of the cells. In the case of poorly soluble protein, compounds including, but not limited to, polyethylene imine (PEI) may be added to induce the precipitation of partially soluble protein. The precipitated protein may then be conveniently collected by centrifugation. Recombinant host cells may be disrupted or

homogenized to release the inclusion bodies from within the cells using a variety of methods known to those of ordinary skill in the art. Host cell disruption or homogenization may be performed using well known techniques including, but not limited to, enzymatic cell disruption, sonication, dounce homogenization, or high pressure release disruption. In one embodiment of the method of fee present invention, the high pressure release technique is used to disrupt the E. coli host cells to release the inclusion bodies of the GH, e.g., hGH polypeptides. When handling inclusion bodies of GH, e.g., hGH polypeptide, it may be advantageous to minimize fee homogenization time on repetitions in order to maximize the yield of inclusion bodies without loss due to factors such as solubilization, mechanical shearing or proteolysis.
[415] Insoluble or precipitated GH, e.g., hGH polypeptide may then be solubilized using
any of a number of suitable solubilization agents known to the art. The GH, e.g., hGH polyeptide
may be solubilized with urea or guanidine hydrochloride. The volume of the solubilized GH, e.g.,
hGH polypeptide should be minimized so that large batches may be produced using conveniently
manageable batch sizes. This factor may be significant in a large-scale commercial setting where
the recombinant host may be grown in batches feat are thousands of liters in volume. In addition,,
when manufacturing GH, e.g., hGH polypeptide in a large-scale commercial setting, in particular
for human pharmaceutical uses, the avoidance of harsh chemicals that can damage the machinery
and container, or the protein product itself, should be avoided, if possible. It has been shown in)
the method of the present invention that the milder denaturing agent urea can be used to solubilize
fee GH, e.g., hGH polypeptide inclusion bodies in place of the harsher denaturing agent guanidine
hydrochloride. The use of urea significantly reduces the risk of damage to stainless steel
equipment utilized in the manufacturing and purification process of GH, e.g., hGH polypeptide
while efficiently solubilizing the GH, e.g., hGH polypeptide inclusion bodies.
[416] In fee case of soluble hGH protein, fee hGH may be secreted into fee periplasmic
space or into fee culture medium. In addition, soluble hGH may be present in fee cytoplasm of the host cells. It may be desired to concentrate soluble hGH prior to performing purification steps. Standard techniques known to those of ordinary skill in fee art may be used to concentrate soluble hGH from, for example, cell lysates or culture medium. In addition, standard techniques known to those of ordinary skill in fee art may be used to disrupt host cells and release soluble hGH from fee cytoplasm or periplasmic space of fee host cells.

[417] When GH, e.g., hGH polypeptide is produced as a fusion protein, the fusion
sequence may be removed. Removal of a fusion sequence may be accomplished by enzymatic or chemical cleavage. Enzymatic removal of fusion sequences may be accomplished using methods known to those of ordinary skill in the art. The choice of enzyme for removal of the fusion sequence will be determined by the identity of the fusion, and the reaction conditions will be specified by the choice of enzyme as will be apparent to one of ordinary skill in the art. Chemical cleavage may be accomplished using reagents known to those of ordinary skill in the art, including but not limited to, cyanogen bromide, TEV protease, and other reagents. The cleaved GH, e.g., hGH polypeptide may be purified from the cleaved fusion sequence by methods known to those of ordinary skill in the art. Such methods will be determined by the identity and properties of the fusion sequence and the GH, e.g., hGH polypeptide, as will be apparent to one of ordinary skill in the art. Methods for purification may include, but are not limited to, size-exclusion chromatography, hydrophobic interaction chromatography, ion-exchange chromatography or dialysis or any combination thereof.
[418] The GH, e.g., hGH polypeptide may also be purified to remove DNA from the'
protein solution. DNA may be removed by any suitable method known to the art, such as' precipitation or ion exchange chromatography, but may be removed by precipitation with a nucleic ' acid precipitating agent, such as, but not limited to, protamine sulfate. The GH, e.g.^ hGH. polypeptide may be separated from the precipitated DNA using standard well known methods including, but not limited to, centrifiigation or filtration. Removal of host nucleic acid molecules is an important factor in a setting where the GH, e.g., hGH polypeptide is to be used to treat humans and the methods of the present invention reduce host cell DNA to pharmaceutical^ acceptable levels.
[419] Methods for small-scale or large-scale fermentation can also be used in protein
expression, including but not limited to, fermentors, shake flasks, fluidized bed bioreactors,
hollow fiber bioreactors, roller bottle culture systems, and stirred tank bioreactor systems. Each of
these methods can be performed in a batch, fed-batch, or continuous mode process.
[420] Human GH polypeptides of the invention can generally be recovered using methods
standard in the art For example, culture medium or cell lysate can be centrifuged or filtered to remove cellular debris. The supernatant may be concentrated or diluted to a desired volume or diafiltered into a suitable buffer to condition the preparation for further purification. Further

purification of the GH, e.g., hGH polypeptide of the present invention includes separating
deamidated and clipped forms of the GH, e.g., hGH polypeptide variant from the intact form.
[421] Any of the following exemplary procedures can be employed for purification of GH,
e.g., hGH polypeptides of the invention: affinity chromatography; anion- or cation-exchange chromatography (using, including but not limited to, DEAE SEPHAROSE); chromatography on silica; reverse phase HPLC; gel filtration (using, including but not limited to, SEPHADEX G-75); hydrophobic interaction chromatography; size-exclusion chromatography, metal-chelate chromatography; ultrafiltration/diafiltration; ethanol precipitation; ammonium sulfate precipitation; chromatofocusing; displacement chromatography; electrophoretic procedures (including but not limited to preparative isoelectric focusing), differential solubility (including but not limited to ammonium sulfate precipitation), SDS-PAGE, or extraction.
[422] Proteins of the present invention, including but not limited to, proteins comprising
unnatural amino acids, peptides comprising unnatural amino acids, antibodies to proteins comprising unnatural amino acids, binding partners for proteins comprising unnatural amino acids, etc., can be purified, either partially or substantially to homogeneity, according to standard procedures known to and used by those of skill in the art. Accordingly, polypeptides of the invention can be recovered and purified by any of a number of methods known to those of ordinary skill in the art, including but not limited to, ammonium sulfate or ethanol precipitation, acid or base extraction, column chromatography, affinity column chromatography, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, hydroxylapatite chromatography, lectin chromatography, gel electrophoresis and the like. Protein refolding steps can be used, as desired, in making correctly folded mature proteins. High performance liquid chromatography (HPLC), affinity chromatography or other suitable methods can be employed in final purification steps where high purity is desired. In one embodiment, antibodies made against unnatural amino acids (or proteins or peptides comprising unnatural amino acids) are used as purification reagents, including but not limited to, for affinity-based purification of proteins or peptides comprising one or more unnatural amino acid(s). Once purified, partially or to homogeneity, as desired, the polypeptides are optionally used for a wide variety of utilities, including but not limited to, as assay components, therapeutics, prophylaxis, diagnostics, research reagents, and/or a$ immunogens for antibody production.

[423] In addition to other references noted herein, a variety of purification/protein folding
methods aTe known to those of ordinary skill in the art, including, but not limited to, those set forth in R. Scopes, Protein Purification, Springer-Verlag, N.Y. (1982); Deutscher, Methods in Enzvmologv Vol. 182: Guide to Protein Purification, Academic Press, Inc. N.Y. (1990); Sandana, (1997) Bioseparation of Proteins. Academic Press, Inc.; Bollag et al. (1996) Protein Methods. 2nd Edition Wiley-Liss, NY; Walker, (1996) The Protein Protocols Handbook Humana Press, NJ, Harris and Angal, (1990) Protein Purification Applications: A Practical Approach IRL Press at Oxford, Oxford, England; Harris and Angal, Protein Purification Methods: A Practical Approach IRL Press at Oxford, Oxford, England; Scopes, (1993) Protein Purification: Principles and Practice 3rd Edition Springer Verlag, NY; Janson and Ryden, (1998) Protein Purification: Principles. High Resolution Methods and Applications, Second Edition Wiley-VCH, NY; and Walker (1998), Protein Protocols on CD-ROM Humana Press, NJ; and the references cited therein.
[424] One advantage of producing a protein or polypeptide of interest with an unnatural
amino acid in a eukaryotic host cell or non-eukaryotic host cell is that typically the proteins or polypeptides will be folded in their native conformations. However, in certain embodiments of the invention, those of skill in the art will recognize that, after synthesis, expression1 and/or purification, proteins or peptides can possess a conformation different from the -desired conformations of the relevant polypeptides. In one aspect of the invention, the expressed protein is optionally denatured and then Tenatured. This is accomplished utilizing methods known in the art, including but not limited to, by adding a chaperonin to the protein or polypeptide of interest, by solubilizing the proteins in a chaotropic agent such as guanidine HC1, utilizing protein disulfide isomerase, etc.
[425] In general, it is occasionally desirable to denature and reduce expressed
polypeptides and then to cause the polypeptides to re-fold into the preferred conformation. For example, guanidine, urea, DTT, DTE, and/or a chaperonin can be added to a translation product of interest Methods of reducing, denaturing and renaturing proteins are known to those of ordinary skill in the art (see, the references above, and Debinski, et al. (1993) J. Biol. Chem.. 268: 14065-14070; Kreitman and Pastan (1993) Bioconiug. Chem., 4: 581-585; and Buchner, et al., (1992) Anal. Biochem.. 205: 263-270). Debinski, et al., for example, describe the denaturation and

reduction of inclusion body proteins in guanidine-DTE. The proteins can be refolded in a redox buffer containing, including but not limited to, oxidized glutathione and L-arginine. Refolding reagents can be flowed or otherwise moved into contact with the one or more polypeptide or other expression product, or vice-versa.
[426] hi the case of prokaryotic production of GH, e.g., hGH polypeptide, the GH, e.g.,
hGH polypeptide thus produced may be misfolded and thus lacks or has reduced biological
activity. Thebioactivity ofthe protein may be restored by "refolding". In general, misfolded GH,
e.g., hGH polypeptide is refolded by solubilizing (where the GH, e.g., hGH polypeptide is also
insoluble), unfolding and reducing the polypeptide chain using, for example, one or more
chaotropic agents (e.g. urea and/or guanidine) and a reducing agent capable of reducing disulfide
bonds (e.g. dithiothreitol, DTT or 2-mercaptoethanol, 2-ME). At a moderate concentration of
chaotrope, an oxidizing agent is thai added (e.g., oxygen, cystine or cystamine), which allows the
reformation of disulfide bonds. GH, e.g., hGH polypeptide may be refolded using standard
methods known in the art, such as those described in U.S. Pat. Nos. 4,511,502, 4,511,503, and
4,512,922, which are incorporated by reference herein. The GH, e.g., hGH polypeptide may also
be cofolded with other proteins to form heterodimers or heteromultimers. \*
[427] After refolding or cofolding, the GH, e.g. hGH polypeptide may be further purified.
Purification of GH, e.g., hGH may be accomplished using a variety of techniques known to those
of ordinary skill in the art, including hydrophobic interaction chromatography, size exclusion
chromatography, ion exchange chromatography, reverse-phase high performance liquid
chromatography, affinity chromatography, and the like or any combination thereof. Additional
purification may also include a step of drying or precipitation ofthe purified protein.
[428] After purification, GH, e.g., hGH may be exchanged into different buffers and/or
concentrated by any of a variety of methods known to the art, including, but not limited to, diafiltration and dialysis. GH, e.g., hGH that is provided as a single purified protein may be subject to aggregation and precipitation.
[429] The purified GH, e.g., hGH may be at least 90% pure (as measured by reverse
phase high performance liquid chromatography, RP-HPLC, or sodium dodecyl sulfate-polyacrylamide gel electrophoresis, SDS-PAGE) or at least 95% pure, or at least 98% pure, or at least 99% or greater pure. Regardless ofthe exact numerical value ofthe purity ofthe GH, e.g.,

hGH, the GH, e.g., hGH is may be sufficiently pure for use as a pharmaceutical product or for
further processing, such as conjugation with a water soluble polymer such as PEG,
{4301 Certain GH, e.g., hGH molecules may be used as therapeutic agents in the absence
of other active ingredients or proteins (other than excipients, carriers, and stabilizers, serum albumin and the like), or they may be complexed with another protein or a polymer.
[431] General Purification Methods Any one of a variety of isolation steps may be
performed on the cell lysate, extract, culture medium, inclusion bodies, periplasmic space of the host cells, cytoplasm of the host cells, or other material, comprising GH, e.g., hGH polypeptide or on any GH, e.g., hGH polypeptide mixtures resulting from any isolation steps including, but not limited to; affinity chromatography, ion exchange chromatography, hydrophobic interaction chromatography, gel filtration chromatography, high performance liquid chromatography ("HPLC"), reversed phase-HPLC (teRP-HPLC"), expanded bed adsorption, or any combination and/or repetition thereof and in any appropriate order.
[432] Equipment and other necessary materials used in performing the techniques
described herein are commercially available. Pumps, fraction collectors, monitors, recorders, and entire systems are available from, for example, Applied Biosystems (Foster City, CA), Bio-Rad Laboratories, Inc. (Hercules, CA), and Amersham Biosciences, Iiic. (Piscataway, NJ). Chromatographic materials including, but not limited to, exchange matrix materials, media, and buffers are also available from such companies.
[433J Equilibration, and other steps in the column chromatography processes described
herein such as washing and elution, may be more rapidly accomplished using specialized equipment such as a pump. Commercially available pumps include, but are not limited to, HILOAD® Pump P-50, Peristaltic Pump P-l, Pump P-901, and Pump P-903 (Amersham Biosciences, Piscataway, NJ).
[434] Examples of fraction collectors include RediFrac Fraction Collector, FRAC-100
and FRAC-200 Fraction Collectors, and SUPERFRAC® Fraction Collector (Amersham Biosciences, Piscataway, NJ). Mixers are also available to form pH and linear concentration gradients. Commercially available mixers include Gradient Mixer GM-1 and In-Line Mixers (Amersham Biosciences, Piscataway, NJ).
[435] The chromatographic process may be monitored using any commercially available
monitor. Such monitors may be used to gather information like UV, pH, and conductivity.

Examples of detectors include Monitor UV-1, UVICORD® S II, Monitor UV-M II, Monitor UV-900, Monitor UPC-900, Monitor pH/C-900, and Conductivity Monitor (Amersham Biosciences, Piscataway, NJ). Indeed, entire systems are commercially available including the various AKTA® systems from Amersham Biosciences (Piscataway, NJ).
[436J In one embodiment of the present invention, for example, the GH, e.g., hGH
polypeptide may be reduced and denatured by first denaturing the resultant purified GH, e.g., hGH polypeptide in urea, followed by dilution into TRIS buffer containing a reducing agent (such as DTT) at a suitable pH. In another embodiment, the GH, e.g., hGH polypeptide is denatured in urea in a concentration range of between about 2 M to about 9 M, followed by dilution in TRIS buffer at a pH in the range of about 5.0 to about 8.0. The refolding mixture of this embodiment may then be incubated. In one embodiment, the refolding mixture is incubated at room temperature for four to twenty-four hours. The reduced and denatured GH, e.g., hGH polypeptide mixture may then be further isolated or purified.
[437] As stated herein, the pH of the first GH, e.g., hGH polypeptide mixture,may be
adjusted prior to performing any subsequent isolation steps. In addition, the first GH, e.g., hGH polypeptide mixture or any subsequent mixture thereof may be concentrated using techniques known in the art. Moreover, the elution buffer comprising the first GH, e.g:, hGH polypeptide mixture or any subsequent mixture thereof may be exchanged for a buffer suitable for, Jhe next isolation step using techniques known to those of ordinary skill in the art.
[438] Ion Exchange Chromatography In one embodiment, and as an optional, additional
step, ion exchange chromatography may be performed on the first GH, e.g., hGH polypeptide mixture. See generally ION EXCHANGE CHROMATOGRAPHY: PRINCIPLES AND METHODS (Cat. No. 18-1114-21, Amersham Biosciences (Piscataway, NJ)). Commercially availahle ion exchange columns include HTTRAP®, HIPREP®, and HELOAD® Columns (Amersham Biosciences, Piscataway, NJ). Such columns utilize strong anion exchangers such as Q SEPHAROSE® Fast Flow, Q SEPHAROSE® High Performance, and Q SEPHAROSE® XL; strong cation exchangers such as SP SEPHAROSE® High Performance, SP SEPHAROSE® Fast Flow, and SP SEPHAROSE® XL; weak anion exchangers such as DEAE SEPHAROSE® Fast Flow; and weak cation exchangers such as CM SEPHAROSE Fast Flow (Amersham Biosciences, Piscataway, NJ). Anion or cation exchange column chromatography may be performed on the GH, e.g., hGH polypeptide at any stage of the purification process to isolate substantially purified GH, e.g., hGH

polypeptide. The cation exchange chromatography step may be performed using any suitable
cation exchange matrix. Useful cation exchange matrices include, but are not limited to, fibrous,
porous, non-porous, microgranular, beaded, or cross-linked cation exchange matrix materials.
Such cation exchange matrix materials include, but are not limited to, cellulose, agarose, dextran,
polyacrylate, polyvinyl, polystyrene, silica, polyether, or composites of any of the foregoing.
[439] The cation exchange matrix may be any suitable cation exchanger including strong
and weak cation exchangers. Strong cation exchangers may remain ionized over a wide pH range
and thus, may be capable of binding GH, e.g., hGH over a wide pH range. Weak cation
exchangers, however, may lose ionization as a function of pH. For example, a weak cation
exchanger, may lose charge when the pH drops below about pH 4 or pH 5. Suitable strong cation
exchangers include, but are not limited to, charged functional groups such as sulfopropyl (SP),
methyl sulfonate (S), or sulfoethyl (SE). The cation exchange matrix may be a strong cation
exchanger, preferably having a GH, e.g., hGH binding pH range of about 2.5 to about 6.0.
Alternatively, the strong cation exchanger may have a GH, e.g., hGH binding pH range of about
pH 2.5 to about pH 5.5. The cation exchange matrix may be a strong cation exchanger having a
GH, e.g., hGH binding pH of about 3.0. Alternatively, the cation exchange matrix may be a
strong cation exchanger, preferably having a GH, e.g., hGH binding pH range of about 6.0 to
about 8.0. The cation exchange matrix may be a strong cation exchanger preferably having a
GH, e.g., hGH binding pH range of about 8.0 to about 12.5. Alternatively, the strong cation
exchanger may have a GH, e.g., hGH binding pH range of about pH 8.0 to about pH 12.0.
[440] Prior to loading the GH, e.g., hGH, the cation exchange matrix may be equilibrated,
for example, using several column volumes of a dilute, weak acid, e.g., four column volumes of 20 mM acetic acid, pH 3. Following equilibration, the GH, e.g., hGH may be added and the column may be washed one to several times, prior to elution of substantially purified GH, e.g., hGH, also using a weak acid solution such as a weak acetic acid or phosphoric acid solution. For example, approximately 2-4 column volumes of 20 mM acetic acid, pH 3, may be used to wash the column. Additional washes using, e.g., 2-4 column volumes of 0.05 M sodium acetate, pH 5.5, or 0.05 M sodium acetate mixed with 0.1 M sodium, chloride, pH 5.5, may also be used. Alternatively, using methods known in the art, the cation exchange matrix may be equilibrated using several column volumes of a dilute, weak base.

[441] Alternatively, substantially purified GH, e.g., hGH may be eluted by contacting the
cation exchanger matrix with a buffer having a sufficiently low pH or ionic strength to displace the GH, e.g., hGH from the matrix. The pH of the elution buffer may range from about pH 2.5 to about pH 6.0. More specifically, the pH of the elution buffer may range from about pH 2.5 to about pH 5.5, about pH 2.5 to about pH 5.0. The elution buffer may have a pH of about 3.0. In addition, the quantity of elution buffer may vary widely and will generally be in the range of about 2 to about 10 column volumes.
[442] Following adsorption of the GH, e.g., hGH polypeptide to the cation exchanger
matrix, substantially purified hGH polypeptide may be eluted by contacting the matrix with a buffer having a sufficiently high pH or ionic strength to displace the GH, e.g., hGH polypeptide from the matrix. Suitable buffers for use in high pH elution of substantially purified GH, e.g., hGH polypeptide may find use herein include, but are not limited to, citrate, phosphate, fonnate, acetate, HEPES, and MES buffers ranging in concentration from at least about 5 mM to. at least about 100 mM.
[443] Reverse-Phase Chromatography RP-HPLC may be performed to purify proteins
following suitable protocols that are known to those of ordinary skill in the art. See, eg., Pearson et al., ANALBIOCHEM. (1982) 124:217-230 (1982); Rivier et al., J. CHROM. (1983) 268:112-119; Kunitani et al., J. CHROM. (1986) 359:391-402. RP-HPLC may be performed on the GH, e.g., hGH polypeptide to isolate substantially purified GH, e.g., hGH polypeptide. In this regard, silica derivatized resins with alkyl functionalities with a wide variety of lengths, including, but not limited to, at least about C3 to at least about C30, at least about C3 to at least about C20J or at least about C3 to at least about Cis, resins may be used. Alternatively, a polymeric resin may be used. For example, TosoHaas Amberchrome CGlOOOsd resin may be used, which is a styrene polymer resin. Cyano or polymeric resins with a wide variety of alkyl chain lengths may also be used. Furthermore, the RP-HPLC column may be washed with a solvent such as ethanol. The Source RP column is another example of a RP-HPLC column.
[444] A suitable elution buffer containing an ion pairing agent and an organic modifier
such as methanol, isopTOpanol, tetrahydrofuran, acetonitrile or ethanol, may be used to elute the GH, e.g., hGH polypeptide from the RP-HPLC column. The most commonly used ion pairing agents include, but are not limited to, acetic acid, formic acid, perchloric acid, phosphoric acid, trifluoroacetic acid, heptafluorobutyric acid, triethylamine, tetramethylammonium,

tetrabutylammonium, and triethylammonium acetate. Elution may be performed using one or more gradients or isocratic conditions, with gradient conditions preferred to reduce the separation time and to decrease peak width. Another method involves the use of two gradients with different solvent concentration ranges. Examples of suitable elution buffers for use herein may include, but are not limited to, ammonium acetate and acetonitrile solutions.
(445] Hydrophobic Interaction Chromatography Purification Techniques Hydrophobic
interaction chromatography (HIC) may be performed on the GH, e.g., hGH polypeptide. See
generally HYDROPHOBIC INTERACTION CHROMATOGRAPHY HANDBOOK: PRINCIPLES AND
METHODS (Cat. No. 18-1020-90, Amersham Biosciences (Piscataway, NJ) which is incorporated by reference herein. Suitable HIC matrices may include, but are not limited to, alkyl- or aryl-substituted matrices, such as butyl-, hexyl-, octyl- or phenyl-substituted matrices including agarose, crossrlinked agarose, sepharose, cellulose, silica, dextran, polystyrene, poly(methacrylate) matrices, and mixed mode resins, including but not limited to, a polyethyleneamine resin or a butyl- or phenyl-substituted poly(methacrylate) matrix. Commercially available sources for hydrophobic interaction column chromatography include, but are not limited to, HrERAP®, HIPREP®, and HILOAD® columns (Amersham Biosciences, Piscataway, NJ). Briefly, prior to loading, the HIC column may be equilibrated using standard buffers known to those of ordinary skill in the art, such as an acetic acid/sodium chloride solution or HEPES containing ammonium sulfate. Ammonium sulfate may be used as the buffer for loading the HIC column. After loading the GH, e.g., hGH polypeptide, the column may then washed using standard buffers and conditions to remove unwanted materials but retaining the GH, • e.g., hGH polypeptide on the HIC column. The GH, e.g., hGH polypeptide may be eluted with about 3 to about 10 column volumes of a standard buffer, such as a HEPES buffer containing EDTA and lower ammonium sulfate concentration than the equilibrating buffer, or an acetic -* acid/sodium chloride buffer, among others. A decreasing linear salt gradient using, for example, a: gradient of potassium phosphate, may also be used to elute the GH, e.g., hGH molecules. The.
' -",. "v ".
eluant may then be concentrated, for example, by filtration such as diafiltration or ultrafiltratipn. -'•'
Diafiltration may be utilized to remove the salt used to elute the GH, e.g., hGH'polypeptide,
[446] Other Purification Techniques Yet another isolation step using, for example, gel
filtration (GEL FILTRATION: PRINCIPLES AND METHODS (Cat. No. 18-1022-18, Amersham Biosciences, Piscataway, NJ) which is incorporated by reference herein, hydroxyapatite '

chromatography (suitable matrices include, but are not limited to, HA-Ultrogel, High Resolution (Calbiochem), CHT Ceramic Hydroxyapatite (BioRad), Bio - Gel HTP Hydroxyapatite (BioRad)), HPLC, expanded bed adsorption, ultrafiltration, diafiltration, lyophilization, and the like, may be performed on the first GH, e.g., hGH polypeptide mixture or any subsequent mixture thereof, to remove any excess salts and to replace the buffer with a suitable buffer for fee next isolation step or even formulation of fee final drug product.
[447] The yield of GH, e.g., hGH polypeptide, including substantially purified GH, e.g.,
hGH polypeptide, may be monitored at each step described herein using techniques known to
those of ordinary skill in the art. Such techniques may also be used to assess the yield of
substantially purified GH, e.g., hGH polypeptide following the last isolation step. For example,
the yield of GH, e.g., hGH polypeptide may be monitored using any of several reverse phase high
pressure liquid chromatography columns, having a variety of alkyl chain lengths such as cyano
RP-HPLC, CigRP-HPLC; as well as cation exchange HPLC and gel filtration HPLC.
[448] In specific embodiments of fee present invention, the yield of GH, e.g., hGH after each ;;
purification step may be at least about 30%, at least about 35%, at least about 40%, at least about •'
45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about ^
70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about,".;'
91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about ?j
96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, or at least*-
about 99.99%, of the GH, e.g., hGH in fee starting material for each purification step.
[449] Purity may be determined using standard techniques, such as SDS-PAGE, or by
measuring GH, e.g., hGH polypeptide using Western blot and ELISA assays. For example, polyclonal antibodies may be generated against proteins isolated from negative control yeast fermentation and the cation exchange recovery. The antibodies may also be used to probe for fee presence of contaminating host cell proteins.
[450] RP-HPLC material Vydac C4 (Vydac) consists of silica gel particles, fee surfaces of
which cany C4-alkyl chains. The separation of GH, e.g., hGH polypeptide from fee proteinaceous impurities is based on differences in the strength of hydrophobic interactions. Elution is performed wife an acetonitrile gradient in diluted trifluoroacetic acid. Preparative HPLC is performed using a stainless steel column (filled wife 2.8 to 3.2 liter of Vydac C4 silicagel). The Hydroxyapatite Ultrogel eluate is acidified by adding trifluoroacetic acid and loaded onto fee Vydac C4 column.

For washing and elution an acetonitrile gradient iji diluted trifluoroacetic acid is used. Fractions are collected and immediately neutralized with phosphate buffer. The GH, e.g., hGH polypeptide fractions which are within the IPC limits are pooled.
[451] DEAE Sepharose (Pharmacia) material consists of diethylaminoethyl (DEAE)-
groups which are covalently bound to the surface of Sepharose beads. The binding of GH, e.g.,
hGH polypeptide to the DEAE groups is mediated by ionic interactions. Acetonitrile and
trifluoroacetic acid pass through the column without being retained. After these substances have
been washed off, trace impurities are removed by washing the column with acetate buffer at a low
pH. Then the column is washed with neutral phosphate buffer and GH, e.g., hGH polypeptide is
eluted with a buffer with increased ionic strength. The column is packed with DEAE Sepharose
fast flow. The column volume is adjusted to assure a GH, e.g., hGH polypeptide load in the range
of 3-10 mg GH, e.g., hGH polypeptide/ml gel. The column is washed with water and equilibration **
buffer (sodium/potassium phosphate). The pooled fractions of the HPLC eluate are loaded and the
column is washed with equilibration buffer. Then the column is washed with washing 'buffer
(sodium acetate buffer) followed by washing with equilibration buffer. Subsequently, GH, e.g.,
hGH polypeptide is eluted from the column with elution buffer (sodium chloride,
sodium/potassium phosphate) and collected in a single fraction in accordance with the master
elution profile. The eluate of the DEAE Sepharose column is adjusted to the specified
conductivity. The resulting drug substance is sterile filtered into Teflon bottles and stored at -70°C
[452] Additional methods that may be employed include, but are not limited to, steps to
remove endotoxins. Endotoxins are lipopoly-saccharides (LPSs) which are located on the outer
membrane of Gram-negative host cells, such as, for example, Escherichia coli. Methods for
reducing endotoxin levels are known to one of ordinary skill in the art and include, but are not
limited to, purification techniques using silica supports, glass powder or hydroxyapatite, reverse-
phase, affinity, size-exclusion, anion-exchange chromatography, hydrophobic interaction
chromatography, a combination of these methods, and the like. Modifications or additional
methods may be required to remove contaminants such as co-migrating proteins from the
polypeptide of interest. Methods for measuring endotoxin levels are known to one of ordinary
skill in the art and include, but are not limited to, Limulus Amebocyte Lysate (LAL) assays.
[453J A wide variety of methods and procedures can be used to assess the yield and purity
of a GH, e.g., hGH protein one or more non-naturally encoded amino acids, including but not

limited to, the Bradford assay, SDS-PAGE, silver stained SDS-PAGE, coomassie stained SDS-PAGE, mass spectrometry (including but not limited to, MALDI-TOF) and other methods for characterizing proteins known to one of ordinary skill in the art
[454] Additional methods include, but are not limited to: SDS-PAGE coupled with protein
staining methods, immunoblotting, matrix assisted laser desorption/ionization-mass spectrometry
(MALDI-MS), liquid chromatography/mass spectrometry, isoelectric focusing, analytical anion
exchange, chromatofocusing, and circular dichroism.
VHI. Expression in Alternate Systems
[455] Several strategies have been employed to introduce unnatural amino acids into
proteins in non-recombinant host cells, mutagenized host cells, or in cell-free systems. These systems are also suitable for use in making the GH, e.g., hGH polypeptides of the present invention. Derivatization of amino acids with reactive side-chains such as Lys, Cys and Tyr resulted in the conversion of lysine to N -acetyl-lysines Chemical synthesis also provides r«'a straightforward method to incorporate unnatural amino acids. With the recent development of enzymatic ligation and native chemical ligation of peptide fragments, it is possible to make larger proteins. See, e.g., P. E. Dawson and S. B. H. Kent, Annu. Rev. Biochem. 69:923 (2000). Chemical peptide ligation and native chemical ligation are described in U.S. Patent No. 6,184,344, U.S. Patent Publication No. 2004/0138412, U.S. Patent Publication No. 2003/0208046, WO 02/098902, and WO 03/042235, which are incorporated by reference herein. A general in vitro biosynthetic method in which a suppressor tRNA chemically acylated with the desired unnatural amino acid is added to an in vitro extract capable of supporting protein biosynthesis, has been used to site-specifically incorporate over 100 unnatural amino acids into a variety of proteins of virtually any size. See, e.g., V. W. Cornish, D. Mendel and P. G. Schultz, Angew. Chem. Int. Ed. End., 1995, 34:621 (1995); CJ. Noren, S.J. Anthony-Cahill, M.C. Griffith, P.G. Schultz, A general method for site-specific incorporation of unnatural amino acids into proteins, Science 244:182-188 (1989); and, J.D. Bain, C.G. Glabe, TA. Dix, A.R. Chamberlin, E.S. Diala, Biosynthetia site-specific incorporation of a non-natural amino acid into a polypeptide, J. Am. Chem. Soc. 111:8013-8014 (1989). A broad range of functional groups has been introduced into proteins for studies of protein stability, protein folding, enzyme mechanism, and signal transduction.

[456] An in vivo method, termed selective pressure incorporation, was developed to
exploit the promiscuity of wild-type synthetases. See, e.g*, N. Budisa, C. Minks, S. Alefelder, W.
Wenger, R M. Dong, L. Moroder and R. Huber, FASEBI, 13:41 (1999). An auxotrophic strain,
in which the relevant metabolic pathway supplying the cell with a particular natural amino acid is
switched off, is grown in minimal media containing limited concentrations of the natural amino
acid, while transcription of the target gene is repressed. At the onset of a stationary growth phase,
the natural amino acid is depleted and replaced with the unnatural amino acid analog. Induction of
expression of the recombinant protein results in the accumulation of a protein containing the
unnatural analog. For example, using this strategy, o, m and p-fluorophenylalanines have been
incorporated into proteins, and exhibit two characteristic shoulders in the UV spectrum which can
be easily identified, see, e.g., C. Minks, R. Huber, L. Moroder and N. Budisa, Anal. Biochem.,
284:29 (2000); trifluoromethionine has been used to replace methionine in bacteriophage T4,
lysozyme to study its interaction with chitooligosaccharide ligands by l9F NMR, see, e.g., H.
Duewel, E. Daub, V. Robinson and J. F. Honek, Biochemistry. 36:3404 (1997); and
trifluoroleucine has been incorporated in place of leucine, resulting.in increased thermal and ..
chemical stability of a leucine-zipper protein. See, eg., Y. Tang, G. Ghirlanda, W. A. Petka, T. v
Nakajima, W, F. DeGrado and D. A. Tirrell, Angew Chem. Int. Ed. Engl., 40:1494 (2001). *.
Moreover, selenomethionine and telluromethionine are incorporated into various recombinant v.;
proteins to facilitate the solution of phases in X-ray crystallography. See, e.g:9 W. A. ^
Hendrickson, J. R. Horton and D. M. Lemaster, EMBO J.. 9:1665 (1990); J. O. Boles, K.
Lewinski, M. Kunkle, J. D. Odom, B. Dunlap, L. Lebioda and M. Hatada, Nat Struct BioL, 1:283
(1994); N. Budisa, B. Steipe, P. Demange, C. Eckerskorn, J. Kellermann and R. Huber, Eur. J.
Biochem., 230:788 (1995); and, N. Budisa, W. Karnbrock, S. Steinbacher, A. Humm, L. Prade, T.
Neuefeind, L. Moroder and R. Huber, J. Mol. Biol., 270:616 (1997). Methionine analogs with
alkene or alkyne functionalities have also been incorporated efficiently, allowing for additional
modification of proteins by chemical means. See, e.g.t J. C. van Hest and D. A. Tirrell, FEBS
Lett., 428:68 (1998); J. C van Hest, K. L. Kiick and D. A. Tirrell, J. Am. Chem. Soc. 122:1282
(2000); and, K. L. Kiick and D. A. Tirrell, Tetrahedron, 56:9487 (2000); U.S. Patent No.
6,586,207; U.S. Patent Publication 2002/0042097, which are incorporated by reference herein.
[457J The success of this method depends on the recognition of the unnatural amino acid
analogs by aminoacyl-tRNA synthetases, which, in general, require high selectivity to insure the

fidelity of protein translation. One way to expand the scope of this method is to relax the substrate
specificity of aminoacyl-tRNA synthetases, which has been achieved in a limited number of cases.
For example, replacement of Ala by Gly in Escherichia coli phenylalanyl-tRNA synthetase
(PheRS) increases the size of substrate binding pocket, andTesults in the acylation of tRNAPhe by
p-Cl~phenylalanine (p-Cl-Phe). See, M. Ibba, P. Kast and H. Hennecke, Biochemistry, 33:7107
(1994). An Escherichia coli strain harboring this mutant PheRS allows the incorporation of p-Cl-
phenylalanine or p-Br-phenylalanine in place of phenylalanine. See, e.g., M. Ibba and H.
Hennecke, FEBS Lett., 364:272 (1995); and, N. Sharma, R. Furter, P. Kast and D. A. Tirrell,
FEBS Lett., 467:37 (2000). Similarly, a point mutation Phel30Ser near the amino acid binding
site of Escherichia coli tyrosyl-tRNA synthetase was shown to allow azatyrosine to be
incorporated more efficiently than tyrosine. See, F. Hamano-Takaku, T. Iwama, S. Saito-Yano, K.
Takaku, Y. Monden, M. Kitabatake, D. Soil and S. Nishimura, J. BioL Chem,. 275:40324 (2000).
[458] Another strategy to incorporate unnatural amino acids into proteins in vivo is to
modify synthetases that have proofreading mechanisms. These synthetases cannot discriminate and therefore activate amino acids that are structurally similar to the cognate natural amino acids. This error is corrected at a separate site, which deacylates the mischarged amino acid from the tRNA to maintain the fidelity of protein translation. If the proofreading activity of the synthetase is disabled, structural analogs that are misactivated may escape the editing function* and be incorporated. This approach has been demonstrated recently with the valyl-tRNA synthetase (ValRS). See, V. Doling, H. D. Mootz, L. A. Nangle, T. L. Hendrickson, V. de Crecy-Lagard, P. Schimmel and P. Marliere, Science,, 292:501 (2001). ValRS can misaminoacylate tRNAVal with Cys, Thr, or aminobutyrate (Abu); these noncognate amino acids are subsequently hydrolyzed by the editing domain. After random mutagenesis of the Escherichia coli chromosome, a mutant Escherichia coli strain was selected that has a mutation in the editing site of ValRS. This edit-defective ValRS incorrectly charges tRNAVal with Cys. Because Abu sterically resembles Cys (-SH group of Cys is replaced with -CH3 in Abu), the mutant ValRS also incorporates Abu into proteins when this mutant Escherichia coli strain is grown in the presence of Abu. Mass spectrometric analysis shows that about 24% of valines are replaced by Abu at each valine position in the native protein.
[459] Solid-phase synthesis and semisynthetic methods have also allowed for the
synthesis of a number of proteins containing novel amino acids. For example, see the following

publications and references cited within, which are as follows: Crick, F.H.C, Barrett, L. Brenner, S. Watts-Tobin, R. General nature of the genetic code for proteins. Nature, 192:1227-1232 (1961); Hofinann, JL, Bohn, H. Studies on polypeptides. XXXVI. The effect ofpyrazole-imidazole replacements on the S-protein activating potency of an S-peptide fragment, J. Am Chem. 88(24):5914-5919 (1966); Kaiser, E.T. Synthetic approaches to biologically active peptides and proteins including enyzmes, Ace Chem Res. 22:47-54 (1989); Nakatsuka, T., Sasaki, T., Kaiser, E.T. Peptide segment coupling catalyzed by the semisynthetic enzyme thiosubtilisin, J Am Chem Soc, 109:3808-3810 (1987); Schnolzer, M., Kent, S B H. Constructing proteins by dovetailing unprotected synthetic peptides: backbone-engineered HIV protease, Science, 256(5054):221-225 (1992); Chaiken, LM. Semisynthetic peptides and proteins, CRC Crit Rev Biochem. 11(3):255-301 (1981); Offord, R.E. Protein engineering by chemical means? Protein Eng., 1(3):151-157 (1987); and, Jackson, D.Y., Buraier, J., Quan, C, Stanley, M., Tom, L, Wells, J.A. A Designed' Peptide Ligasefor Total Synthesis of Ribonuclease A with Unnatural Catalytic Residues, Science, / 266(5183);243 (1994).
[460] Chemical modification has been used to introduce a variety of unnatural side
chains, including cofactors, spin labels and oligonucleotides into proteins in vitro. See, e.g., Corey, D.R., Schultz, P.G. Generation of a hybrid sequence-specific single-stranded deoxyribonuclease, Science, 238(4832): 1401-1403 (1987); Kaiser, E.T., Lawrence D.S., Rokita, S.E. The chemical modification of enzymatic specificity, Annn Rev Biochem. 54:565-595 (1985); Kaiser, E.T., Lawrence, D.S. Chemical mutation ofenyzme active sites, Science, 226(4674):505-511 (1984); Neet, K.E., Nanci A, Koshland, D.E. Properties of thiol-subtilisin, J Biol. Chem, 243(24):6392-6401 (1968); Polgar, L. et MX. Bender. A new enzyme containing a synthetically formed active site. Thiol-subUlisin. J. Am Chem Soc, 88:3153-3154 (1966); and, Pollack, S.J., Nakayama, G. Schultz, P.G. Introduction of nucleophiles and spectroscopic probes into antibody combining sites, Science. 242(4881): 1038-1040 (1988).
[461] Alternatively, biosynthetic methods that employ chemically modified aminoacyl-
tRNAs have been used to incorporate several biophysical probes into proteins synthesized in vitro. See the following publications and references cited within: Brunner, J. New Photolabeling and crosslinMng methods, Annu. Rev Biochem, 62:483-514 (1993); and, Krieg, U.C., Walter, P., Hohnson, A.E. Photocrosslinking of the signal sequence of nascent preprolactin of the 54-

kilodalton polypeptide of the signal recognition particle, Proc. Natl. Acad. Sci, 83(22):8604-8608 (1986).
[462] Previously, it has been shown that unnatural amino acids can be site-specifically
incorporated into proteins in vitro by the addition of chemically aminoacylated suppressor tRNAs
to protein synthesis reactions programmed with a gene containing a desired amber nonsense
mutation. Using these approaches, one can substitute a number of the common twenty amino
acids with close structural homologues, e.g., fluorophenylalanine for phenylalanine, using strains
auxotropic for a particular amino acid. See, e.g.t Noren, CJ., Anthony-Cahill, Griffith, M.C.,
Schultz, P.G. A general method for site-specific incorporation of unnatural amino acids into
proteins, Science, 244: 182-188 (1989); M.W. Nowak, et al., Science 268:439-42 (1995); Bain,
J.D., Glabe, C.G., Dix, T.A., Chamberlin, A.R., Diala, E.S. Biosynthetic site-specific .
Incorporation of a non-natural amino acid into a polypeptide, J. Am Chem Soc. 111:8013-8014
(1989); N. Budisa et al., FASEB J. 13:41-51 (1999); Ellman, JA., Mendel, D., Anthony-Cahill, S., Noren, CJ;, Schultz, P.G. Biosynthetic method for introducing unnatural amino acids site-
specifically into proteins. Methods in Enz.. vol. 202, 301-336 (1992); and, Mendfel, D., Cornish, •■*
V.W. & Schultz, P.G. Site-Directed Mutagenesis with an Expanded Genetic Code, Annu Rev f:
Biophvs. Biomol Struct. 24, 435-62 (1995). >
[463] For example, a suppressor tRNA was prepared that recognized the stop codon UAG )
and was chemically aminoacylated with an unnatural amino acid. Conventional site-directed ,, mutagenesis was used to introduce the stop codon TAG, at the site of interest in the protein gene.. See, e.g., Sayers, J.R., Schmidt, W. Eckstein, F. 5'-3f Exonucleases in phosphoroihioate-based olignoucleotide-directed mutagensis, Nucleic Acids Res. 16(3):791-802 (1988). When the acylated suppressor tRNA and the mutant gene were combined in an in vitro transcription/translation system, the unnatural amino acid was incorporated in response to the UAG codon which gave a protein containing that amino acid at the specified position. Experiments using [ H]-Phe and experiments with a-hydroxy acids demonstrated that only the desired amino acid is incorporated at the position specified by the UAG codon and that this amino acid is not incorporated at any other site in the protein. See, e.g., Noren, et al, supra; Kobayashi et al., (2003) Nature Structural Biology 10(6):425-432; and, Ellman, J.A., Mendel, D., Schultz, P.G. Site-specific incorporation of novel backbone structures into proteins, Science. 255(5041):197-200 (1992).

[464] A tRNA may be aminoacylated with a desired amino acid by any method or
technique, including but not limited to, chemical or enzymatic aminoacylation.
[465] Aminoacylation may be accomplished by aminoacyl tRNA synthetases or by other
enzymatic molecules, including but not limited to, ribozymes. The term "ribozyme" is interchangeable with "catalytic RNA." Cech and coworkers (Cech, 1987, Science, 236:1532-1539; McCorWe et al., 1987, Concepts Biochem. 64:221-226) demonstrated the presence of naturally occurring RNAs that can act as catalysts (ribozymes). However, although these natural RNA catalysts have only been shown to act on ribonucleic acid substrates for cleavage and splicing, the recent development of artificial evolution of ribozymes has expanded the repertoire of catalysis td-various chemical reactions. Studies have identified RNA molecules that can catalyze aminoacyl-RNA bonds on their own (2^3'-termini (Illangakekare et al., 1995 Science 267:643-647), and an RNA molecule which can transfer an amino acid from one RNA molecule to another : (Lohse et al., 1996, Nature 381:442-444).
[466} U.S. Patent Application Publication 2003/0228593, which is incorporated by
■i
reference herein, describes methods to construct ribozymes and their use in aminoacylation of tRNAs with naturally encoded and non-naturally encoded amino acids. Substrate-immobilized forms of enzymatic molecules that can aminoacylate tRNAs, including but not limited to, ribozymes, may enable efficient affinity purification of the aminoacylated products. Examples of suitable substrates include agarose, sepharose, and magnetic beads. The production and use of a ; substrate-immobilized form of ribozyme for aminoacylation is described in Chemistry and Biology 2003, 10:1077-1084 and U.S. Patent Application Publication 2003/0228593, which are incorporated by reference herein.
[467] Chemical aminoacylation methods include, but are not limited to, those
introduced by Hecht and coworkers (Hecht, S. M. Ace. Chem. Res. 1992, 25, 545; Heckler, T. G.; Roesser, J. R.; Xu, C; Chang, P.; Hecht, S. M. Biochemistry 1988, 27, 7254; Hecht, S. M.; Alford, B..L.; Kuroda, Y.; Kitano, S. J. Biol. Chem. 1978,253,4517) and by Schultz, Chamberlin, Dougherty and others (Cornish, V. W.; Mendel, D.; Schultz, P. G.,Angew. Chem. hit Ed. Engl. 1995, 34, 621; Robertson, S. A.; Ellman, J. A.; Schultz, P. G. J. Am. Chem. Soc. 1991, 113,2722; Noren, C. J.; Anthony-Cahill, S. J.; Griffith, M. C; Schultz, P. G. Science 1989, 244, 182; Bain, J. D.; Glabe, C. G.; Dix, T. A.; Chamberlin, A. R. J. Am. Chem. Soc. 1989,111, 8013; Bain, J. D. et

al. Nature 1992, 356, 537; Gallivan, J. P.; Lester, H. A.; Dougherty, D. A. Chem. Biol. 1997, 4, 740; Turcatti, et al. J. Biol. Chem. 1996, 271, 19991; Nowak, M. W. et al. Science, 1995, 268, 439; Saks, M. E. et al. J. Biol. Chem. 1996, 271, 23169; Hohsaka, T. et al. J. Am. Chem. Soc. 1999, 121, 34), which are incorporated by reference herein, to avoid the use of synthetases in aminoacylation. Such methods or other chemical aminoacylation methods may be used to aminoacylate tRNA molecules.
[468] Methods for generating catalytic RNA may involve generating separate pools of
randomized ribozyme sequences, performing directed evolution on the pools, screening the pools for desirable aminoacylation activity, and selecting sequences of those ribozymes exhibiting desired aminoacylation activity.
[469] Ribozymes can comprise motifs and/or regions that facilitate acylation activity,
such as a GGU motif and a U-rich region. For example, it has been reported that U-rich regions can facilitate recognition of an amino acid substrate, and a GGU-motif can form base pairs with the 3' termini of a tRNA. In combination, the GGU and motif and U-rich region facilitate simultaneous recognition of both the amino acid and tRNA simultaneously, and thereby facilitate aminoacylation of the 3' terminus of the tRNA.
[470] Ribozymes can be generated by in vitro selection using a partially randomized
r24mini conjugated with tRNA ncccG> followed by systematic engineering of a consensus sequence found in the active clones. An exemplary ribozyme obtained by this method is termed 'Tx3 ribozyme" and is described in U.S. Pub. App. No. 2003/0228593, the contents of which is * incorporated by reference herein, acts as a versatile catalyst for the synthesis of various aminoacyl-tRNAs charged with cognate non-natural amino acids.
[471] Immobilization on a substrate may be used to enable efficient affinity purification
of the aminoacylated tRNAs. Examples of suitable substrates include, but are not limited to, agarose, sepharose, and magnetic beads. Ribozymes can be immobilized on resins by taking advantage of the chemical structure of RNA, such as the 3-cis-diol on the ribose of RNA can be oxidized with periodate to yield the corresponding dialdehyde to facilitate immobilization of the RNA on the resin. Various types of resins can be used including inexpensive hydrazide resins wherein reductive amination makes the interaction between the resin and the ribozyme an irreversible linkage. Synthesis of aminoacyl-tRNAs can be significantly facilitated by this on-

column aminoacylation technique. Kourouklis et al. Methods 2005; 36:239-4 describe a column-based aminoacylation system.
[472] Isolation of the aminoacylated tRNAs can be accomplished in a variety of ways.
One suitable method is to elute the aminoacylated tRNAs from a column with a buffer such as a sodium acetate solution with 10 mM EDTA, a buffer containing 50 mM N-(2-hydroxyethyl)piperazine-N,-(3-propanesiilfonic acid), 12.5 mM KC1, pH 7.0, 10 mM EDTA, or simply an EDTA buffered water (pH 7.0).
[473] The aminoacylated tRNAs can be added to translation reactions in order to
incorporate the amino acid with which the tRNA was aminoacylated in a position of choice in a polypeptide made by the translation reaction. Examples of translation systems in which the aminoacylated tRNAs of the present invention may be used include, but are not limited to cell lysates. Cell lysates provide reaction components necessary for in vitro translation of a polypeptide from an input mRNA. Examples of such reaction components include but are not limited to ribosomal proteins, rRNA, amino acids, tRNAs, GIT, ATP, translation initiation and elongation factors and additional factors associated with translation. Additionally, translation systems may be batch translations or compartmentalized translation. Batch translation systems combine reaction components in a single compartment while compartmentalized translation systems separate the translation reaction components from reaction products that can inhibit the translation efficiency. Such translation systems are available commercially.
[474] Further, a coupled transcription/translation system may be used. Coupled
transcription/translation systems allow for both transcription of an input DNA into a corresponding mRNA, which is in turn translated by the reaction components. An example of a commercially available coupled transcription/translation is the Rapid Translation System (RTS, Roche Inc.). The system includes a mixture containing E. coli lysate for providing translational components such as ribosomes and translation factors. Additionally, an RNA polymerase is included for the transcription of the input DNA into an mRNA template for use in translation. RTS can use compartmentalization of the reaction components by way of a membrane interposed between reaction compartments, including a supply/waste compartment and a transcription/translation compartment.

[475] Aminoacylation of tRNA may be performed by other agents, including but not
limited to, transferases, polymerases, catalytic antibodies, multi-functional proteins, and the like.
[476] Lu et al. in Mol Cell. 2001 Oct;8(4):759-69 describe a method in which a protein is
chemically ligated to a synthetic peptide containing unnatural amino acids (expressed protein ligation).
[477] Microinjection techniques have also been use incorporate unnatural amino acids
into proteins. See, e.g., M. W. Nowak, P. C. Kearney, J. R. Sampson, M. E. Saks, C. G. Labarca, S. K. Silverman, W. G. Zhong, J. Thorson, J. N. Abelson, N. Davidson, P. G. Schulteu D. A. Dougherty and H. A. Lester, Science, 268:439 (1995); and, D. A. Dougherty, Curr. Opin. Chem. Biol., 4:645 (2000). A Xenopus oocyte was coinjected wife two RNA species made in vitro: an mRNA encoding the target protein with a UAG stop codon at the amino acid position of interest and an amber suppressor tRNA aminoacylated with the desired unnatural amino acid. The translational machinery of the oocyte then inserts the unnatural amino acid at the position specified by UAG. This method has allowed in vivo structure-function studies of integral membrane proteins, which are generally not amenable to in vitro expression systems. Examples include the incorporation of a fluorescent amino acid into tachykinin neurokinin-2 receptor to measure distances by fluorescence resonance energy transfer, see, e.g., G. Turcatti, K. Nemeth, M. D. Edgerton, U. Meseth, F. Talabot, M. Peitsch, J. Knowles, H. Vogel and A. Chollet, J. Biol. Chem.. 271:19991 (1996); the incorporation of biotinylated amino acids to identify surface-exposed residues in ion channels, see, e.g., J. P. Gallivan, H. A. Lester and D. A. Dougherty, Chem. Biol.. 4:739 (1997); the use of caged tyrosine analogs to monitor conformational changes in an ion channel in real time, see, e.g., J. C. Miller, S. K. Silverman, P. M. England, D. A. Dougherty and H. A. Lester, Neuron, 20:619 (1998); and, the use of alpha hydroxy amino acids to change ion channel backbones for probing their gating mechanisms. See, e.g., P. M. England, Y. Zhang, D. A. Dougherty and H. A. Lester, Celt, 96:89 (1999); and, T. Lu, A. Y. Ting, J. Mainland, L. Y. Jan, P. G. Schultz and J. Yang, Nat Neuroscu 4:239 (2001).
[478] The ability to incorporate unnatural amino acids directly into proteins in vivo offers
a wide variety of advantages including but not limited to, high yields of mutant proteins, technical ease, the potential to study the mutant proteins in cells or possibly in living organisms and the use of these mutant proteins in therapeutic treatments and diagnostic uses. The ability to include unnatural amino acids with various sizes, acidities, nucleophilicities, hydrophobicities, and other

properties into proteins can greatly expand our ability to rationally and systematically manipulate the structures of proteins, both to probe protein function and create new proteins or organisms with novel properties.
[479] In one attempt to site-specifically incorporate para-F-Phe, a yeast amber suppressor
tRNAPheCUA /phenylalanyl-tRNA synthetase pair was used in a p-F-Phe resistant, Phe
auxotrophic Escherichia coli strain. See, e.g~, R. Furten Protein Sci.« 7:419 (1998).
[480] It may also be possible to obtain expression of a GH, e.g., hGH polynucleotide of
the present invention using a cell-free (in-vitro) translational system/Translation systems may be cellular or cell-free, and may be prokaryotic or eukaryotic. Cellular translation systems include, but are not limited to, whole cell preparations such as permeabilized cells or cell cultures wherein a desired nucleic acid sequence can be transcribed to mRNA and the mRNA translated. Cell-free translation systems are commercially available and many different types and systems are well- \ known. Examples of cell-free systems include, but are not limited to,- prokaryotic lysates such as \ Escherichia coli lysates, and eukaryotic lysates such as wheat germ extracts, insect cell lysates, rabbit reticulocyte lysates, rabbit oocyte lysates and human cell lysates. Eukaryotic extracts or * lysates may be preferred when the resulting protein is glycosylated, phosphorylated or otherwise modified because many such modifications are only possible in eukaryotic systems. Some of these : extracts and lysates are available commercially (Promega; Madison, Wis.; Stratagene; La Jolla, Calif; Amersham; Arlington Heights, HI.; GIBCO/BRL; Grand Island, N.Y.). Membranous extracts, such as the canine pancreatic extracts containing microsomal membranes, are also available which are useful for translating secretory proteins. In these systems, which can include either mRNA as a template (in-vitro translation) or DNA as a template (combined in-vitro transcription and translation), the in vitro synthesis is directed by the ribosomes. Considerable effort has been applied to the development of cell-free protein expression systems. See, e.g., Kim, D.M. and J JR.. Swartz, Biotechnology and Bioengineering, 1A :309-316 (2001); Kim, D.M. and J.R. Swartz, Biotechnology Letters, 22, 1537-1542, (2000); Kim, D.M., and J.R. Swartz, Biotechnology Progress, 16, 385-390, (2000); Kim, D.M., and J.R. Swartz, Biotechnology and Bioengineering, 66,180-188, (1999); and Patnaik, R. and J.R. Swartz, Biotechniques 24, 862-868, (1998); U.S. Patent No. 6,337,191; U.S. Patent Publication No. 2002/0081660; WO 00/55353; WO 90/05785, which are incorporated by reference herein. Another approach that may be applied to the expression of GH, e.g., hGH polypeptides comprising a non-naturally encoded amino acid

includes the mRNA-peptide fusion technique. See, e.g., R. Roberts and J. Szostak, Proc. Natl Acad. Sci. (USA) 94:12297-12302 (1997); A. Frankel, et al., Chemistry & Biology 10:1043-1050 (2003). In this approach, an mRNA template linked to puromycin is translated into peptide on the ribosome. If one or more tRNA molecules has been modified, non-natural amino acids can be incorporated into the peptide as well. After the last mRNA codon has been read, puromycin captures the C-terminus of the peptide. If the resulting mRNA-peptide conjugate is found to have interesting properties in an in vitro assay, its identity can be easily revealed from the mRNA sequence. In this way, one may screen libraries of GH, e.g., hGH polypeptides comprising one or more non-naturally encoded amino acids to identify polypeptides having desired properties. More recently, in vitro ribosome translations with purified components have been reported that permit the synthesis of peptides substituted with non-naturally encoded amino acids. See, e.g., A. Forster etaUProc. Natl Acad. Sci. (USA) 100:6353 (2003).
[481] Reconstituted translation systems may also be used. Mixtures of purified translation
factors have also been used successfully to translate mRNA into protein as well as combinations
of lysates or lysates supplemented with purified translation factors such as initiation factor-1 (IF-
1), IF-2, IF-3 (a or j5), elongation factor T (EF-Tu), or termination factors. Cell-free systems may
also be coupled transcription/translation systems wherein DNA is introduced to the system,
transcribed into mRNA and the mRNA translated as described in Current Protocols in Molecular
Biology (F. M. Ausubel et al. editors, Wiley Interscience, 1993), which is hereby specifically
incorporated by reference. RNA transcribed in eukaryotic transcription system may be in the form
of heteronuclear RNA (hnRNA) or 5-end caps (7-methyl guanosine) and 3-end poly A tailed
mature mRNA, which can be an advantage in certain translation systems. For example, capped
mRNAs are translated with high efficiency in the reticulocyte lysate system.
DC Macromolecular Polymers Coupled to GH, e.g.f hGH Polypeptides
[482] Various modifications to the non-natural amino acid polypeptides described herein
can be effected using the compositions, methods, techniques and strategies described herein. These modifications include the incorporation of further functionality onto the non-natural amino acid component of the polypeptide, including but not limited to, a label; a dye; a polymer; a water-soluble polymer; a derivative of polyethylene glycol; a photocrosslinker; a radionuclide; a cytotoxic compound; a drug; an affinity label; a photoaffinity label; a reactive compound; a resin; a second protein or polypeptide or polypeptide analog; an antibody or antibody fragment; a metal

chelator; a cofactor; a fatty acid; a carbohydrate; a polynucleotide; a DNA; a RNA; an antisense polynucleotide; a saccharide; water-soluble dendrimer; a cyclodextrin; an inhibitory ribonucleic acid; a biomaterial; a nanoparticle; a spin label; a fluorophore, a metal-containing moiety; a radioactive moiety; a novel functional group; a group that covalently or noncovalently interacts with other molecules; a photocaged moiety; an actinic radiation excitable moiety; a photoisomerizable moiety; biotin; a derivative of biotin; a biotin analogue; a moiety incorporating a heavy atom; a chemically cleavable group; a photocleavable group; an elongated side chain; a carbon-linked sugar, a redox-active agent; an amino thioacid; a toxic moiety; an isotopically labeled moiety; a biophysical probe; a phosphorescent group; a chemiluminescent group; an electron dense group; a magnetic group; an intercalating group; a chromophore; an energy transfer agent; a biologically active agent; a detectable label; a small molecule; a quantum dot; a nanotransmitter; a radionucleotide; a radiotransmitter; a neutron-capture agent; or any combination of the above, or any other desirable compound or substance. As an illustrative, non-limiting example of the compositions, methods, techniques and strategies described herein, the following description will focus on adding macromolecular polymers to the non-natural amino acid polypeptide with the understanding that the compositions, methods, techniques and strategies described thereto are also applicable (with appropriate modifications, if necessary and for which one of skill in the art could make with the disclosures herein) to adding other functionalities, including but not limited to those listed above.
[483] A wide variety of macromolecular polymers and other molecules can be linked to '
GH, e.g., hGH polypeptides of the present invention to modulate biological properties of the GH, e.g., hGH polypeptide, and/or provide new biological properties to the GH, e.g., hGH molecule. These macromolecular polymers can be linked to the GH, e.g., hGH polypeptide via a naturally encoded amino acid, via a non-naturally encoded amino acid, or any functional substituent of a natural or non-natural amino acid, or any substituent or functional group added to a natural or non-natural amino acid. The molecular weight of the polymer may be of a wide range, including but not limited to, between about 100 Da and about 100,000 Da or more. The molecular weight of the polymer may be between about 100 Da and about 100,000 Da, including but not limited to, 100,000 Da, 95,000 Da, 90,000 Da, 85,000 Da, 80,000 Da, 75,000 Da, 70,000 Da, 65,000 Da, 60,000 Da, 55,000 Da, 50,000 Da, 45,000 Da, 40,000 Da, 35,000 Da, 30,000 Da, 25,000 Da, 20,000 Da, 15,000 Da, 10,000 Da, 9,000 Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000 Da, 4,000 Da,

3,000 Da, 2,000 Da, 1,000 Da, 900 Da, 800 Da, 700 Da, 600 Da, 500 Da, 400 Da, 300 Da, 200 Da, and 100 Da. In some embodiments, the molecular weight of the polymer is between about 100 Da and 50,000 Da. In some embodiments, the molecular weight of the polymer is between about 100 Da and 40,000 Da. In some embodiments, the molecular weight of the polymer is between about 1,000 Da and 40,000 Da. La some embodiments, the molecular weight of the polymer is between about 5,000 Da and 40,000 Da. In some embodiments, the molecular weight of the polymer is between about 10,000 Da and 40,000 Da.
[484] The present invention provides substantially homogenous preparations of
polymerrprotein conjugates. "Substantially homogenous" as used herein means that polymerrprotein conjugate molecules are observed to be greater than half of the total protein. The polymerrprotein conjugate has biological activity and the present "substantially homogenous" PEGylated GH, e.g., hGH polypeptide preparations provided herein are those which are homogenous enough to display the advantages of a homogenous preparation, e.g., ease in clinical application in predictability of lot to lot pharmacokinetics.
[485] One may also choose to prepare a mixture of polymenprotein conjugate molecules,
and the advantage provided herein is that one may select the proportion of mono-polymerrprotein conjugate to include in the mixture. Thus, if desired, one may prepare a mixture of various proteins with various numbers of polymer moieties attached (i.e., di-, tri-, tetra-, etc.) and combine said conjugates with the mono-polymenprotein conjugate prepared using the methods of the present invention, and have a mixture with a predetermined proportion of mono-polymenprotein conjugates.
[486] The polymer selected may be water soluble so that the protein to which it is
attached does not precipitate in an aqueous environment, such as a physiological environment. The polymer may be branched or unbranched. For therapeutic use of the end-product preparation, the polymer will be pharmaceutical^ acceptable.
[487] Examples of polymers include but are not limited to polyalkyl ethers and alkoxy-
capped analogs thereof (e.g., polyoxyethylene glycol, polyoxyethylene/propylene glycol, and
methoxy or ethoxy-capped analogs thereof, especially polyoxyethylene glycol, the latter is also
known as polyethyleneglycol or PEG); polyvinylpyrrolidones; polyvinylalkyl ethers;
polyoxazolines, polyalkyl oxazolines and polyhydroxyalkyl oxazolines; polyacrylamides,
polyalkyl acrylamides, and polyhydroxyalkyl acrylamides (e.g.,

polyhydroxypropybnethacrylamide and derivatives thereof); polyhydroxyalkyl acrylates; polysialic acids and analogs thereof; hydrophilic peptide sequences; polysaccharides and their derivatives, including dextran and dextran derivatives, e.g., carboxymethyldextran, dextran sulfates, aminodextran; cellulose and its derivatives, e.g;, carboxymethyl cellulose, hydroxyalkyl celluloses; chitin and its derivatives, e.g., chitosan, succinyl chitosan, carboxymethylchitin, carboxymethylchitosan; hyaluronic acid and its derivatives; starches; alginates; chondroitin sulfate; albumin; pullulan and carboxymethyl pullulan; polyaminoacids and derivatives thereof, e.g., polyglutamic acids, polylysines, polyaspartic acids, polyaspartamides; maleic anhydride copolymers such as: styrene maleic anhydride copolymer, divinylethyl ether maleic anhydride copolymer; polyvinyl alcohols; copolymers thereof; terpolymers thereof; mixtures thereof; and derivatives of the foregoing.
[488] The proportion of polyethylene glycol molecules to protein molecules will vary, as
will their concentrations in the reaction mixture, hi general, the optimum ratio (in terms of efficiency of reaction in that there is minimal excess unreacted protein or polymer) may be determined by the molecular weight of the polyethylene glycol selected and on the number of available reactive groups available. As relates to molecular weight, typically the higher the molecular weight of the polymer, the fewer number of polymer molecules which may be attached to the protein. Similarly, branching of the polymer should be taken into account when optimizing these parameters. Generally, the higher the molecular weight (or the more branches) the higher the polymerrprotein ratio.
[489J As used herein, and when contemplating PEG:GH, e.g., hGH polypeptide
conjugates, the term "therapeutically effective amount" refers to an amount which gives the desired benefit to a patient The amount will vary from one individual to another and will depend upon a number of factors, including the overall physical condition of the patient and the underlying cause of the condition to be treated. The amount of GH, e.g.,hGH polypeptide used for therapy gives an acceptable rate of change and maintains desired response at a beneficial level. A therapeutically effective amount of the present compositions may be readily ascertained by one of ordinary skill in the art using publicly available materials and procedures.
[490] The water soluble polymer may be any structural foim including but not limited to
linear, forked or branched. Typically, the water soluble polymer is a poly(alkylene glycol), such as

poly(ethyIene glycol) (PEG), but other water soluble polymers can also be employed. By way of example, PEG is used to describe certain embodiments of this invention.
[491] PEG is a well-known, water soluble polymer that is commercially available or can
be prepared by ring-opening polymerization of ethylene glycol according to methods known to those of ordinary skill in the art (Sandler and Karo, Polymer Synthesis, Academic Press, New York, Vol. 3, pages 138-161). The term "PEG" is used broadly to encompass any polyethylene glycol molecule, without regard to size or to modification at an end of the PEG, and can be represented as linked to the GH, e.g., hGH polypeptide by the formula: XO-(CH2CH20)n-CH2CH2"Y
where n is 2 to 10,000 and X is H or a terminal modification, including but not limited to, a CM alkyl, a protecting group, or a terminal functional group.
[492] hi some cases, a PEG used in the invention terminates on one end with hydroxy or
methoxy, i.e., X is H or CH3 ("methoxy PEG"). Alternatively, the PEG can terminate with a reactive group, thereby forming a Afunctional polymer. Typical reactive groups can include those reactive groups that are commonly used to react with the functional groups found in the 20 common amino acids (including but not limited to, maleimide groups, activated carbonates (including but not limited to,.p-nitrophenyl ester), activated esters (including but not limited to, N-hydroxysuccinimide, p-nitrophenyl ester) and aldehydes) as well as functional groups that are. inert to the 20 common amino acids but that react specifically with complementary functional groups present in non-naturally encoded amino acids (including but not limited to, azide groups, alkyne. groups). It is noted that the other end of the PEG, which is shown in the above formula by Y, will attach either directly or indirectly to a GH, e.g., hGH polypeptide via a naturally-occurring or non-naturally encoded amino acid. For instance, Y may be an amide, carbamate or urea linkage to an amine group (including but not limited to, the epsilon amine of lysine or the TV-terminus) of the polypeptide. Alternatively, Y may be a maleimide linkage to a thiol group (including but not limited to, the thiol group of cysteine). Alternatively, Y may be a linkage to a residue not commonly* accessible via the 20 common amino acids. For example, an azide group on the PEG can be reacted with an alkyne group on the GH, e.g., hGH polypeptide to form a Huisgen [3+2] cycloaddition product Alternatively, an alkyne group on the PEG can be reacted with an azide group present in a non-naturally encoded amino acid to form a similar product In some embodiments, a strong nucleophile (including but not limited to, hydrazine, hydrazide,

hydroxylamine, semicarbazide) can be reacted with an aldehyde or ketone group present in a non-naturally encoded amino acid to form a hydrazone, oxime or semicarbazone, as applicable, which in some cases can be further reduced by treatment with an appropriate reducing agent. Alternatively, the strong nucleophile can be incorporated into the GH, e.g., hGH polypeptide via a non-naturally encoded amino acid and used to react preferentially with a ketone or aldehyde group present in the water soluble polymer.
f493] Any molecular mass for a PEG can be used as practically desired, including but not
limited to, from about 100 Daltons (Da) to 100,000 Da or more as desired (including but not limited to, sometimes 0.1-50 kDa or 10-40 kDa). The molecular weight of PEG may be of a wide range, including but not limited to, between about 100 Da and about 100,000 Da or more. The molecular weight of PEG may be between about 100 Da and about 100,000 Da, including but not limited to, 100,000 Da, 95,000 Da, 90,000 Da, 85,000 Da, 80,000 Da, 75,000 Da, 70,000 Da, 65,000 Da, 60,000 Da, 55,000 Da, 50,000 Da, 45,000 Da, 40,000 Da, 35,000 Da, 30,000 Da, , 25,000 Da, 20,000 Da, 15,000 Da, 10,000 Da, 9,000 Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000 Da, 4,000 Da, 3,000 Da, 2,000 Da, 1,000 Da, 900 Da, 800 Da, 700 Da, 600 Da, 500 Da, 400 Da, 300 • Da, 200 Da, and 100 Da. In some embodiments, fee molecular weight of PEG is between about . 100 Da and 50,000 Da. In some embodiments, the molecular weight of PEG is between about 100 Da and 40,000 Da. In some embodiments, the molecular weight of PEG is between about 1,000 Da and 40,000 Da. In some embodiments, the molecular weight of PEG is between about 5,000.; Da and 40,000 Da. In some embodiments, the molecular weight of PEG is between about 10,000 • Da and 40,000 Da. Branched chain PEGs, including but not limited to, PEG molecules with each chain having a MW ranging from 1-100 kDa (including but not limited to, 1-50 kDa or 5-20 kDa) can also be used. The molecular weight of each chain of the branched chain PEG may be, including but not limited to, between about 1,000 Da and about 100,000 Da or more. The molecular weight of each chain of the branched chain PEG may be between about 1,000 Da and about 100,000 Da, including but not limited to, 100,000 Da, 95,000 Da, 90,000 Da, 85,000 Da, 80,000 Da, 75,000 Da, 70,000 Da, 65,000 Da, 60,000 Da, 55,000 Da, 50,000 Da, 45,000 Da, 40,000 Da, 35,000 Da, 30,000 Da, 25,000 Da, 20,000 Da, 15,000 Da, 10,000 Da, 9,000 Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000 Da, 4,000 Da, 3,000 Da, 2,000 Da, and 1,000 Da. In some embodiments, the molecular weight of each chain of the branched chain PEG is between about 1,000 Da and 50,000 Da. In some embodiments, the molecular weight of each chain of the

branched chain PEG is between about 1,000 Da and 40,000 Da. In some embodiments, the molecular weight of each chain of the branched chain PEG is between about 5,000 Da and 40,000 Da. In some embodiments, the molecular weight of each chain of the branched chain PEG is between about 5,000 Da and 20,000 Da. A wide range of PEG molecules are described in, including but not limited to, the Shearwater Polymers, Inc. catalog, Nefctar Therapeutics catalog, incorporated herein by reference.
[494] Generally, at least one terminus of the PEG molecule is available for reaction with
the non-naturally-encoded amino acid. For example, PEG derivatives bearing alkyne and azide moieties for reaction with amino acid side chains can be used to attach PEG to non-naturally encoded amino acids as described herein. If the non-naturally encoded amino acid comprises an azide, then the PEG will typically contain either an alkyne moiety to effect formation of the [3+2] cycloaddition product or an activated PEG species (i.e., ester, carbonate) containing a phosphine : group to effect formation of the amide linkage. Alternatively, if the non-naturally encoded amino : acid comprises an alkyne, then the PEG will typically contain an azide moiety to effect formation of the [3+2] Huisgen cycloaddition product. If the non-naturally encoded amino acid comprises a carbonyl group, the PEG will typically comprise a potent nucleophile (including but not limited to, ■■' a hydrazide, hydrazine, hydroxylamine, or semicarbazide functionality) in order to effect . formation of corresponding hydrazone, oxime, and semicarbazone linkages, respectively. In other ; alternatives, a reverse of the orientation of the reactive groups described above can be used, i.e., an ► azide moiety in the non-naturally encoded amino acid can be reacted with a PEG derivative containing an alkyne.
[495] In some embodiments, the GH, e.g., hGH polypeptide variant with a PEG derivative
contains a chemical functionality that is reactive with the chemical functionality present on the side chain of the non-naturally encoded amino acid.
[496] The invention provides in some embodiments azide- and acetylene-containing
polymer derivatives comprising a water soluble polymer backbone having an average molecular weight from about 800 Da to about 100,000 Da. The polymer backbone of the water-soluble polymer can be poly(ethylene glycol). However, it should be understood that a wide variety of water soluble polymers including but not limited to poly(ethylene)glycol and other related polymers, including poly(dextran) and poly(propylene glycol), are also suitable for use in the

practice of this invention and that the use of the term PEG or poly(ethylene glycol) is intended to encompass and include all such molecules. The term PEG includes, but is not limited to, poly(ethylene glycol) in any of its forms, including bifunctional PEG, multiarmed PEG, derivatized PEG, forked PEG, branched PEG, pendent PEG (i.e. PEG or related polymers having one or more functional groups pendent to the polymer backbone), or PEG with degradable linkages therein.
[497] PEG is typically clear, colorless, odorless, soluble in water, stable to heat, inert to
many chemical agents, does not hydrolyze or deteriorate, and is generally non-toxic. Polyethylene glycol) is considered to be biocompatible, which is to say that PEG is capable of coexistence with living tissues or organisms without causing harm. More specifically, PEG is substantially non-immunogenic, which is to say that PEG does not tend to produce an immune response in the body. When attached to a molecule having some desirable function in the body, such as a biologically active agent, the PEG tends to mask the agent and can reduce or eliminate any immune response ; so that an organism can tolerate the presence of the agent. PEG conjugates tend not to produce a substantial immune response or cause clotting or other undesirable effects. PEG having the 5 formula - CH2CH20«-(CH2CH20)n - CH2CH2--, where n is from about 3 to about 4000, typically from about 20 to about 2000, is suitable for use in the present invention. PEG having a molecular ; weight of from about 800 Da to about 100,000 Da are in some embodiments of the present,; invention particularly useful as the polymer backbone. The molecular weight of PEG may be of a ,. wide range, including but not limited to, between about 100 Da and about 100,000 Da or more. The molecular weight of PEG may be between about 100 Da and about 100,000 Da, including but not limited to, 100,000 Da, 95,000 Da, 90,000 Da, 85,000 Da, 80,000 Da, 75,000 Da, 70,000 Da, 65,000 Da, 60,000 Da, 55,000 Da, 50,000 Da, 45,000 Da, 40,000 Da, 35,000 Da, 30,000 Da, 25,000 Da, 20,000 Da, 15,000 Da, 10,000 Da, 9,000 Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000 Da, 4,000 Da, 3,000 Da, 2,000 Da, 1,000 Da, 900 Da, 800 Da, 700 Da, 600 Da, 500 Da, 400 Da, 300 Da, 200 Da, and 100 Da. In some embodiments, the molecular weight of PEG is between about 100 Da and 50,000 Da. In some embodiments, the molecular weight of PEG is between about 100 Da and 40,000 Da. In some embodiments, the molecular weight of PEG is between about 1,000 Da and 40,000 Da. In some embodiments, the molecular weight of PEG is between about 5,000

Da and 40,000 Da. In some embodiments, the molecular weight of PEG is between about 10,000 Da and 40,000 Da.
[498] The polymer backbone can be linear or branched. Branched polymer backbones are
generally known in the art Typically, a branched polymer has a central branch core moiety and a
plurality of linear polymer chains linked to the central branch core. PEG is commonly used in
branched foims that can be prepared by addition of ethylene oxide to various polyols, such as
glycerol, glycerol oligomers, pentaerythritol and sorbitol. The central branch moiety can also be
derived from several amino acids, such as lysine. The branched polyethylene glycol) can be
represented in general form as R(-PEG-OH)m in which R is derived from a core moiety, such as
glycerol, glycerol oligomers, or pentaerythritol, and m represents the number of arms. Multi-
armed PEG molecules, such as those described in U.S. Pat. Nos. 5,932,462; 5,643,575; 5,229,490;
4,289,872; U.S. Pat Appl. 2003/0143596; WO 96/21469; and WO 93/21259, each of which is
incorporated by reference herein in its entirety, can also be used as the polymer backbone.
[499] Branched PEG can also be in the form of a forked PEG represented by PEG(— .
YCHZa}n> where Y is a Unking group and Z is an activated terminal group linked to CH by a chain of atoms of defined length.
[500] Yet another branched form, the pendant PEG, has reactive groups, such as
carboxyl, along the PEG backbone rather than at the end of PEG chains.
[501] In addition to these forms of PEG, the polymer can also be prepared with weak or
degradable1 linkages in the backbone. For example, PEG can be prepared with ester linkages in the polymer backbone that are subject to hydrolysis. As shown below, this hydrolysis results in cleavage of the polymer into fragments of lower molecular weight: -PEG-C02-PEG-+H20 -» PEG-CO2H+HO-PEG-
It is understood by those of ordinary skill in the art that the term poly(ethylene glycol) or PEG represents or includes all the forms known in the art including but not limited to those disclosed herein.
[502] Many other polymers are also suitable for use in the present invention. In some
embodiments, polymer backbones that are water-soluble, with from 2 to about 300 termini, are particularly useful in the invention. Examples of suitable polymers include, but are not limited to, other poly(alkylene glycols), such as poly(propylene glycol) (lTPG"), copolymers thereof

(including but not limited to copolymers of ethylene glycol and propylene glycol), terpolymers
thereof, mixtures thereof, and the like. Although the molecular weight of each chain of the
polymer backbone can vary, it is typically in the range of from about 800 Da to about 100,000 Da,
often from about 6,000 Da to about 80,000 Da. The molecular weight of each chain of the
polymer backbone may be between about 100 Da and about 100,000 Da, including but not limited
to, 100,000 Da, 95,000 Da, 90,000 Da, 85,000 Da, 80,000 Da, 75,000 Da, 70,000 Da, 65,000 Da,
60,000 Da, 55,000 Da, 50,000 Da, 45,000 Da, 40,000 Da, 35,000 Da, 30,000 Da, 25,000 Da,
20,000 Da, 15,000 Da, 10,000 Da, 9,000 Da, 8,000 Da, 7,000 Da, 6,000 Da, 5,000 Da, 4,000 Da,
3,000 Da, 2,000 Da, 1,000 Da, 900 Da, 800 Da, 700 Da, 600 Da, 500 Da, 400 Da, 300 Da, 200 Da,
and 100 Da. In some embodiments, the molecular weight of each chain of the polymer backbone
is between about 100 Da and 50,000 Da. In some embodiments, the molecular weight of each
chain of the polymer backbone is between about 100 Da and 40,000 Da. In some embodiments, •
the molecular weight of each chain of the polymer backbone is between about 1,000 Da and •■
40,000 Da. In some embodiments, the molecular weight of each chain of the polymer backbone is
between about 5,000 Da and 40,000 Da. In some embodiments, the molecular weight pf each ;;
chain of the polymer backbone is between about 10,000 Da and 40,000 Da.
[503] Those of ordinary skill in the art will recognize that the foregoing list for
substantially water soluble backbones is by no means exhaustive and is merely illustrative, and .. that all polymeric materials having the qualities described above are contemplated as being ■ suitable for use in the present invention.
[504] In some embodiments of the present invention the polymer derivatives are "multi-
functional", meaning that the polymer backbone has at least two termini, and possibly as many as
about 300 termini, functionalized or activated with a functional group. Multifunctional polymer
derivatives include, but are not limited to, linear polymers having two termini, each terminus
being bonded to a functional group which may be the same or different
[505] In one embodiment, the polymer derivative has the structure:
X—A—POLY— B—N=N=N
wherein:
N=N=N is an azide moiety;

B is a linking moiety, which may be present or absent;
POLY is a water-soluble non-antigenic polymer,
A is a linking moiety, which may be present or absent and which may be the same as B or
different; and
X is a second functional group.
Examples of a linking moiety for A and B include, but are not limited to, a multiply-functionalized alkyl group containing up to 18, and may contain between 1-10 carbon atoms. A heteroatom such as nitrogen, oxygen or sulfur may be included with the alkyl chain. The alkyl chain may also be branched at a heteroatom. Other examples of a linking moiety for A and B include, but are not limited to, a multiply functionalized aryl group, containing up to 10 and may contain 5-6 carbon atoms. The aryl group may be substituted with one more carbon atoms, nitrogen, oxygen or sulfur atoms. Other examples of suitable linking groups include those linking groups described in U.S. Pat. Nos. 5,932,462; 5,643,575; and U.S. Pat. Appl. Publication 2003/0143596, each of which is incorporated by reference herein. Those of ordinary skill in the art will recognize that the foregoing list for linking moieties is by no means exhaustive and is merely illustrative, and that all ' linking moieties having the qualities described above are contemplated to be suitable for use in the ' present invention.
[506] Examples of suitable functional groups for use as X include, but are not limited to, '
hydroxyl, protected hydroxyl, alkoxyl, active ester, such as N-hydroxysuccinimidyl esters and 1-benzotriazolyl esters, active carbonate, such as N-hydroxysuccinimidyl carbonates and 1-benzotriazolyl carbonates, acetal, aldehyde, aldehyde hydrates, alkenyl, acrylate, methacrylate, acrylamide, active sulfone, amine, aminooxy, protected amine, hydrazide, protected hydrazide, protected thiol, carboxylic acid, protected carboxylic acid, isocyanate, isothiocyanate, maleimide, vinylsulfone, dithiopyridine, vinylpyridine, iodoacetamide, epoxide, glyoxals, diones, mesylates, tosylates, tresylate, alkene, ketone, and azide. As is understood by those of ordinary skill in the art, the selected X moiety should be compatible with the azide group so that reaction with the azide group does not occur. The azide-containing polymer derivatives may be homobifunctional, meaning that the second functional group (i.e., X) is also an azide moiety, or heterobifunctional, meaning that the second functional group is a different functional group.

[507] The term "protected" refers to the presence of a protecting group or moiety that
prevents reaction of the chemically reactive functional group under certain reaction conditions. The protecting group will vary depending on the type of chemically reactive group heing protected. For example, if the chemically reactive group is an amine or a hydrazide, the protecting group can be selected from the group of tert-butyloxycarbonyl (t-Boc) and 9-fluorenylmethoxycarbonyl (Fmoc). If the chemically reactive group is a thiol, the protecting group can be orthopyridyldisulfide. If the chemically reactive group is a carboxylic acid, such as butanoic or propionic acid, or a hydroxyl group, the protecting group can be benzyl or an alkyl group such as methyl, ethyl, or tert-butyl. Other protecting groups known in the art may also be used in the present invention.
1508] Specific examples of terminal functional groups in the literature include, but are not
limited to, N-succinimidyl carbonate (see e.g., U.S. Pat. Nos. 5,281,698, 5,468,478), amine (see, ■ e.g., Buckmann et al. Makromol. Chem. 182:1379 (1981), Zalipsky et al. Eur. Polym. J. 19:1177 (1983)), hydrazide (See, e.g., Andresz et al. Makromol. Chem. 179:301 (1978)), succinimidyl propionate and succinimidyl butanoate (see, e.g., Olson et al. in Poly(ethylejie glycol) Chemistry & Biological Applications, pp 170-181, Harris & Zalipsky Eds., ACS, Washington, D.C., 1997; see also U.S. Pat. No. 5,672,662), succinimidyl succinate (See, e.g., Abuchowski et al. Cancer Biochem. Biophys. 7:175 (1984) and Joppich et al. Makromol. Chem. 180:1381 (1979), succinimidyl ester (see, e.g., U.S. Pat. No. 4,670,417), benzotriazole carbonate (see, e.g., U.S. Pat No. 5,650,234), glycidyl ether (see, e.g., Pitha et al. Eur. J Biochem. 94:11 (1979), Elling et al., Biotech. Appl. Biochem. 13:354 (1991), oxycarbonylimidazole (see, e.g., Beauchamp, et al., Anal. Biochem. 131:25 (1983), Tondelli et al. J. Controlled Release 1:251 (1985)), p-nitrophenyl carbonate (see, e.g., Veronese, et al., Appl. Biochem. Biotech., 11: 141 (1985); and Sartore et al., Appl. Biochem. Biotech., 27:45 (1991)), aldehyde (see, e.g., Harris et al. J. Polym. Sci. Chem. Ed. 22:341 (1984), U.S. Pat. No. 5,824,784, U.S. Pat No. 5,252,714), maleimide (see, e.g., Goodson et al. Biotechnology (NY) 8:343 (1990), Romani et al. in Chemistry of Peptides and Proteins 2:29 (1984)), and Kogan, Synthetic Comm. 22:2417 (1992)), orthopyridyl-disulfide (see, e.g., Woghiren, et al. Bioconj. Chem. 4:314(1993)), acrylol (see, e.g., Sawhney et al., Macromolecules, 26:581 (1993)), vinylsulfone (see, e.g., U.S. Pat. No. 5,900,461). All of the above references and patents are incorporated herein by reference

[509] In certain embodiments of the present invention, the polymer derivatives of the
invention comprise a polymer backbone having the structure:
X—CH2CH20-(CH2CH20)n -CH2CH2 -N=N=N wherein:
X is a functional group as described above; and
n is about 20 to about 4000.
In another embodiment, the polymer derivatives of the invention comprise a polymer backbone
having the structure:
X—CH2CH20-(CH2CH20)n «CH2CH2 - 0-(CH2)m-W-N=N=N wherein:
W is an aliphatic or aromatic linker moiety comprising between 1-10 carbon atoms;
n is about 20 to about 4000; and
X is a functional group as described above, m is between 1 and 10.
[510] The azide-containing PEG derivatives of the invention can be prepared by a variety .
of methods known in the art and/or disclosed herein. In one method, shown below, a water soluble
polymer backbone having an average molecular weight from about 800 Da to about 100,000 Da,
the polymer backbone having a first terminus bonded to a first functional group and a second :
terminus bonded to a suitable leaving group, is reacted with an azide anion (which may be paired r
with any of a number of suitable counter-ions, including sodium, potassium, tert-butylammonium .
and so forth). The leaving group undergoes a nucleophilic displacement and is replaced by the
azide moiety, affording the desired azide-containing PEG polymer.
X-PEG-L + N3" -> X-PEG- N3
[511] As shown, a suitable polymer backbone for use in the present invention has the
formula X-PEG-L, wherein PEG is poly(ethylene glycol) and X is a functional group which does not react with azide groups and L is a suitable leaving group. Examples of suitable functional groups include, but are not limited to, hydroxyl, protected hydroxyl, acetal, alkenyl, amine, aminooxy, protected amine, protected hydrazide, protected thiol, carboxylic acid, protected carboxylic acid, maleimide, dithiopyridine, and vinylpyridine, and ketone. Examples of suitable

leaving groups include, but are not limited to, chloride, bromide, iodide, mesylate, tresylate, and
tosylate.
[512] In another method for preparation of the azide-containing polymer derivatives of
the present invention, a linking agent bearing an azide functionality is contacted with a water
soluble polymer backbone having an average molecular weight from about 800 Da to about
100,000 Da, wherein the linking agent bears a chemical functionality that will react selectively
with a chemical functionality on the PEG polymer, to form an azide-containing polymer derivative
product wherein the azide is separated from the polymer backbone by a linking group.
[513] An exemplary reaction scheme is shown below:
X-PEG-M +N-linker-N=N=N -» PG-X-PEG-linker-N-N=N
wherein:
PEG is poly(ethylene glycol) and X is a capping group such as alkoxy or a functional group as
described above; and
M is a functional group that is not reactive with the azide functionality but that will react '
efficiently and selectively with the N functional group.
[514] Examples of suitable functional groups include, but are not limited to, M being a :
carboxylic acid, carbonate or active ester if N is an amine; M being a ketone if N is a hydrazide or "
aminooxy moiety; M being a leaving group if N is a nucleophile.
[515] Purification of the crude product may be accomplished by known methods
including, but are not limited to, precipitation of the product followed by chromatography, if
necessary.
[516] A more specific example is shown below in the case of PEG diamine, in which one
of the amines is protected by a protecting group moiety such as tert-butyl-Boc and the resulting
mono-protected PEG diamine is reacted with a linking moiety that bears the azide functionality:
BocHN-PEG-NH2 + H02C-(CH2)3-N=N=N
[517] In this instance, the amine group can be coupled to the carboxylic acid group using
a variety of activating agents such as thionyl chloride or carbodiimide reagents and N-hydroxysuccinimide or N-hydroxybenzotriazole to create an amide bond between the monoamine PEG derivative and the azide-bearing linker moiety. After successful formation of the amide

bond, the resulting N-tert-butyl-Boc-protected azide-containing derivative can be used directly to modify bioactive molecules or it can be further elaborated to install other useful functional groups. For instance, the N-t-Boc group can be hydrolyzed by treatment with strong acid to generate an omega-amino-PEG-azide. The resulting amine can be used as a synthetic handle to install other useful functionality such as maleimide groups, activated disulfides, activated esters and so forth for the creation of valuable heterobifunctional reagents.
[518] Heterobifunctional derivatives are particularly useful when it is desired to attach
different molecules to each terminus of the polymer. For example, the omega-N-amino-N-azido
PEG would allow the attachment of a molecule having an activated electrophilic group, such as an
aldehyde, ketone, activated ester, activated carbonate and so forth, to one terminus of the PEG and
a molecule having an acetylene group to the other terminus of the PEG.
[519] hi another embodiment of the invention, the polymer derivative has the structure:
X—A—POLY— B-OC-R
wherein:
R can be either H or an alkyl, alkene, alkyoxy, or aryl or substituted aryl group;
B is a linking moiety, which may be present or absent;
POLY is a water-soluble non-antigenic polymer;
A is a linking moiety, which may be present or absent and which may be the same as B or
different; and
X is a second functional group.
[520] Examples of a linking moiety for A and B include, but are not limited to, a
multiply-fonctionalized alkyl group containing up to 18, and may contain between 1-10 carbon
atoms. A heteroatom such as nitrogen, oxygen or sulfur may be included with the alkyl chain.
The alkyl chain may also be branched at a heteroatom. Other examples of a linking moiety for A
and B include, but are not limited to, a multiply functionalized aryl group, containing up to 10 and
may contain 5-6 carbon atoms. The aryl group may be substituted with one more carbon atoms,
nitrogen, oxygen, or sulfur atoms. Other examples of suitable linking groups include those linking
groups described in U.S. Pat. Nos. 5,932,462 and 5,643,575 and U.S. Pat. Appl. Publication
2003/0143596, each of which is incorporated by reference herein. Those of ordinary skill in the

art will recognize that the foregoing list for linking moieties is by no means exhaustive and is
intended to be merely illustrative, and that a wide variety of linking moieties having the qualities
described above are contemplated to be useful in the present invention.
[521] Examples of suitable functional groups for use as X include hydroxyl, protected
hydroxyl, alkoxyi, active ester, such as N-hydroxysuccimmidyl esters and 1-benzotriazolyl esters,
active carbonate, such as N-hydroxysuccinhnidyl carbonates and 1-benzotriazolyl carbonates,
acetal, aldehyde, aldehyde hydrates, alkenyl, acrylate, methacrylate, acrylamide, active sulfone,
amine, aminooxy, protected amine, hydrazide, protected hydrazide, protected thiol, carboxylic
acid, protected carboxylic acid, isocyanate, isothiocyanate, maleimide, vinylsulfone,
dithiopyridine, vinylpyridine, iodoacetamide, epoxide, glyoxals, diones, mesylates, tosylates, and
tresylate, alkene, ketone, and acetylene. As would be understood, the selected X moiety should be
compatible with the acetylene group so that reaction with the acetylene group does not occur. The ■
acetylene-containing polymer derivatives may be homobifiinctional, meaning that the second
functional group (i.e., X) is also an acetylene moiety, or heterobifiinctiona], meaning that the
second functional group is a different functional group.
[522] In another embodiment of the present invention, the polymer derivatives comprise
a polymer backbone having the structure:
X—CH2CH20-(CH2CH20)n -CH2CH2 - 0-(CH2VOCH
wherein:
X is a functional group as described above;
n is about 20 to about 4000; and
m is between 1 and 10.
Specific examples of each of the heterobifunctional PEG polymers are shown below.
[523J The acetylene-containing PEG derivatives of the invention can be prepared using
methods known to those of ordinary skill in the art and/or disclosed herein. In one method, a water
soluble polymer backbone having an average molecular weight from about 800 Da to about
100,000 Da, the polymer backbone having a first terminus bonded to a first functional group and a
second terminus bonded to a suitable nucleophilic group, is reacted with a compound that bears
both an acetylene functionality and a leaving group that is suitable for reaction with the
nucleophilic group on the PEG. When the PEG polymer bearing the nucleophilic moiety and the

molecule bearing the leaving group are combined, the leaving group undergoes a nucleophilic displacement and is replaced by the nucleophilic moiety, affording the desired acetylene-containing polymer.
X-PEG-Nu + L-A-C ^ X-PEG-Nu-A-CsCR'
[524] As shown, a preferred polymer backbone for use in the reaction has the formula X-
PEG-Nu, wherein PEG is poly(ethyiene glycol), Nu is a nucleophilic moiety and X is a functional
group that does not react with Nu, L or the acetylene functionality.
[525] Examples of Nu include, but are not limited to, amine, alkoxy, aryloxy, sulfhydryl,
imino, carboxylate, hydxazide, aminoxy groups that would react primarily via a SN2-type
mechanism. Additional examples of Nu groups include those functional groups that would react
primarily via an nucleophilic addition reaction. Examples of L groups include chloride, bromide,
iodide, mesylate, tresylate, and tosylate and other groups expected to undergo nucleophilic
displacement as well as ketones, aldehydes, thioesters, olefins, alpha-beta unsaturated carbonyl
groups, carbonates and other electrophilic groups expected to undergo addition by nucleophiles.
[526] In another embodiment of the present invention, A is an aliphatic linker of between
1-10 carbon atoms or a substituted aryl ring of between 6-14 carbon atoms. X is a functional group
which does not react with azide groups and L is a suitable leaving group
[527] In another method for preparation of the acetylene-containing polymer derivatives
of the invention, a PEG polymer having an average molecular weight from about 800 Da to about
100,000 Da, bearing either a protected functional group or a capping agent at one terminus and a
suitable leaving group at the other terminus is contacted by an acetylene anion.
[528] An exemplary reaction scheme is shown below:
X-PEG-L + -OCR' ^ X-PEG-CsCR'
wherein:
PEG is pply(ethylene glycol) and X is a capping group such as alkoxy or a functional group as
described above; and
R' is either H, an alkyl, alkoxy, aryl or aryloxy group or a substituted alkyl, alkoxyl, aryl or
aryloxy group.

[529] In the example above, the leaving group L should be sufficiently reactive to
undergo SN2-type displacement when contacted with a sufficient concentration of the acetylene anion. The reaction conditions required to accomplish SN2 displacement of leaving groups by acetylene anions are known to those of ordinary skill in the art.
[530] Purification of the crude product can usually be accomplished by methods known
in the art including, but are not limited to, precipitation of the product followed by chromatography, if necessary.
[531] Water soluble polymers can be linked to the GH, e.g., hGH polypeptides of the
invention. The water soluble polymers may be linked via a non-naturally encoded amino acid
incorporated in the GH, e.g., hGH polypeptide or any functional group or substituent of a non-
naturally encoded or naturally encoded amino acid, or any functional group or substituent added to .
a non-naturally encoded or naturally encoded amino acid. Alternatively, the water soluble
polymers are linked to a GH, e.g., hGH polypeptide incorporating a non-naturally encoded amino .
acid via a naturally-occurring amino acid (including but not limited to, cysteine, lysine or the
amine group of the N-terminal residue). In some cases, the GH, e.g., hGH polypeptides of the .;
invention comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more than 10 non-natural amino acids, wherein *'
one or more non-naturally-encoded amino acid(s) are linked to water soluble polymer(s)
(including but not limited to, PEG and/or oligosaccharides). In some cases, the GH, e.g., hGH
polypeptides of the invention further comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 40, or more than 10..
naturally-encoded amino acid(s) linked to water soluble polymers. In some cases, the GH, e.g.,
hGH polypeptides of the invention comprise one or more non-naturally encoded amino acid(s)
linked to water soluble polymers and one or more naturally-occurring amino acids linked to water
soluble polymers. In some embodiments, the water soluble polymers used in the present invention
enhance the serum half-life of the GH, e.g., hGH polypeptide relative to the unconjugated form.
[532] The number of water soluble polymers linked to a GH, e.g., hGH polypeptide (i.e.,
the extent of PEGylation or glycosylation) of the present invention can be adjusted to provide an altered (including but not limited to, increased or decreased) pharmacologic, pharmacokinetic or pharmacodynamic characteristic such as in vivo half-life. In some embodiments, the half-life of GH, e.g., hGH is increased at least about 10, 20, 30, 40, 50, 60, 70, 80, 90 percent, 2- fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 11-fold, 12-fold, 13-fold, 14-fold, 15-fold, 16-fold, 17-fold,

18-fold, 19-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40-fold, 50-fold, or at least about 100-fold over an unmodified polypeptide.
PEG derivatives containing a strong nucleophilic group (i.e., hydrazide, hydrazine, hydroxvlamine or semicarbazide)
[533] In one embodiment of the present invention, a GH, e.g., hGH polypeptide
comprising a carbonyl-containing non-naturally encoded amino acid is modified with a PEG
derivative that contains a terminal hydrazine, hydroxylamine, hydrazide or semicarbazide moiety
that is linked directly to the PEG backbone.
[534] In some embodiments, the hydroxylamine-terminal PEG derivative will have the
structure:
RO-(CH2CH20)„-0-(CH2)m-0-NH2
where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10 and n is 100-1,000 (i.e., average
molecular weight is between 5-40 kDa).
[535] In some embodiments, the hydrazine- or hydrazide-containing PEG derivative will
have the structure:
RO-(CH2CH20)n-0-(CH2)m-X-NH-NH2
where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10 and n is ,100-1,000 and X is
optionally a carbonyl group (C=0) that can be present or absent.
[536] In some embodiments, the semicarbazide-containing PEG derivative will have the.
structure:
RO-(CH2CH20)n -0-(CH2)m-NH-C(0)-NH-NH2
where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10 and n is 100-1,000.
[537] In another embodiment of the invention, a GH, e.g., hGH polypeptide comprising a
carbonyl-containing amino acid is modified with a PEG derivative that contains a terminal
hydroxylamine, hydrazide, hydrazine, or semicarbazide moiety that is linked to the PEG backbone
by means of an amide linkage.
[538] In some embodiments, the hydroxylamine-terminal PEG derivatives have the
structure:
RO-(CH2CH20)n-0-(CH2)2-NH"C(0)(CH2)m»0-NH2

where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10 and n is 100-1,000 (i.e., average
molecular weight is between 5-40 kDa).
[539J h some embodiments, the hydrazine- or hydrazide-containing PEG derivatives have
the structure:
RO where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10, n is 100-1,000 and X is
optionally a carbonyl group (C=0) that can be present or absent
[540] In some embodiments, the semicarbazide-containing PEG derivatives have the
structure:
RO where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10 and n is 100-1,000.
[541] In another embodiment of the invention, a GH, e.g., hGH polypeptide comprising a
carbonyl-containing amino acid is modified with a branched PEG derivative that contains a
terminal hydrazine, hydroxylamine, hydrazide or semicarbazide moiety, with each chain of the
branched PEG having a MW ranging from 10-40 kDa and, may be from 5-20 kDa.
[542] In another embodiment of the invention, a GH, e.g., hGH polypeptide comprising a
non-naturally encoded amino acid is modified with a PEG derivative having a branched structure.
For instance, in some embodiments, the hydrazine- or hydrazide-terminal PEG derivative will
have the following structure:
^OKCH2CH2OVO-(CH2)2-N^^
where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10 and n is 100-1,000, and X is
optionally a carbonyl group (C=0) that can be present or absent.
[543] In some eriibodiments, the PEG derivatives containing a semicarbazide group will
have the structure:
^O^CH2CH2OVOKCT2)^
where R is a simple alkyl (methyl, ethyl, propyl, etc.), X is optionally NH, O, S, C(O) or not
present, mris 2-10 and n is 100-1,000.
[544] In some embodiments, the PEG derivatives containing a hydroxylamine group will
have the structure:
[RO-(CH2CH20)n-0-(CH2)2-C(0)-NH-CH2-CH2]2CH-X"(CH2)m"0-NH2

where R is a simple alkyl (methyl, ethyl, propyl, etc.), X is optionally NH, O, S, C(O) or not present, m is 2-10 and n is 100-1,000.
[545] The degree and sites at which the water soluble polymer(s) are linked to the hGH
polypeptide can modulate the binding of the hGH polypeptide to the hGH polypeptide receptor at Site 1. In some embodiments, the invention provides a GH, e.g., hGH, that is linked to at least one PEG by an oxime bond, where the PEG used in the reaction to form the oxime bond is a linear, 30 kDa monomethoxy-poly(ethylene glycol)-2-aminooxy ethylamine carbamate hydrochloride, as shown in FIG. 19. FIG. 20 presents an illustrative example of the synthesis of a linear, 30 kDa monomethoxy-poly(ethylene glycol)-2-aminooxy ethylamine carbamate hydrochloride useful in the synthesis of certain embodiments of the invention.
[546] By way of example only and not as a limitation on the types or classes of PEG
reagents that may be used with the compositions, methods, techniques and strategies described herein, FIG. 21 presents further illustrative examples of hydroxylamine-containing PEG reagents that can react with carbonyl-containing non-natural amino acid polypeptides to form oxime-containing non-natural amino acid polypeptides linked to the PEG group, as well as examples of carbonyl-containing PEG reagents that can react with react with oxime-containing non-natural amino acid polypeptides or hydroxylamine-containing non-natural amino acid polypeptides to form new oxime-containing non-natural amino acid polypeptides linked to PEG groups. FIG. 22 presents four illustrative examples of synthetic methods for forming hydroxylamine-containing PEG reagents, or protected forms of hydroxylamine-containing PEG reagents, or masked forms of hydroxylamine-containing PEG reagents. FIG. 23 presents an illustrative example of synthetic methods for forming amide-linked hydroxylamine-containing PEG reagents, or protected forms of amide-linked hydroxylamine-containing PEG reagents, or masked forms of amide-linked hydroxylamine-containing PEG reagents. FIG. 24 and FIG. 25 present an illustrative examples of synthetic methods for forming carbamate-linked hydroxylamine-containing PEG reagents, or protected forms of caibamate-linked hydroxylamine-containing PEG reagents, or masked forms of carbamate-linked hydroxylamine-containing PEG reagents. FIG. 26 presents illustrative examples of synthetic methods for forming simple hydroxylamine-containing PEG reagents, or protected forms of simple hydroxylamine-containing PEG reagents, or masked forms of simple hydroxylamine-containing PEG reagents. Further, FIG. 27 presents illustrative examples of hydroxylamine-containing reagents that have multiple branches of linked PEG groups, and further

shows the reaction of one such hydroxylamine-containing multi-PEG-branched reagents with a carbonyl-containing non-natural amino acid polypeptide to form an oxime-containing non-natural amino acid polypeptide with a linked multi-PEG-branched group.
[547] Further examples of water soluble polymers, e.g., PEGs, useful in the invention,
e.g., PEG modified to be capable of forming an oxime bond, may be found in U.S. Patent Application Nos. 60/638,418; 60/638,527; and 60/639,195, entitled "Compositions containing, methods involving, and uses of non-natural amino acids and polypeptides," filed December 22, 2004, which are incorporated herein by reference in their entirety. Also they are described in U.S. Patent Application Nos. 60/696,210; 60/696,302; and 60/696,068, entitled "Compositions containing, methods involving, and uses of non-natural amino acids and polypeptides," filed July 1, 2005, which are incorporated herein by reference in their entirety.
[548] The degree and sites at which the water soluble polymer(s) are linked to the GH,
e.g., hGH polypeptide can modulate the binding of the GH, e.g., hGH polypeptide to the GH, e.g., hGH polypeptide receptor at Site 1. In some embodiments, the linkages are arranged such that the GH, e.g., hGH polypeptide binds the GH, e.g., hGH polypeptide receptor at Site 1 with a K [549] Methods and chemistry for activation of polymers as well as for conjugation of
peptides are described in the literature and are known in the art. Commonly used methods for
activation of polymers include, but are not limited to, activation of functional groups with
cyanogen bromide, periodate, glutaraldehyde, biepoxides, epichlorohydrin, divinylsulfone,
carbodiimide, sulfonyl halides, trichlorotriazine, etc. (see, R. F. Taylor, (1991), PROTEIN
IMMOBILISATION. FUNDAMENTAL AND APPLICATIONS, Marcel Dekker, N.Y.; S. S. Wong, (1992),
CHEMISTRY OF PROTEIN CONJUGATION AND CROSSLINKING, CRC Press, Boca Raton; G. T.
Hermanson et a/., (1993), IMMOBILIZED AFFINITY LIGAND TECHNIQUES, Academic Press, N.Y.;
Dunn, R.L., et al, Eds. POLYMERIC DRUGS AND DRUG DELIVERY SYSTEMS, ACS
Symposium Series Vol. 469, American Chemical Society, Washington, D.C. 1991).
[550] Several reviews and monographs on the functionalization and conjugation of PEG
are available. See, for example, Harris, Macromol. Chem. Phys. C25: 325-373 (1985); Scouten, Methods in Enzymology 135: 30-65 (1987); Wong et al, Enzyme Microb. Technol 14: 866-874

(1992); Delgado et al9 Critical Reviews in Therapeutic Drug Carrier Systems 9: 249-304 (1992); Zalipsky, Bioconjugate Chem. 6: 150-165 (1995).
[551] Methods for activation of polymers can also be found in WO 94/17039, U.S. Pat.
No. 5,324,844, WO 94/18247, WO 94/04193, U.S. Pat. No. 5,219,564, U.S. Pat No. 5,122,614, WO 90/13540, U.S. Pat No. 5,281,698, and WO 93/15189, and for conjugation between activated polymers and enzymes including but not limited to Coagulation Factor Vm (WO 94/15625), hemoglobin (WO 94/09027), oxygen carrying molecule (U.S. Pat No. 4,412,989), ribonuclease and superoxide dismutase (Veronese at ah, App. Biochem. Biotech. 11: 141-52 (1985)). All references and patents cited are incorporated by reference herein.
[552] PEGylation (i.e., addition of any water soluble polymer) of GH, e.g., hGH
polypeptides containing a non-naturally encoded amino acid, such as /?-azido-L-phenylalanine, is
carried out by any convenient method. For example, GH, e.g., hGH polypeptide is PEGylated
with an alkyne-terminated mPEG derivative. Briefly, an excess of solid mPEG(5000)-O-CH2-
OCH is added, with stirring, to an aqueous solution of p-azido-L-Phe-containing GH, e.g., hGH
polypeptide at room temperature. Typically, the aqueous solution is buffered with a buffer having -
a pKa near the pH at which the reaction is to be carried out (generally about pH 4-10). Examples
of suitable buffers for PEGylation at pH 7.5, for instance, include, but are not limited to, HEPES,
phosphate, borate, TRIS-HC1, EPPS, and TES. The pH is continuously monitored and adjusted if
necessary. The reaction is typically allowed to continue for between about 1-48 hours.
[553] The reaction products are subsequently subjected to hydrophobic interaction
chromatography to separate the PEGylated GH, e.g., hGH polypeptide variants from free mPEG(5000)-O-CH2-C=CH and any high-molecular weight complexes of the pegylated GH, e.g., hGH polypeptide which may form when unblocked PEG is activated at both ends of the molecule, thereby crosslinking GH, e.g., hGH polypeptide variant molecules. The conditions during hydrophobic interaction chromatography are such that free mPEG(5000)-O-CH2-CsCH flows through the column, while any crosslinked PEGylated GH, e.g., hGH polypeptide variant complexes elute after the desired forms, which contain one GH, e.g., hGH polypeptide variant molecule conjugated to one or more PEG groups. Suitable conditions vary depending on the relative sizes of the cross-linked complexes versus the desired conjugates and are readily determined by those of ordinary skill in the art. The eluent containing the desired conjugates is concentrated by ultrafiltration and desalted by diafiltration.

[554] If necessary, the PEGylated GH, e.g., hGH polypeptide obtained from the
hydrophobic chromatography can be purified further by one or more procedures known to those of ordinary skill in the art including, but are not limited to, affinity chromatography, anion- or cation-exchange chromatography (using, including but not limited to, DEAE SEPHAROSE); chromatography on silica; reverse phase HPLC; gel filtration (using, including but not limited to, SEPHADEX G-75); hydrophobic interaction chromatography; size-exclusion chromatography, metal-chelate chromatography; ultrafiltration/diafiltration; ethanol precipitation; ammonium sulfate precipitation; chromatofocusing; displacement chromatography; electrophoretic procedures (including but not limited to preparative isoelectric focusing), differential solubility (including but not limited to ammonium sulfate precipitation), or extraction. Apparent molecular weight may be estimated by GPC by comparison to globular protein standards (Preneta, AZ in PROTEIN PURIFICATION METHODS, A PRACTICAL APPROACH (Harris & Angal, Eds.) IRL Press 1989, 293-306). The purity of the GH; e.g., hGH-PEG conjugate can be assessed by proteolytic degradation (including but not limited to, trypsin cleavage) followed by mass spectrometry analysis. Pepinsky KB.,etaLfJ.PharmcoL &Exp. Ther. 297(3): 1059-66 (2001).
[555J PEGylation (i.e., addition of any water soluble polymer) of GH, e.g., hGH
polypeptides containing a non-naturally encoded amino acid containing a carbonyl group, e.g., such as p-acetyl-L-phenylalanine, is also carried out by any convenient method. As a nonexclusive example, a GH, hGH polypeptide containing a carbonyl-containing non-naturally encoded amino acid, e.g., j>acetyl-L-phenylalanine, is PEGylatedwith an aminooxy ethylamine carbamate mPEG derivative of MW about 0.1-100 kDa, or about 1-100 kDa, or about 10-50 kDa, or about 20-40 kDa, or e.g., 30 kDa. Briefly, an excess of solid MPEG-oxyamine e.g., mPEG(30,000>O-CO-NH^CH2)rONH3+ (a linear 30kDa monomethoxy-poly(ethylene glycol>2-aminooxy ethylamine carbamate hydrochloride, 3 OK MPEG-oxyamine) is added, with stirring, to an aqueous solution of p-acetyl-L-phenylalanine-containing GH, e.g., hGH polypeptide at room temperature. The molar ratio of PEGrGH, e.g., hGH can be about 2-15, or about 5-10, or about 5, 6, 7, 8, 9 or 10. Typically, the aqueous solution is buffered with a buffer having a pKa near the pH at which the reaction is to be carried out (generally about pH 2-8). An of a suitable buffer for PEGylation at pH 4.0, for instance, includes, but is not limited to, a sodium acetate/glycine buffer adjusted to pH 4.0 by addition of acetic acid. The reaction is typically allowed to continue for

between about 1-60 hours, or about 10-50 hours, or about 18-48 hours, or about 39-50 hours, at
room temperature with gentle shaking. PEGylation can be confirmed by SDS gel.
[5561 The reaction products are subsequently subjected to purification from, e.g., from
free 30K MPEG-oxyamine and any high-molecular weight complexes of the PEGylated GH, e.g.,
hGH polypeptide which may form when unblocked PEG is activated at both ends of the molecule,
thereby crosslinking GH, e.g., hGH polypeptide variant molecules. Any suitable purification
method may be used, e.g., column chromatography such as a SourceQ column run with SourceQ
Buffer A and SourceQ Buffer B. The reaction mixture may be diluted with TRIS base and
SourceQ Buffer A and MilliQ water prior to loading on die column. The eluent containing the
desired conjugates can be further concentrated by ultrafiltration and desalted by diafiltration.
[557] If necessary, the PEGylated GH, e.g., hGH polypeptide obtained from the
chromatography can be purified further by one or more procedures known to those of ordinary
skill in the art and described herein (see, e.g., above). The final PEGylated GH, e.g., hGH
polypeptide, may be obtained at a purity of greater than 50, 60, 70, 80, 90, 95, 99, 99.9, or
99.99%. Purity may be determined by methods known in the art* Exemplary non-limiting
methods of assessing purity include SDS-PAGE, measuring GH, e,g., hGH using Western blot and
ELISA assays, Bradford assay, mass spectrometry (including, but no limited to, MALDI-TOF),
HPLC methods such as RP HPLC, cation exchange HPLC, and gel filtration HPLC, and other
methods for characterizing proteins known to those of ordinary skill in the art.
[558] A water soluble polymer linked to an amino acid of a GH, e.g., hGH polypeptide of"
the invention can be further derivatized or substituted without limitation.
Azide-containing PEG derivatives
(5591 In another embodiment of the invention, a GH, e.g., hGH polypeptide is modified
with a PEG derivative that contains an azide moiety that will react with an alkyne moiety present
on the side chain of the non-naturally encoded amino acid. In general, the PEG derivatives will
have an average molecular weight ranging from 1-100 kDa and, in some embodiments, from 10-
40kDa. .
[560] In some embodiments, the azide-terminal PEG derivative will have the structure:
RO-(CH2CH20)n-0-(CH2)m-N3
where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10 and n is 100-1,000 (i.e., average
molecular weight is between 5-40 kDa).
2

[561] In another embodiment, the azide-terminal PEG derivative will have the structure:
RO-(CH2CH20)n -0-(CH2)m-NH-C(OHCH2)p-N3
where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10, p is 2-10 and n is 100-1,000
(i.e., average molecular weight is between 5-40 kDa).
[562] In another embodiment of the invention, a GH, e.g., hGH polypeptide comprising a
alkyne-containing amino acid is modified with a branched PEG derivative that contains a terminal
azide moiety, with each chain of the branched PEG having a MW ranging from 10-40 kDa and ,
may be from 5-20 kDa. For instance, in some embodiments, the azide-terminal PEG derivative
will have the following structure:
|TRO-(CH2CH^
where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10, p is 2-10, and n is 100-1,000, and
X is optionally an O, N, S or carbonyl group (C=0), in each case that can be present or absent.
Alkyne-containing PEG derivatives
[563] hi another embodiment of the invention, a GH, e.g., hGH polypeptide is modified
with a PEG derivative that contains an alkyne moiety that will react with an azide moiety present
on the side chain of the non-naturally encoded amino acid.
[564] In some embodiments, the alkyne-terminal PEG derivative will have the following
structure:
RO-(CH2CH2OVO-(CH2)m-OCH
where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10 and n is 100-1,000 (i.e., average .
molecular weight is between 5-40 kDa).
[565] In another embodiment of the invention, a GH, e.g., hGH polypeptide comprising an
alkyne-containing non-naturally encoded amino acid is modified with a PEG derivative that
contains a terminal azide or terminal alkyne moiety that is linked to the PEG backbone by means
of an amide linkage.
[566] In some embodiments, the alkyne-terminal PEG derivative will have the following
structure:
RO-(CH2CH20)n -0-(CH2)m-NH-C(0)-(CH2)p-OCH
where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10, p is 2-10 and n is 100-1,000.

[567] In another embodiment of the invention, a GH, e.g., hGH polypeptide comprising an
azide-containing amino acid is modified with a branched PEG derivative that contains a terminal
alkyne moiety, with each chain of the branched PEG having a MW ranging from 10-40 kDa and
may be from 5-20 kDa. For instance, in some embodiments, the alkyne-terminal PEG derivative
will have the following structure:
[RO-(CH2CH20)n-0-(^^
where R is a simple alkyl (methyl, ethyl, propyl, etc.), m is 2-10, p is 2-10, and n is 100-1,000, and
X is optionally an O, N, S or carbonyl group (C=0), or not present
Phosphine-contaLain£ PEG derivatives
[568] In another embodiment of the invention, a GH, e.g., hGH polypeptide is modified
with a PEG derivative that contains an activated functional group (including but not limited to,
ester, carbonate) further comprising an aryl phosphine group that will react with an azide moiety
present on the side chain of the non-naturally encoded amino acid. In general, the PEG derivatives
will have an average molecular weight ranging from 1-100 kDa and, in some embodiments, from
10-40 kDa.
[569] In some embodiments, the PEG derivative will have the structure:
Ph2P(H2C)n/SYXxw o
wherein n is 1-10; X can be O, N, S or not present, Ph is phenyl, and W is a water soluble
polymer.
[570] In some embodiments, the PEG derivative will have the structure:
wherein X can be O, N, S or not present, Ph is phenyl, W is a water soluble polymer and R can be H, alkyl, aryl, substituted alkyl and substituted aryl groups. Exemplary R groups include but are not limited to -CH2, -C(CH3)3» -OR\ -NR'R", -SR\ -halogen, -C(0)R>, -CONR'R", -S(0)aR\ -S(0)2NR'R", -CN and -N02. R\ R", R'" and R"" each independently refer to hydrogen, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, including but not limited to, aryl substituted with 1-3 halogens, substituted or unsubstituted alkyl, alkoxy or thioalkoxy groups, or arylalkyl groups. When a compound of the invention includes more than one R group, for example, each of the R groups is independently selected as are each R\ R", R'" and R""

groups when more than one of these groups is present. When R' and R" are attached to the same nitrogen atom, they can be combined with the nitrogen atom to form a 5-, 6-, or 7-membered ring. For example, -NR'R" is meant to include, but not be limited to, 1-pyrrolidinyl and 4-morpholinyl. From the above discussion of substituents, one of skill in the art will understand that the term "alkyl" is meant to include groups including carbon atoms bound to groups other than hydrogen groups, such as haloalkyl (including but not limited to, -CF3 and -CH2CF3) and acyl (including but not limited to, -C(0)CH3, -C(0)CF3, -C(0)CH2OCH3, and the like). Other PEG derivatives and General PEGylation techniques
[571] Other exemplary PEG molecules that may be linked to GH, e.g., hGH polypeptides,
as well as PEGylation methods include those described in, e.g., U.S. Patent Publication No. 2004/0001838; 2002/0052009; 2003/0162949; 2004/0013637; 2003/0228274; 2003/0220447; 2003/0158333; 2003/0143596; 2003/0114647; 2003/0105275; 2003/0105224; 2003/0023023; -2002/0156047; 2002/0099133; 2002/0086939; 2002/0082345; 2002/0072573; 2002/0052430; • 2002/0040076; 2002/0037949; 2002/0002250; 2001/0056171; 2001/0044526; 2001/0021763; . U.S. Patent No. 6,646,110; 5,824,778; 5,476,653; 5,219,564; 5,629,384; 5,736,625; 4,902,502; 5,281,698; 5,122,614; 5,473,034; 5,516,673; 5,382,657; 6,552,167; 6,610,281; 6,515,100; • 6,461,603; 6,436,386; 6,214,966; 5,990,237; 5,900,461; 5,739,208; 5,672,662; 5,446,090; 5,808,096; 5,612,460; 5,324,844; 5,252,714; 6,420,339; 6,201,072; 6,451,346; 6,306,821; 5,559,213; 5,747,646; 5,834,594; 5,849,860; 5,980,948; 6,004,573; 6,129,912; WO 97/32607, EP /• 229,108, EP 402,378, WO 92/16555, WO 94/04193, WO 94/14758, WO 94/17039, WO 94/18247, WO 94/28024, WO 95/00162, WO 95/11924, WO95/13090, WO 95/33490, WO 96/00080, WO 97/18832, WO 98/41562, WO 98/48837, WO 99/32134, WO 99/32139, WO 99/32140, WO 96/40791, WO 98/32466, WO 95/06058, EP 439 508, WO 97/03106, WO 96/21469, WO 95/13312, EP 921 131, WO 98/05363, EP 809 996, WO 96/41813, WO 96/07670, EP 605 963, EP 510 356, EP 400 472, EP 183 503 and EP 154 316, which are incorporated by reference herein. Any of the PEG molecules described herein may be used in any form, including but not limited to, single chain, branched chain, multiarm chain, single functional, bi-functional, multi-functional, or any combination thereof.

Enhancing affinity for serum albumin
[572] Various molecules can also be fused to the GH, e.g., hGH polypeptides of the
invention to modulate the half-life of GH, e.g., hGH polypeptides in serum. In some
embodiments, molecules are linked or fused to GH, e.g., hGH polypeptides of the invention to
enhance affinity for endogenous serum albumin in an animal.
[573] For example, in some cases, a recombinant fusion of a GH, e.g., hGH polypeptide
and an albumin binding sequence is made. Exemplary albumin binding sequences include, but are
not limited to, the albumin binding domain from streptococcal protein G (see, e.g.9 Makrides et al,
J. Pharmacol. Exp. Ther. 277:534-542 (1996) and Sjolander et al, J, Immunol Methods 201:115-
123 (1997)), or albumin-binding peptides such as those described in, e.g., Dennis, et al, X Biol
Chem. 277:35035-35043 (2002).
[574] In other embodiments, the GH, e.g., hGH polypeptides of the present invention are
acylated with fatty acids. In some cases, the fatty acids promote binding to serum albumin. See,'*.
e.g.9Kxatzh&is,etal>Biochem.J. 312:725-731 (1995). V
[575] In other embodiments, the GH, e.g., hGH polypeptides of the invention are fused $
directly with serum albumin (including but not limited to, human serum albumin). Those of skill >')
in the art will recognize that a wide variety of other molecules can also be linked to GH, e.g., hGH •;
in the present invention to modulate binding to serum albumin or other serum components.
X, Glycosylation of GH, e.g*, hGH Polypeptides
[576] The invention includes GH, e.g., hGH polypeptides incorporating one or more non-
naturally encoded amino acids bearing saccharide residues. The saccharide residues may be either
natural (including but not limited to, N-acetylglucosamine) or non-natural (including but not
limited to, 3-fluorogalactose). The saccharides may be linked to the non-naturally encoded amino
acids either by an N- or O-linked glycosidic linkage (including but not limited to, N-
acetylgalactose-L-serine) or a non-natural linkage (including but not limited to, an oxime or the
corresponding C- or S-linked glycoside).
[577] The saccharide (including but not limited to, glycosyl) moieties can be added to GH,
e.g., hGH polypeptides either in vivo or in vitro. In some embodiments of the invention, a GH,
e.g., hGH polypeptide comprising a carbonyl-containing non-naturally encoded amino acid is
modified with a saccharide derivatized with an aminooxy group to generate the corresponding
glycosylated polypeptide linked via an oxime linkage. Once attached to the non-naturally encoded

amino acid, the saccharide may be further elaborated by treatment with glycosyltransferases and other enzymes to generate an oligosaccharide bound to the GH, e.g., hGH polypeptide. See, e.g.9 H. Liu, et al. J. Am. Chem. Soc. 125: 1702-1703 (2003).
[578] In some embodiments of the invention, a GH, e.g., hGH polypeptide comprising a
cafbonyl-containing non-naturally encoded amino acid is modified directly with a glycan with
defined structure prepared as an aminooxy derivative. One of ordinary skill in the art will
recognize that other functionalities, including azide, alkyne, hydrazide, hydrazine, and
semicarbazide, can be used to link the saccharide to the non-naturally encoded amino acid.
[579] In some embodiments of the invention, a GH, e.g., hGH polypeptide comprising an
azide or alkyhyl-containing non-naturally encoded amino acid can then be modified by, including but not limited to, a Huisgen [3+2] cycloaddition reaction with, including but not limited to, alkynyl or azide derivatives, respectively. This method allows for proteins to be modified with extremely high selectivity.
XL GH Supergene Family Member Dimers and Multimers
[580] The present invention also provides for GH supergene family member combinations
(including but not limited to GH, e.g., hGH and hGH analogs) such as homodimers, heterodimers,
homomultimers, or heteromultimers (i.e., trimers, tetramers, etc.) where a GH supergene family
member polypeptide such as GH, e.g., hGH containing one or more non-naturally encoded amino
acids is bound to another GH supergene family member or variant thereof or any other
polypeptide that is a non-GH supergene family member or variant thereof, either directly to the
polypeptide backbone or via a linker. Due to its increased molecular weight compared to
monomers, the GH supergene family member, such as GH, e.g., hGH, dimer or multimer
conjugates may exhibit new or desirable properties, including but not limited to different
pharmacological, pharmacokinetic, pharmacodynamic, modulated therapeutic half-life, or
modulated plasma half-life relative to the monomelic GH supergene family member. In some
embodiments, the GH supergene family member, such as GH, e.g., hGH, dimers of the invention
will modulate the dimerization of the GH supergene family member receptor. In other
embodiments, the GH supergene family member dimers or multimers of the present invention will
act as a GH supergene family member receptor antagonist, agonist, or modulator.
[581] In some embodiments, one or more of the GH, e.g., hGH molecules present in a GH,
e.g., hGH containing dimer or multimer comprises a non-naturally encoded amino acid linked to a

water soluble polymer that is present within the Site II binding region. As such, each of the GH, e.g., hGH molecules of the dimer or multimer are accessible for binding to the GH, e.g., hGH polypeptide receptor via the Site I interface but are unavailable for binding to a second GH, e.g., hGH polypeptide receptor via the Site II interface. Thus, the GH, e.g., hGH polypeptide dimer or multimer can engage the Site I binding sites of each of two distinct GH, e.g., hGH polypeptide receptors but, as the GH, e.g., hGH molecules have a water soluble polymer attached to a non-genetically encoded amino acid present in the Site II region, the GH, e.g., hGH polypeptide receptors cannot engage the Site II region of the GH, e.g., hGH polypeptide ligand and the dimer or multimer acts as a GH, e.g., hGH polypeptide antagonist In some embodiments, one or more of the GH, e.g., hGH molecules present in a GH, e.g., hGH polypeptide containing dimer or multimer comprises a non-naturally encoded amino acid linked to a water soluble polymer that is present within the Site I binding region, allowing binding to the Site II region. Alternatively, in some embodiments one or more of the GH, e.g., hGH molecules present in a GH, e.g., hGH polypeptide containing dimer or multimer comprises a non-naturally encoded amino acid linked to a water soluble polymer that is present at a site that is not within the Site I or Site II binding region, such that both are available for binding. In some embodiments a combination of GH, e.g., ' hGH molecules is used having Site I, Site n, or both available for binding. A combination of GH, e.g., hGH molecules wherein at least one has Site I available for binding, and at least one has Site II available for binding may provide molecules having a desired activity or property. In addition, a combination of GH, e.g., hGH molecules having both Site I and Site II available for binding may produce a super-agonist GH, e.g., hGH molecule.
[582} In some embodiments, the GH supergene family member polypeptides are linked
r directly, including but not limited to, via an Asn-Lys amide linkage or Cys-Cys disulfide linkage. In some embodiments, the linked GH supergene family member polypeptides, and/or the linked non-GH supergene family member, will comprise different non-naturally encoded amino acids to facilitate dimerization, including but not limited to, an alkyne in one non-naturally encoded amino acid of a first GH, e.g., hGH polypeptide and an azide in a second non-naturally encoded amino acid of a second GH supergene family member polypeptide will be conjugated via a Huisgen [3+2] cycloaddition. Alternatively, a first GH supergene family member, and/or the linked non-GH supergene family member, polypeptide comprising a ketone-containing non-naturally encoded amino acid can be conjugated to a second GH supergene family member polypeptide comprising a

hydroxylamine-containing non-naturally encoded amino acid and the polypeptides are reacted via formation of the corresponding oxime.
[583] Alternatively, the two GH supergene family member polypeptides, and/or the linked
non-GH supergene family member, are linked via a linker. Any hetero- or homo-bifunctional linker can be used to link the two GH supergene family members, and/or the linked non-GH supergene family member, polypeptides, which can have the same or different primary sequence. In some cases, the linker used to tether the GH supergene family member, and/or the linked non-GH supergene family member, polypeptides together can be a bifiinctional PEG reagent. The linker may have a wide range of molecular weight or molecular length. Larger or smaller molecular weight linkers may be used to provide a desired spatial relationship or conformation between the GH supergene family member and the linked entity or between the GH supergene family member and the receptor for the GH supergene family member, or between the linked entity and the receptor for the GH supergene family member. Linkers having longer or shorter molecular length may also be used to provide a desired space or flexibility between the GH supergene family member and the linked entity, or between the GH supergene family member and its receptor, or between the linked entity and GH supergene family member receptor. Similarly, a linker having a particular shape or conformation may be utilized to impart a particular shape or conformation to the GH supergene family member or the linked entity, either before or after the GH supergene family member reaches its target This optimization of the spatial relationship between the GH supergene family member and the linked entity may provide new, modulated, or desired properties to the molecule.
[584] In some embodiments, the invention provides water-soluble bifiinctional linkers that
have a dumbbell structure that includes: a) an azide, an alkyne, a hydrazine, a hydrazide, a hydroxylamine, or a carbonyl-containing moiety on at least a first end of a polymer backbone; and b) at least a second functional group on a second end of the polymer backbone. The second functional group can be the same or different as the first functional group. The second functional group, in some embodiments, is not reactive with the first functional group. The invention provides, in some embodiments, water-soluble compounds that comprise at least one arm of a branched molecular structure. For example, the branched molecular structure can be dendritic.

[585] In some embodiments, the invention provides multimers comprising one or more
GH supergene family member, such as GH, e.g., hGH, formed by reactions with water soluble activated polymers that have the structure:
R-(CH2GH2O)n"0-(CH2VX
wherein n is from about 5 to 3,000, m is 2-10, X can be an azide, an alkyne, a hydrazine, a hydrazide, an aminooxy group, a hydroxylamine, an acetyl, or carbonyl-containing moiety, and R is a capping group, a functional group, or a leaving group that can be the same or different as X. R can be, for example, a functional group selected from the group consisting of hydroxy!, protected hydroxy!, alkoxyl, N-hydroxysuccinimidyl ester, 1-benzotriazolyl ester, N-hydroxysuccinimidyl carbonate, 1-benzotriazolyl carbonate, acetal, aldehyde, aldehyde hydrates, alkenyl, acrylate, methacrylate, acrylamide, active sulfone, amine, aminooxy, protected amine, hydrazide, protected hydrazide, protected thiol, carboxylic acid, protected carboxylic acid, isocyanate, isothiocyanate, maleimide, vinylsulfone, dithiopyridine, vinylpyridine, iodoacetamide, epoxide, glyoxals, diones, mesylates, tosylates, and tresylate, alkene, and ketone.
XDL Measurement ofhGH Polypeptide Activity and Affinity ofhGHPolypeptide for
the hGH Polypeptide Receptor
[586] The hGH receptor can be prepared as described in McFarland et aL, Science* 245:
494-499 (1989) and Leung, D., et aL, Nature, 330:537-543 (1987). hGH polypeptide activity can
be determined using standard or known in vitro or in vivo assays. For example, cell lines that
proliferate in the presence of hGH (e.g., a cell line expressing the hGH receptor or a lactogenic
receptor) can be used to monitor hGH receptor binding. See, e.g., Clark, R., et aL, J. BioL Chem.
271(36):21969 (1996); Wada, et aL, MoL Endocrinol. 12:146-156 (1998); Gout, P. W., et aL
Cancer Res. 40, 2433-2436 (1980); WO 99/03887. For a non-PEGylated or PEGYlated hGH
polypeptide comprising a non-natural amino acid, the affinity of the hormone for its receptor can
be measured by using a BIAcore™ biosensor (Pharmacia). See, e.g., U.S. Patent No. 5,849,535;
Spencer, S. A., et al., J. BioL Chem., 263:7862-7867 (1988). In vivo animal models for testing
hGH activity include those described in, e.g., Clark et aL, J. BioL Chem. 271(36):21969-21977
(1996). Assays for dimerization capability of hGH polypeptides comprising one or more non-
naturally encoded amino acids can be conducted as described in Cunningham, B., et aL, Science,
254:821-825 (1991) and Fuh, G., et aL, Science, 256:1677-1680 (1992). All references and
patents cited are incorporated by reference herein.

[587] The compilation of references for assay methodologies is not exhaustive, and those
of ordinary skill in the art will recognize other assays useful for testing for the desired end result.
XU1. Measurement of Potency, Functional In Vivo Half-Life, and Pharmacokinetic
Parameters
[588J An important aspect of the invention is the prolonged biological half-life that is
obtained by construction of the hGH polypeptide with or without conjugation of the polypeptide to a water soluble polymer moiety. The rapid decrease of hGH polypeptide serum concentrations has made it important to evaluate biological responses to treatment with conjugated and non-conjugated hGH polypeptide and variants thereof. The conjugated and non-conjugated hGH polypeptide and variants thereof of the present invention may have prolonged serum half-lives also after subcutaneous or i.v. administration, making it possible to measure by, e.g. ELISA method or by a primary screening assay. ELISA or RIA kits from either BioSource International (Camarillo, CA) or Diagnostic Systems Laboratories (Webster, TX) may be used. Measurement of in vivo biological half-life is carried out as described herein.
[589] The potency and functional in vivo half-life of an hGH polypeptide comprising a
non-naturally encoded amino acid can be determined according to the protocol described in Clark, R., etal, 1 Biol Chem. 271(36):21969-21977 (1996).
[590] Pharmacokinetic parameters for a hGH polypeptide comprising a non-naturally
encoded amino acid can be evaluated in normal Sprague-Dawley male rats (N=5 animals per treatment group). Animals will receive either a single dose of 25 ug/rat iv or 50 ug/rat sc, and approximately 5-7 blood samples will be taken according to a pre-defined time course, generally covering about 6 hours for a GH, e.g., hGH polypeptide comprising a non-naturally encoded amino acid not conjugated to a water soluble polymer and about 4 days for a GH, e.g., hGH polypeptide comprising a non-naturally encoded amino acid and conjugated to a water soluble polymer. Pharmacokinetic data for GH, e.g., hGH polypeptides is well-studied in several species and can be compared directly to the data obtained for GH, e.g., hGH polypeptides comprising a non-naturally encoded amino acid. See Mordenti J., et al, Pharm. Res. 8(11):1351-59 (1991) for studies related to GH, e.g., hGH.
[591] Pharmacokinetic parameters can also be evaluated in a primate, e.g., cynomolgus
monkeys. Typically, a single injection is administered either subcutaneously or intravenously, and serum GH, e.g., hGH, levels are monitored over time. See, e.g., Examples, for further description.

[592] In some embodiments, the invention provides a GH, e.g., hGH, having an average
serum half-life of at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 4, 15, 16, or more than 16 hours when administered to a mammal subcutaneously. In some embodiments, the invention provides a GH, e.g., hGH, having an average serum half-life of at least about 0.25, 0.5, 0.75, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more than 12 hours when administered to a mammal subcutaneously. An "average" serum half-life is the mean of at least three animals, or at least four animals, or at least five animals, or more than five animals. The mammal is, in some embodiments, is a rat; in some embodiments, the mammal is a primate, such as a cynomolgus monkey, or such as a human. In some embodiments, the invention provides a PEGylated GH, e.g., a PEGylated hGH, that has an average serum half-life in a mammal that is at least about 2-, 3-, 4-, 5_, 6-, 7-, 8-, 9-, 10-, 11-, 12-, 13-, 14-, 15- 16- 17- 18-, 19-, 20-, 21-, 22-, 23-, 24-, 25-, 30-, 35-, 40-, 45-, 50-fold, or more than 50-fold the average serum half-life of the GH, e.g., hGH, in its non-PEGylated form, when administered subcutaneously. In some embodiments, the invention provides a PEGylated GH, e.g., a PEGylated hGH, that has an average serum half-life in a mammal that is at least about 2-, 3-, 4-, 5-, 6-, 7-, 8-, 9-, 10-, 11-, 12-, 13-, 14-, 15- 16- 17- 18-, 19-, 20-, 21-, 22-, 23-, 24-, 25-, 30-, 35-, 40-, 45-, 50-fold, or more than 50-fold the average serum half-life of the GH, e.g., hGH, in its non-PEGylated form, when administered intravenously. An "average" serum half-life is the mean of at least three animals, or at least four animals, or at least five animals, or more than five animals. The mammal is, in some embodiments, is a rat; in some embodiments, the mammal is a primate, such as a cynomolgus monkey, or such as a human. In some embodiments, the GH is a GH, e.g., hGH. In some embodiments, the growth hormone is linked by a covalent bond to at least one water-soluble polymer, where the covalent bond is an oxime bond. The GH can be a GH, e.g., hGH. In some embodiments, the GH, e.g., hGH, includes a non-naturally encoded amino acid, such as a carbonyl-containing non-naturally encoded amino acid. In some embodiments, the non-naturally encoded amino acid is a ketone-containing amino acid, e.g., para-acetylphenylalanine. In some embodiments, the GH, e.g., hGH, contains a non-naturally encoded amino acid, e.g., para-acetylphenylalanine, substituted at a position in the GH, e.g., hGH corresponding to amino acid 35 in SEQ ID NO: 2. The water-soluble polymer may be a PEG. Suitable PEGs include linear and branched PEGs; any PEG described herein may be used. In certain embodiments, the PEG is a linear PEG of about 0.1-100 kDa, or about 1-100 kDa, or about 10-50 kDa, or about 20-40 kDa, or about 30 kDa. In some embodiments, the

pharmaceutical composition contains a GH, e.g., hGH, linked to a 30 kDa PEG by an oxime bond, where the oxime bond is between a para-acetylphenylalanine in the GH located at a position corresponding to amino acid 35 in SEQ ID NO: 2 and the PEG.
[593J The specific activity of GH, e.g., hGH polypeptides in accordance with this
invention can be determined by various assays known in (he art. The biological activity of fee GH, e.g., hGH polypeptide muteins, or fragments thereof, obtained and purified in accordance with this invention can be tested by methods described or referenced herein or known to those of ordinary skill in the art.
XTV. Administration and Pharmaceutical Compositions
[594] The polypeptides or proteins of the invention (including but not limited to, GH,
e.g., hGH, synthetases, proteins comprising one or more unnatural amino acid, etc.) are optionally employed for therapeutic uses, including but not limited to, in combination with a suitable * pharmaceutical carrier. Such compositions, for example, comprise a therapeutically effective amount of the compound, and a pharmaceutical^ acceptable carrier or excipient. Such a carrier or excipient includes, but is not limited to, saline, buffered saline, dextrose, water, glycerol, ethanol, and/or combinations thereof. The formulation is made to suit the mode of administration. In general, methods of administering proteins are known to those of ordinary skill in the art and can be applied to administration of the polypeptides of the invention.
[595] In some embodiments, the invention provides a pharmaceutical composition that
contains a hormone composition comprising a growth hormone linked by a covalent bond to at least one water-soluble polymer, where the covalent bond is an oxime bond; and a pharmaceutically acceptable excipient The GH can be a hGH. In some embodiments, the GH, e.g., hGH, includes a non-naturally encoded amino acid, such as a carbonyl-containing non-naturally encoded amino acid. In some embodiments, the non-naturally encoded amino acid is a ketone-containing amino acid, e.g., para-acetylphenylalanine. In some embodiments, the GH, e.g., hGH, contains a non-naturally encoded amino acid, e.g., para-acetylphenylalanine, substituted at a position in the GH, e.g., hGH corresponding to amino acid 35 in SEQ ID NO: 2. The water-soluble polymer may be a PEG. Suitable PEGs include linear and branched PEGs; any PEG described herein may be used. In certain embodiments, the PEG is a linear PEG of about 0.1-100 kDa, or about 1-100 kDa, or about 10-50 kDa, or about 20-40 kDa, or about 30 kDa. In some embodiments, the pharmaceutical composition contains a GH, e.g., a GH, e.g., hGH, linked to a 30

kDa PEG by an oxirae bond, where the oxime bond is between a para-acetylphenylalanine in the GH located at a position corresponding to amino acid 35 in SEQ ID NO: 2 and the PEG.
[596] Therapeutic compositions comprising one or more polypeptide of the invention are
optionally tested in one or more appropriate in vitro and/or in vivo animal models of disease, to confirm efficacy, tissue metabolism, and to estimate dosages, according to methods known to those of ordinary skill in the art. In particular, dosages can be initially determined by activity, stability or other suitable measures of unnatural herein to natural amino acid homologies (including but not limited to, comparison of a GH, e.g., hGH polypeptide modified to include one or more unnatural amino acids to a natural amino acid GH, e.g., hGH polypeptide), i.e., in a relevant assay.
[597] Administration is by any of the routes normally used for introducing a molecule
into ultimate contact with blood or tissue cells. The unnatural amino acid polypeptides of the invention are administered in any suitable manner, optionally with one or more pharmaceutically acceptable carriers. Suitable methods of administering such polypeptides in the context of the present invention to a patient are available, and, although more than one route can be used to administer a particular composition, a particular route can often provide a more immediate and more effective action or reaction than another route.
[598] Pharmaceutically acceptable carriers are determined in part by the particular
composition being administered, as well as by the particular method used to administer the composition. Accordingly, there is a wide variety of suitable formulations of pharmaceutical compositions of the present invention.
[599] hGH polypeptides of the invention, including but not limited to PEGylated hGH,
may be administered by any conventional route suitable for proteins or peptides, including, but not limited to parenterally, e.g. injections including, but not limited to, subcutaneously or intravenously or any other form of injections or infusions. Polypeptide compositions can be administered by a number of routes including, but not limited to oral, intravenous, intraperitoneal, intramuscular, transdermal, subcutaneous, topical, sublingual, or rectal means. Compositions comprising non-natural amino acid polypeptides, modified or unmodified, can also be administered via liposomes. Such administration routes and appropriate formulations are generally known to those of skill in the art. The hGH polypeptide comprising a non-naturally

encoded amino acid, including but not limited to PEGylated hGH, may be used alone or in combination with other suitable components such as a pharmaceutical carrier.
[600] The GH, e.g., hGH polypeptide comprising a non-natural amino acid, alone or in
combination with other suitable components, can also be made into aerosol formulations (i.e., they can be '^nebulized") to be administered via inhalation. Aerosol formulations can be placed into pressurized acceptable propellants, such as dichlorodifluoromethane, propane, nitrogen, and the like.
[601J Formulations suitable for parenteral administration, such as, for example, by
intraarticular (in the j oints), intravenous, intramuscular, intradermal, intraperitoneal, and subcutaneous routes, include aqueous and non-aqueous, isotonic sterile injection solutions, which can contain antioxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient, and aqueous and non-aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives. The formulations of hGH can be presented in unit-dose or multi-dose sealed containers, such as ampules and vials.
[602] Parenteral administration and intravenous administration are preferred methods of
administration. In particular, the routes of administration already in use for natural amino acid homologue therapeutics (including but not limited to, those typically used for EPO, GH, G-CSF, GM-CSF, IFNs, interleukins, antibodies, and/or any other pharmaceutical^ delivered protein), along with formulations in current use, provide preferred routes of administration and formulation for the polypeptides of the invention.
[603] The dose administered to a patient, in the context of the present invention, is
sufficient to have a beneficial therapeutic response in the patient over time, or other appropriate activity, depending on the application. The dose is determined by the efficacy of the particular vector, or formulation, and the activity, stability or serum half-life of the unnatural amino acid polypeptide employed and the condition of the patient, as well as the body weight or surface area of the patient to be treated. The size of the dose is also determined by the existence, nature, and extent of any adverse side-effects that accompany the administration of a particular vector, formulation, or the like in a particular patient.

[604] In determining the effective amount of the vector or formulation to be administered
in the treatment or prophylaxis of disease (including but not limited to, cancers, inherited diseases, diabetes, AIDS, or the like), the physician evaluates circulating plasma levels, formulation toxicities; progression of the disease, and/or where relevant, the production of anti- unnatural amino acid polypeptide antibodies.
[605J The dose administered, for example, to a 70 kilogram patient, is typically in the
range equivalent to dosages of currently-used therapeutic proteins, adjusted for the altered activity or serum half-life of the relevant composition. The vectors or pharmaceutical formulations of this invention can supplement treatment conditions by any known conventional therapy, including antibody administration, vaccine administration, administration of cytotoxic agents, natural amino acid polypeptides, nucleic acids, nucleotide analogues, biologic response modifiers, and the like.
[606] For administration, formulations of the present invention are administered at a rate
determined by the LD-50 or ED-50 of the relevant formulation, and/or observation of any side-effects of the unnatural amino acid polypeptides at various concentrations, including but not limited to, as applied to the mass and overall health of the patient. Administration can be accomplished via single or divided doses.
[607] If a patient undergoing infusion of a formulation develops fevers, chills, or muscle
aches, he/she receives the appropriate dose of aspirin, ibuprofen, acetaminophen or other pain/fever controlling drug. Patients who experience reactions to the infusion such as fever, ■ muscle aches, and chills are premedicated 30 minutes prior to the future infusions with either aspirin, acetaminophen, or, including but not limited to, diphenhydramine. Meperidine is used for more severe chills and muscle aches that do not quickly respond to antipyretics and antihistamines. Cell infusion is slowed or discontinued depending upon the severity of the reaction.
[608] Human GH polypeptides of the invention can be administered directly to a
mammalian subject. Administration is by any of the routes normally used for introducing hGH polypeptide to a subject. The hGH polypeptide compositions according to embodiments of the present invention include those suitable for oral, rectal, topical, inhalation (including but not limited to, via an aerosol), buccal (including but not limited to, sub-lingual), vaginal, parenteral (including but not limited to, subcutaneous, intramuscular, intradermal, intraarticular, intrapleural,

intraperitoneal, inracerebral, intraarterial, or intravenous), topical (i.e., both skin and mucosal surfaces, including airway surfaces) and transdermal administration, although the most suitable route in any given case will depend on the nature and severity of the condition being treated. Administration can be either local or systemic. The formulations of compounds can be presented in unit-dose or multi-dose sealed containers, such as ampoules and vials. GH, e.g., hGH polypeptides of the invention can be prepared in a mixture in a unit dosage injectable form (including but not limited to, solution, suspension, or emulsion) with a pharmaceutically acceptable carrier. GH, e.g., hGH polypeptides of the invention can also be administered by continuous infusion (using, including but not limited to, minipumps such as osmotic pumps), single bolus or slow-release depot formulations.
[609] Formulations suitable for administration include aqueous and non-aqueous
solutions, isotonic sterile solutions, which can contain antioxidants, buffers, bacteriostats, and ' solutes that render the formulation isotonic, and aqueous and non-aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives. Solutions and suspensions can be prepared from sterile powders, granules, and tablets of the kind previously described.
[610] Freeze-drying is a commonly employed technique for presenting proteins which
serves to remove water from the protein preparation of interest. Freeze-drying, or lyophilization, is a process by which the material to be dried is first frozen and then the ice or frozen solvent is removed by sublimation in a vacuum environment. An excipient may be included in pre-lyophilized formulations to enhance stability during the freeze-drying process and/or to improve stability of the lyophilized product upon storage. Pikal, M. Biopharm. 3(9)26-30 (1990) and Arakawa et al. Pharm. Res. 8(3):285-291 (1991).
[611] The spray drying of pharmaceuticals is also known to those of Ordinary skill in the
art. For example, see Broadhead, J. et al., 'The Spray Drying of Pharmaceuticals," in Drug Dev. Ind. Pharm, 18 (11 & 12), 1169-1206 (1992). In addition to small molecule pharmaceuticals, a variety of biological materials have been spray dried and these include: enzymes, sera, plasma, micro-organisms and yeasts. Spray drying is a useful technique because it can convert a liquid pharmaceutical preparation into a fine, dustless or agglomerated powder in a one-step process. The basic technique comprises the following four steps: a) atomization of the feed solution into a spray; b) spray-air contact; c) drying of fee spray; and d) separation of the dried product from the

drying air, U.S. Patent Nos. 6,235,710 and 6,001,800, which are incorporated by reference herein, describe the preparation of recombinant erythropoietin by spray drying.
[612] The pharmaceutical compositions of the invention may comprise a pharmaceutically
acceptable carrier, excipient, or stabilizer. Pharmaceutically acceptable carriers are determined in part by the particular composition being administered, as well as by the particular method used to administer the composition. Accordingly, there is a wide variety of suitable formulations of pharmaceutical compositions (including optional pharmaceutically acceptable carriers, excipients, or stabilizers) of the present invention (see, e.g., Remington's Pharmaceutical Sciences, 17 ed. 1985)). [613]
[614] Suitable carriers include buffers containing succinate, phosphate, borate, HEPES,
citrate, histidine or histidine derivatives, imidazole, acetate, bicarbonate, and other organic acids; antioxidants including but not limited to, ascorbic acid; low molecular weight polypeptides including but not limited to those less than about 10 residues; proteins, including but not limited to, serum albumin, gelatin, or immunoglobulins; hydrophilic polymers including but not limited to, polyvinylpyrrolidone; amino acids including but not limited to, glycine, glutamine, asparagine, arginine, histidine or histidine derivatives, methionine, glutamate, or lysine; monosaccharides, disaccharides, and other carbohydrates, including but not limited to, trehalose, sucrose, glucose, mannose, or dextrins; chelating agents including but not limited to, EDTA; divalent metal ions including but not limited to, zinc, cobalt, or copper; sugar alcohols including but not limited to, mannitol or sorbitol; salt-forming counter ions including but not limited to, sodium; and/or nonionic surfactants including but not limited to, Tween™ (including but not limited to, Tween 80 (polysorbate 80) and Tween 20 (polysorbate 20), Pluronics™ and other pluronic acids, including but not limited to, and other pluronic acids, including but not limited to, pluronic acid F68 (poloxamer 188), or PEG. Suitable surfactants include for example but are not limited to polyethers based upon poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide), i.e., (PEO-PPO-PEO), or poly(propylene oxide)-poly(ethylene oxide)-poly(propylene oxide), i.e., (PPO-PEO-PPO), or a combination thereof. PEO-PPO-PEO and PPO-PEO-PPO are commercially available under the trade names Pluronics , R-Pluronics , Tetronics and R-Tetronics (BASF Wyandotte Corp., Wyandotte, Mich.) and are further described in U.S. Pat. No. 4,820,352 incorporated herein in its entirety by reference. Other ethylene/polypropylene block polymers

may be suitable surfactants. A surfactant or a combination of surfactants may be used to stabilize PEGylated hGH against one or more stresses including but not limited to stress that results from agitation. Some of the above may be referred to as tcbulking agents." Some may also be referred to as "tonicity modifiers."
[615] GH, e.g., hGH polypeptides of the invention, including those linked to water soluble
polymers such as PEG can also be administered by or as part of sustained-release systems. Sustained-release compositions include, including but not limited to, semi-permeable polymer matrices in the form of shaped articles, including but not limited to, films, or microcapsules. Sustained-release matrices include from biocompatible materials such as poly(2-hydroxyethyl methacrylate) (Langer et al.9 J. Biomed. Mater. Res., 15: 267-277 (1981); Langer, Chem. Tech., 12: 98-105 (1982), ethylene vinyl acetate (Langer et al9 supra) or poly-D-(-)-3-hydroxybutyric acid (EP 133,988), polylactides (polylactic acid) (U.S. Patent No. 3,773,919; EP 58,481), polyglycolide (polymer of glycolic acid), polylactide co-glycolide (copolymers of lactic acid and glycolic acid) polyanhydrides, copolymers of L-glutamic acid and gamma-ethyl-L-glutamate (Sidman et al.9 Biopolymers, 22, 547-556 (1983), poly(ortho)esters, polypeptides, hyaluronic acid, collagen, chondroitin sulfate, carboxylic acids, fatty acids, phospholipids, polysaccharides, nucleic acids, polyamino acids, amino acids such as phenylalanine, tyrosine, isoleucine, polynucleotides, polyvinyl propylene, polyvinylpyrrolidone and silicone. Sustained-release compositions also include a liposomally entrapped compound. Liposomes containing the compound are prepared by methods known per se: DE 3,218,121; Eppstein et al9 Proc. Natl Acad. Sci. U.S.A.9 82: 3688-3692 (1985); Hwang et al.9 Proc. Natl Acad. Sci. U.S.A., 77: 4030-4034 (1980); EP 52,322; EP 36,676; U.S. Patent No. 4,619,794; EP 143,949; U.S. Patent No. 5,021,234; Japanese Pat. Appln. 83-118008; U.S. Pat Nos. 4,485,045 and 4,544,545; and EP 102,324. All references and patents cited are incorporated by reference herein.
[616] Liposomally entrapped GH, e.g., hGH polypeptides can be prepared by methods
described in, e.g., DE 3,218,121; Eppstein et aL9 Proc. Natl Acad. Sci. U.SA.9 82: 3688-3692 (1985); Hwang et al9 Proc. Natl. Acad. Sci. U.S.A.9 IT. 4030-4034 (1980); EP 52,322; EP 36,676; U.S. Patent No. 4,619,794; EP 143,949; U.S. Patent No. 5,021,234; Japanese Pat. Appln. 83-118008; U.S. Patent Nos. 4,485,045 and 4,544,545; and EP 102,324. Composition and size of liposomes are well known or able to be readily determined empirically by one of ordinary skill in the art Some examples of liposomes as described in, e.g., Park JW, et al.9 Proc. Natl. Acad. Set

USA 92:1327-1331 (1995); Lasic D and Papahadjopoulos D (eds): MEDICAL APPLICATIONS OF LIPOSOMES (1998); Drummond DC, et al, Liposomal drug delivery systems for cancer therapy, in Teicher B (ed): CANCER DRUG DISCOVERY AND DEVELOPMENT (2002); Park JW, et al9 Clin. Cancer Res. 8:1172-1181 (2002); Nielsen UB, et al, Biochim. Biophys. Acta 1591(1-3):109-118 (2002); Mamot C, et al, Cancer Res. 63: 3154-3161 (2003). All references and patents cited are incorporated by reference herein.
[617] The dose administered to a patient in the context of the present invention should be
sufficient to cause a beneficial response in the subject over time. Generally, the total pharmaceutically effective amount of the GH, e.g., hGH polypeptide of the present invention administered parenterally per dose is in the range of about 0.01 /ig/kg/day to about 100 jtig/kg, or about 0.05 mg/kg to about 1 mg/kg, of patient body weight, although this is subject to therapeutic discretion. The frequency of dosing is also subject to therapeutic discretion, and may be more frequent or less frequent than the commercially available GH, e.g., hGH polypeptide products approved for use in humans. Generally, a PEGylated GH, e.g., hGH polypeptide of the invention can be administered by any of the routes of administration described. above. In some embodiments, the invention provides a composition comprising any of the GH, e.g., hGH, described herein in a pharmaceutical composition that is sufficiently stable for the storage and dosing regimens described herein. Methods of testing stability are known in the art.
XV. Therapeutic Uses ofGH, e.g., hGH Polypeptides of the Invention
[618] The GH, e.g., hGH polypeptides of the invention are useful for treating a wide range
of disorders.
[619] The GH, e.g., hGH agonist polypeptides of the invention may be useful, for
example, for treating growth deficiency, immune disorders, and for stimulating heart function. Individuals with growth deficiencies include, e.g., individuals with Turner's Syndrome, GH» deficient individuals (including children), children who experience a slowing or retardation in their normal growth curve about 2-3 years before their growth plate closes (sometimes known as "short normal children"), and individuals where the insulin-like growth factor-I (IGF-I) response to GH has been blocked chemically (i.e., by glucocorticoid treatment) or by a natural condition such as in adult patients where the IGF-I response to GH is naturally reduced. The hGH polypeptides of the invention may be useful for treating individuals with the following conditions:

pediatric growth hormone deficiency, idiopathic short stature, adult growth hormone deficiency of childhood onset, adult growth hormone deficiency of adult onset, or secondary growth hormone deficiency. Adults diagnosed with growth hormone deficiency in adulthood may have had a pituitary tumor or radiation. Conditions including but not limited to, metabolic syndrome, head injury, obesity, osteoporosis, or depression may result in growth hormone deficiency-like symptoms in adults.
[620] An agonist GH, e.g., hGH variant may act to stimulate the immune system of a
mammal by increasing its immune function, whether the increase is due to antibody mediation or
cell mediation, and whether the immune system is endogenous to the host treated with the GH,
e.g., hGH polypeptide or is transplanted from a donor to the host recipient given the GH, e.g.,
hGH polypeptide (as in bone marrow transplants). "Immune disorders" include any condition in
which the immune system of an individual has a reduced antibody or cellular response to antigens
than normal, including those individuals with small spleens with reduced immunity due to drug
(e.g., chemotherapeutic) treatments. Examples individuals with immune disorders include, e.g.,
elderly patients, individuals undergoing chemotherapy or radiation therapy, individuals recovering
from a major illness, or about to undergo surgery, individuals with AIDS, Patients with congenital
and acquired B-cell deficiencies such as hypogammaglobulinemia, common varied
agammaglobulinemia, and selective immunoglobulin deficiencies (e.g., IgA deficiency, patients
infected with a virus such as rabies with an incubation time shorter than die immune response of
the patient; and individuals with hereditary disorders such as diGeorge syndrome.
[621] GH, e.g., hGH antagonist polypeptides of the invention may be useful for the
treatment of gigantism and acromegaly, diabetes and complications (diabetic retinopathy, diabetic neuropathy) arising from diabetes, vascular eye diseases (e.g., involving proliferative neovascularization), nephropathy, and GH-responsive malignancies.
[622] Vascular eye diseases include, e.g., retinopathy (caused by, e.g., pre-maturity or
sickle cell anemia) and macular degeneration.
[623] GH-responsive malignancies include, e.g., Wilm's tumor, sarcomas (e.g., osteogenic
sarcoma), breast, colon, prostate, and thyroid cancer, and cancers of tissues that express GH receptor mRNA (i.e., placenta, thymus, brain, salivary gland, prostate, bone marrow, skeletal muscle, trachea, spinal cord, retina, lymph node and from Burkitt's lymphoma, colorectal carcinoma, lung carcinoma, lymphoblastic leukemia, and melanoma).

[624] The GH, e.g., hGH agonist polypeptides of the invention may be useful, for
example, for treating chronic renal failure, growth failure associated with chronic renal insufficiency (CRI), short stature associated with Turner Syndrome, pediatric Prader-Willi Syndrome (PWS), HIV patients with wasting or cachexia, children bom small for gestational age (SGA), obesity, and osteoporosis.
[625] Average quantities of the GH, e.g., hGH may vary and in particular should be based
upon the recommendations and prescription of a qualified physician. The exact amount of GH, e.g., hGH is a matter of preference subject to such factors as the exact type of condition being treated, the condition of the patient being treated, as well as the other ingredients in the composition .The invention also provides for administration of a therapeutically effective amount of another active agent. The amount to be given may be readily determined by one of ordinary skill in the art based upon therapy with hGH.
[626] Pharmaceutical compositions of the invention may be manufactured in a
conventional manner.
[627] In some embodiments the invention provides a method of treatment that includes
administering to an individual in need of treatment an effective amount of a hormone composition comprising a growth hormone (GH) linked by covalent bond(s) to at least one water-soluble polymer, wherein the covalent bond(s) is an oxime bond. In some embodiments, the methods include administering to the individual, e.g., human, a GH, e.g., hGH. In some embodiments, the GH, e.g., hGH, includes a non-naturally encoded amino acid, such as a carbonyl-containing non-naturally encoded amino acid. In some embodiments, the non-naturally encoded amino acid is a ketone-containing amino acid, e.g., para-acetylphenylalanine. In some embodiments, the GH, e.g., hGH, contains a non-naturally encoded amino acid, e.g., para-acetylphenylalanine, substituted at a position in the GH, e.g., hGH corresponding to amino acid 35 in SEQ ID NO: 2. The water-soluble polymer may be a PEG. Suitable PEGs include linear and branched PEGs; any PEG described herein may be used. In certain embodiments, the PEG is a linear PEG of about 0.1-100 kDa, or about 1-100 kDa, or about 10-50 kDa, or about 20-40 kDa, or about 30 kDa. In some embodiments, the pharmaceutical composition contains a GH, e.g., a GH, e.g., hGH, linked to a 30 kDa PEG by an oxime bond, where the oxime bond is between a para-acetylphenylalanine in the GH located at a position corresponding to amino acid 35 in SEQ ID NO: 2 and the PEG. In some embodiments, the individual who is treated suffers from pediatric growth hormone deficiency,

idiopathic short stature, adult growth hormone deficiency of childhood onset, adult growth hormone deficiency of adult onset, or secondary growth hormone deficiency.
[628] The GH, e.g., hGH, can be administered to the individual in any suitable form
route, dose, frequency, and duration, as described herein and as known in the art. In some embodiments, the invention provides a method of treatment that includes administering to an individual in need of treatment an effective amount of a hormone composition comprising a growth hormone (GH) linked by covalent bond(s) to at least one water-soluble polymer, wherein the water-soluble polymer is a linear polymer, and wherein the hormone composition is given at a frequency of no more than about once every other day, once every 3, 4, 5, or 6 days, once per week, once per every 8, 9, 10, 11,12, or 13 days, once per two weeks, once per every 15, 16, 17, 18, 19, or 20 days, once per three weeks, once per 22, 23, 24, 25, 26,27,28, 29, or 30 days, once per month, or less than about once per month. It will be appreciated that frequency of administration may be altered at the discretion of the individual or, more typically, the treating professional, and that any combination of frequencies may be used. In some embodiments, the GH composition is administered no more that about once per week, once per two weeks, once per three weeks, or once per month. In some embodiments, the GH composition is administered no more that about once per week, once per two weeks, or once per month. In some embodiments, the GH composition is administered no more that about once per week. In some embodiments, the GH composition is administered no more that about once per two weeks. In some embodiments, the GH composition is administered no more that about once per month.
{629] The invention also provides for administration of a therapeutically effective amount
of another active agent along with hGH of the present invention. The amount to be given may be
readily determined by one of ordinary skill in the art based upon therapy with hGH.
[630] Pharmaceutical compositions of the invention may be manufactured in
conventional manner.
EXAMPLES
[631] The following examples are offered to illustrate, but not to limit the claimed
invention.

Example 1
[632] This example describes one of the many potential sets of criteria for the selection of
preferred sites of incorporation of non-naturally encoded amino acids into hGH.
[633] This example demonstrates how preferred sites within the hGH polypeptide were
selected for introduction of a non-naturally encoded amino acid. The crystal structure 3HHR, composed of hGH complexed with two molecules of the extracellular domain of receptor (hGHbp), was used to determine preferred positions into which one or more non-naturally encoded amino acids could be introduced- Other hGH structures (e.g. 1AXT) were utilized to examine potential variation of primary and secondary structural elements between crystal structure datasets. The coordinates for these structures are available from the Protein Data Bank (PDB) (Bernstein et al. X Mol Biol. 1997, 112, pp 535) or via The Research Collaborator/ for Structural Bioinformatics PDB available on the World Wide Web at rcsb.org. The structural model 3HHR contains the entire mature 22 kDa sequence of hGH with the exception of residues 148 - 153 and the C-terminal F191 residue which were omitted due to disorder in the crystal. Two disulfide bridges are present, formed by C53 and C165 and C182 and C185. Sequence numbering used in this example is according to the amino acid sequence of mature hGH (22 kDa variant) shown in SEQ ID N0:2.
[634] The following criteria were used to evaluate each position of hGH for the
introduction of a non-naturally encoded amino acid: the residue (a) should not interfere with binding of either hGHbp based on structural analysis of 3HHR, 1AXI, and 1HWG (crystallographic structures of hGH conjugated with hGHbp monomer or dimer), b) should not be affected by alanine or homolog scanning mutagenesis (Cunningham et al. Science (1989) 244:1081-1085 and Cunningham et al. Science (1989) 243:1330-1336), (c) should be surface exposed and exhibit minimal van der Waals or hydrogen bonding interactions with surrounding residues, (d) should be either deleted or variable in hGH variants (e.g. Tyr35, Lys38, Phe92, Lysl40), (e) would result in conservative changes upon substitution with a non-naturally encoded amino acid and (f) could be found in either highly flexible regions (including but not limited to CD loop) or structurally rigid regions (including but not limited to Helix B). In addition, further calculations were performed on the hGH molecule, utilizing the Cx program (Pintar et al. (2002) Bioinformatics, 18, pp 980) to evaluate the extent of protrusion for each protein atom. As a result,

in some embodiments, one or more non-naturally encoded encoded amino acids are incorporated at, but not limited to, one or more of the following positions of hGH: before position 1 (i.e. at the N-terminus), 1, 2, 3,4, 5, 8, 9,11, 12, 15,16, 19, 22, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44,45, 46, 47, 48, 49, 52, 55, 57, 59, 65, 66, 69, 70, 71, 74, 88, 91, 92, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 111, 112, 113, 115, 116, 119, 120, 122, 123, 126, 127, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 159, 161, 168, 172, 183, 184, 185, 186,187, 188, 189, 190, 191,192 (i.e., at the carboxyl terminus of the protein) (SEQ ID NO: 2 or the corresponding amino acids in SEQ ID NO: 1 or 3).
[635] In some embodiments, one or more non-naturally encoded amino acids are
substituted at one or more of the following positions: 29, 30, 33, 34, 35, 37, 39, 40, 49, 57, 59, 66, 69, 70, 71, 74, 88, 91, 92, 94, 95, 98, 99, 101, 103, 107, 108, 111, 122, 126, 129, 130, 131, 133, 134, 135, 136, 137, 139, 140, 141, 142, 143, 145, 147, 154, 155, 156, 159, 183, 186, and 187 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3).
[636] In some embodiments, one or more non-naturally encoded amino acids are
substituted at one or more of the following positions: 29, 33, 35, 37, 39,49, 57, 69, 70, 71,74, 88, 91, 92, 94, 95, 98, 99, 101, 103, 107, 108, 111, 129, 130, 131, 133, 134, 135, 136, 137, 139, 140, 141, 142, 143, 145, 147, 154, 155, 156, 186, and 187 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3).
[637] In some embodiments, one or more non-naturally encoded amino acids are
substituted at one or more of the following positions: 35, 88, 91, 92, 94, 95, 99, 101, 103, 111, 131, 133, 134, 135, 136, 139, 140, 143, 145, and 155 (SEQ ID NO: 2 or the corresponding amino acidsofSEQIDNO:lor3).
[638] In some embodiments, one or more non-naturally encoded amino acids are
substituted at one or more of the following positions: 30, 74, 103 (SEQ ID NO: 2 or the
corresponding amino acids of SEQ ID NO: 1 or 3). In some embodiments, one or more non-
naturally encoded amino acids are substituted at one or more of the following positions: 35, 92,
143,145 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3).
[639] In some embodiments, the non-naturally occurring amino acid at one or more of
these positions is linked to a water soluble polymer, including but not limited to, positions: before position 1 (i.e. at the N-terminus), 1, 2, 3, 4, 5, 8, 9, 11, 12, 15, 16, 19, 22, 29, 30, 32, 33, 34, 35,

36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 55, 57, 59, 65, 66, 69, 70, 71, 74, 88, 91, 92, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 111, 112, 113, 115, 116, 119, 120, 122, 123, 126, 127, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,U44, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 158, 159, 161, 168, 172,183, 184,185,186,187,188,189,190, 191,192 (i.e., at the carboxyl terminus of the protein) (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3). In some embodiments, the non-naturally occurring amino acid at one or more of these positions is linked to a water soluble polymer, including but not limited to, positions: 29, 30, 33, 34, 35, 37, 39, 40, 49, 57, 59, 66, 69, 70, 71, 74, 88, 91, 92, 94, 95, 98, 99, 101, 103, 107, 108, 111, 122, 126, 129, 130, 131, 133,134, 135, 136, 137, 139, 140,141, 142, 143, 145,147,154, 155, 156, 159,183, 186, and 187 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3).
[640] In some embodiments, the non-naturally occurring amino acid at one or more of
these positions is linked to a water soluble polymer, including but not limited to, positions: 29, 33, 35, 37, 39, 49, 57, 69, 70, 71, 74, 88, 91, 92, 94, 95, 98, 99, 101, 103, 107, 108, 111, 129, 130, 131, 133, 134, 135, 136, 137, 139, 140, 141, 142, 143, 145, 147, 154, 155, 156, 186, and 187 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3).
[641] In some embodiments, the non-naturally occurring amino acid at one or more of
these positions is linked to a water soluble polymer, including but not limited to, positions: 35, 88, 91, 92, 94, 95, 99, 101, 103, 111, 131, 133, 134, 135, 136, 139, 140, 143, 145, and 155 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3).
[642] In some embodiments, the non-naturally occurring amino acid at one or more of
these positions is linked to a water soluble polymer, including but not limited to, positions: 30, 74, 103 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3). In some embodiments, the non-naturally occurring amino acid at one or more of these positions is linked to • a water soluble polymer 30, 35, 74,92,103,143,145 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3). In some embodiments, the non-naturally occurring amino acid at one or more of these positions is linked to a water soluble polymer: 35, 92,143,145 (SEQ ID NO: 2 or the corresponding amino acids of SEQ ID NO: 1 or 3).
[643] Some sites for generation of an hGH antagonist include: 1, 2, 3, 4, 5, 8, 9, 11, 12,
15, 16, 19,22, 103, 109, 112, 113, 115, 116, 119, 120, 123, 127, or an addition before position 1, or any combination thereof (SEQ ID NO: 2, or the corresponding amino acid in SEQ ID NO: 1, 3,

or any other GH sequence). These sites were chosen utilizing criteria (c) - (e) of the agonist design. The antagonist design may also include site-directed modifications of site I residues to increase binding affinity to hGHbp.
Example 2
[644] This example details cloning and expression of a hGH polypeptide including a non-
naturally encoded amino acid in E. colL This example also describes one method to assess the
biological activity of modified hGH polypeptides.
[645] Methods for cloning hGH and fragments thereof are detailed in U.S. Patent Nos,
4,601,980; 4,604,359; 4,634,677; 4,658,021; 4,898;830; 5,424,199; and 5,795,745, which are
incorporated by reference herein. cDNA encoding the full length hGH or the mature form of hGH
lacking the N-terminal signal sequence are shown in SEQ ID NO: 21 and SEQ ID NO: 22
respectively.
[646] An introduced translation system that comprises an orthogonal tRNA (O-tRNA)
and an orthogonal aminoacyl tRNA synthetase (O-RS) is used to express hGH containing a non-
naturally encoded amino acid. The O-RS preferentially aminoacylates the O-tRNA with a non-
naturally encoded amino acid. In turn the translation system inserts the non-naturally encoded
amino acid into hGH, in response to an encoded selector codon.
Table 2: O-RS and O-tRNA sequences.



[6471 The transformation of E. coli with plasmids containing the modified hGH gene and
the orthogonal aminoacyl tRNA synthetase/tRNA pair (specific for the desired non-naturally encoded amino acid) allows the site-specific incorporation of non-naturally encoded amino acid into the hGH polypeptide. The transformed E. coli, grown at 37° C in media containing between 0.01 - 100 mM of the particular non-naturally encoded amino acid, expresses modified hGH with high fidelity and efficiency. The His-tagged hGH containing a non-naturally encoded amino acid is produced by the E- coli host cells as inclusion bodies or aggregates. The aggregates are solubilized and affinity purified under denaturing conditions in 6M guanidine HC1. Refolding is performed by dialysis at 4*C overnight in 50mM TRIS-HC1, pH8.0, 40/iM CuS04, and 2% (w/v) Sarkosyl. The material is then dialyzed against 20mM TRIS-HC1, pH 8.0, lOOmM NaCl, 2mM CaCl2, followed by removal of the His-tag. See Boissel et al., (1993) J. Bio. Chem. 268:15983-93. Methods for purification of hGH are known to those of ordinary skill in the art and are confirmed by SDS-PAGE, Western Blot analyses, or electrospray-ionization ion trap mass spectrometry and the like.
[648] Figure 6 is an SDS-PAGE of purified hGH polypeptides. The His-tagged mutant
hGH proteins ware purified using the ProBond Nickel-Chelating Resin (Invitrogen, Carlsbad, CA) via the standard His-tagged protein purification procedures provided by the manufacturer, followed by an anion exchange column prior to loading on the gel. Lane 1 shows the molecular weight marker, and lane 2 represents N-Hfis hGH without incorporation of a non-natural amino acid. Lanes 3-10 contain N-His hGH mutants comprising the non-natural amino acid p-acetyl-phenylalanine at each of the positions Y35, F92, Ylll, G131, R134, K140, Y143, and K145, respectively.
[649] To further assess the biological activity of modified hGH polypeptides, an assay
measuring a downstream marker of hGH's interaction with its receptor was used. The interaction of hGH with its endogenously produced receptor leads to the tyrosine phosphorylation of a signal

transducer and activator of transcription family member, STAT5, in the human IM-9 lymphocyte cell line. Two forms of STAT5, STAT5A and STAT5B were identified from an IM-9 cDNA library. See, e.g., Silva et al., Mol. Endocrinol. (1996) 10(5):508-518. The human growth hormone receptor on IM-9 cells is selective for human growth hormone as neither rat growth hormone nor human prolactin resulted in detectable STAT5 phosphorylation. Importantly, rat GHR (L43R) extra cellular domain and the G120R bearing hGH compete effectively against hGH stimulated pSTAT5 phoshorylation.
[650J IM-9 cells were stimulated with hGH polypeptides of the present invention. The
human IM-9 lymphocytes were purchased from ATCC (Manassas, VA) and grown in RPMI1640 supplemented with sodium pyruvate, penicillin, streptomycin (Invitrogen, Carlsbad, San Diego) and 10% heat inactivated fetal calf serum (Hyclone, Logan, UT). The IM-9 cells were starved overnight in assay media (phenol-red free RPMI, 1 OmM Hepes, 1 % heat inactivated charcoal/dextran treated FBS, sodium pyruvate, penicillin and streptomycin) before stimulation with a 12-point dose range of hGH polypeptides for 10 min at 37°C. Stimulated cells were fixed with 1% formaldehyde before permeabilization with 90% ice-cold methanol for 1 hour on ice. The level of STATS phosphorylation was detected by intra-cellular staining with a primary phospho-STAT5 antibody (Cell Signaling Technology, Beverly, MA) at room temperature for 30 min followed by a PE-conjugated secondary antibody. Sample acquisition was performed on the FACS Array with acquired data analyzed on the Flowjo software (Tree Star Inc., Ashland, OR). EC50 values were derived from dose response curves plotted with mean fluorescent intensity (MFI) against protein concentration utilizing SigmaPlot
[651J Table 3 below summarizes the IM-9 data generated with mutant hGH polypeptides.
Various hGH polypeptides with a non-natural amino acid substitution at different positions were tested with human IM-9 cells as described. Specifically, Figure 7, Panel A shows the IM-9 data for a His-tagged hGH polypeptide, and Figure 7, Panel B shows the IM-9 data for His-tagged hGH comprising the non-natural amino acid p-acetyl-phenylalanine substitution for Y143. The same assay was used to assess biological activity of hGH polypeptides comprising a non-natural amino acid that is PEGylated.



Example 3
[652] This example details introduction of a carbonyl-containing amino acid and
subsequent reaction with an aminooxy-containing PEG.
[653] This Example demonstrates a method for the generation of a hGH polypeptide that
incorporates a ketone-containing non-naturally encoded amino acid that is subsequently reacted,
with an aminooxy-containing PEG of approximately 5,000 MW. Each of the residues 35, 88, 91,
92, 94, 95, 99, 101, 103, 111, 120, 131, 133, 134, 135,136, 139, 140, 143, 145, and 155 identified
according to the criteria of Example 1 (hGH) is separately substituted with a non-naturally
encoded amino acid having the following structure:

[654] The sequences utilized for site-specific incorporation of p-acetyl-phenylalanine into
hGH are SEQ ID NO: 2 (hGH), and SEQ ID NO: 4 (muttRNA, M jannaschii mtRNA^A ), and
16,17 or 18 (TyrRS LW1,5, or 6) described in Example 2 above.
[655] Once modified, the hGH polypeptide variant comprising the carbonyl-containing
amino acid is reacted with an aminooxy-containing PEG derivative of the form:
R-PEG(N)-0-(CH2)n-0-NH2

where R is methyl, n is 3 and N is approximately 5,000 MW. The purified hGH containing p~ acetylphenylalanine dissolved at 10 mg/mL in 25 mM MES (Sigma Chemical, St. Louis, MO) pH 6.0, 25 mM Hepes (Sigma Chemical, St. Louis, MO) pH 7.0, or in 10 mM Sodium Acetate (Sigma Chemical, St. Louis, MO) pH 4.5, is reacted with a 10 to 100-fold excess of aminooxy-containing PEG, and then stirred for 10 - 16 hours at room temperature (Jencks, W. J. Am. Chern. Soc. 1959, 81, pp 475). The PEG-hGH is then diluted into appropriate buffer for immediate purification and analysis.
Example 4
[656] Conjugation with a PEG consisting of a hydroxylamine group linked to the PEG
via an amide linkage.
[657] A PEG reagent having the following structure is coupled to a ketone-containing
non-naturally encoded amino acid using the procedure described in Example 3:
R-PEG(N)-0-(CH2)2-NH-C(0)(CH2)n-0-NH2
where R = methyl, n=4 and N is approximately 20,000 MW. The reaction, purification, and
analysis conditions are as described in Example 3.
Example 5
[658] This example details the introduction of two distinct non-naturally encoded amino
acids into hGH polypeptides.
[659] This example demonstrates a method for the generation of a hGH polypeptide that
incorporates non-naturally encoded amino acid comprising a ketone functionality at two positions
among the following residues: E30, E74, Y103, K38, K41, K140, and K145. The hGH
polypeptide is prepared as described in Examples 1 and 2, except that the selector codon is
introduced at two distinct sites within the nucleic acid.
Example 6
[660] This example details conjugation of hGH polypeptide to a hydrazide-containing
PEG and subsequent in situ reduction.
[661] A hGH polypeptide incorporating a carbonyl-contahiing amino acid is prepared
according to the procedure described in Examples 2 and 3. Once modified, a hydrazide-containing
PEG having the following structure is conjugated to the hGH polypeptide:
R-PEG(N)-0-(CH2)2-NH-C(0)(CH2)n»X-NH-NH2

where R = methyl, n=2 and N = 10,000 MW and X is a carbonyl (C=0) group. The purified hGH containing p-acetylphenylalanine is dissolved at between 0.1-10 mg/mL in 25 mM MES (Sigma Chemical, St Louis, MO) pH 6.0, 25 mM Hepes (Sigma Chemical, St Louis, MO) pH 7.0, or in 10 mM Sodium Acetate (Sigma Chemical, St Louis, MO) pH 4.5, is reacted with a 1 to 100-fold excess of hydrazide-containing PEG, and the corresponding hydrazone is reduced in situ by addition of stock 1M NaCNBEb (Sigma Chemical, St Louis, MO), dissolved in EfeO, to a final concentration of 10-50 mM. Reactions are carried out in the dark at 4 °C to RT for 18-24 hours. Reactions are stopped by addition of 1 M Tris (Sigma Chemical, St Louis, MO) at about pH 7.6 to a final Tris concentration of 50 mM or diluted into appropriate buffer for immediate purification.
Example 7
[662] This example details introduction of an alkyne-containing amino acid into a hGH
polypeptide and derivatization with mPEG-azide.
[663] The following residues, 35, 88, 91, 92, 94, 95, 99, 101, 131, 133, 134, 135, 136,
140, 143, 145, and 155, are each substituted with the following non-naturally encoded amino acid
(hGH;SEQIDNO:2):

[664] The sequences utilized for site-specific incorporation of p-propargyl-tyrosine into
hGH are SEQ ID NO: 2 (hGH), SEQ ID NO: 4 (muttRNA, M. jannaschii mtRNA^A ), and 9, 10
or 11 described in Example 2 above. The hGH polypeptide containing the propargyl tyrosine is
expressed in E. coli and purified using the conditions described in Example 3.
[665] The purified hGH containing propargyl-tyrosine dissolved at between 0.1-10
mg/mL in PB buffer (100 mM sodium phosphate, 0,15 M NaCl, pH = 8) and a 10 to 1000-fold excess of an azide-containing PEG is added to the reaction mixture. A catalytic amount of Q1SO4 and Cu wire are then added to the reaction mixture. After the mixture is incubated (including but not limited to, about 4 hours at room temperature or 37° C, or overnight at 4°C), H2O is added and

the mixture is filtered through a dialysis membrane. The sample can be analyzed for the addition,
including but not limited to, by similar procedures described in Example 3.
[666] In this Example, the PEG will have the following structure:
R-PEG(N)-0-(CH2)2-NH-C(0)(CH2)n-N3
where R is methyl, n is 4 and N is 10,000 MW.
Example 8
[667] This example details substitution of a large, hydrophobic amino acid in a hGH
polypeptide with propargyl tyrosine.
[668] A Phe, Trp or Tyr residue present within one the following regions of hGH: 1-5 (N-
terminus), 6-33 (A helix), 34-74 (region between A helix and B helix, the A-B loop), 75-96 (B
helix), 97-105 (region between B helix and C helix, the B-C loop), 106-129 (C helix), 130-153
(region between C helix and D helix, the C-D loop), 154-183 (D helix), 184-191 (C-terminus)
(SEQ ID NO: 2), is substituted with the following non-naturally encoded amino acid as described
in Example 7:

[669] Once modified, a PEG is attached to the hGH polypeptide variant comprising the
alkyne-containing amino acid. The PEG will have the following structure: Me-PEG(N)-0-(CH2)2-N3
and coupling procedures would follow those in Example 7. This will generate a hGH polypeptide variant comprising a non-naturally encoded amino acid that is approximately isosteric with one of the naturally-occurring, large hydrophobic amino acids and which is modified with a PEG derivative at a distinct site within the polypeptide.
Example 9
[670] This example details generation of a hGH polypeptide homodimer, heterodimer,
homomultimer, or heteromultimer separated by one or more PEG linkers.
[671] The alkyne-containing hGH polypeptide variant produced in Example 7 is reacted
with a Afunctional PEG derivative of the form:

N3-(CH2)n-C(0)-NH-(CH2)2-0-PEG(N)-0-(CH2)2-NH-C(0)-(CH2)n-N3
where n is 4 and the PEG has an average MW of approximately 5,000, to generate the corresponding hGH polypeptide homodimer where the two hGH molecules are physically separated by PEG. I» an analogous manner a hGH polypeptide may be coupled to one or more other polypeptides to form heterodimers, homomultimers, or heteromultimers. Coupling, purification, and analyses will be performed as in Examples 7 and 3.
Example 10
[672] This example details coupling of a saccharide moiety to a hGH polypeptide.
[673] One residue of the following is substituted with the non-naturally encoded amino
acid below: 29, 30, 33, 34, 35, 37, 39, 40,49, 57, 59, 66, 69, 70, 71, 74, 88, 91, 92, 94, 95, 98, 99,
101, 103, 107, 108, 111, 122, 126, 129, 130, 131, 133, 134, 135, 136, 137, 139, 140, 141, 142,
143, 145, 147, 154, 155, 156, 159, 183, 186, and 187 (hGH, SEQ ID NO: 2) as described in
Example 3.

[674] Once modified, the hGH polypeptide variant comprising the carbonyl-containing
amino acid is reacted with a p-linked aminooxy analogue of N-acetylglucosamine (GlcNAc). The hGH polypeptide variant (10 mg/mL) and the aminooxy saccharide (21 mM) are mixed in aqueous 100 mM sodium acetate buffer (pH 5.5) and incubated at 37°C for 7 to 26 hours. A second saccharide is coupled to the first enzymatically by incubating the saccharide-conjugated hGH polypeptide (5 mg/mL) with UDP-galactose (16 mM) and p-l,4-galacytosyltransferase (0.4 units/mL) in 150 mM HEPES buffer (pH 7.4) for 48 hours at ambient temperature (Schanbacher et al. /. Biol Chem. 1970,245, 5057-5061). Example 11
[675] This example details generation of a PEGylated hGH polypeptide antagonist
[676] One of the following residues, 1, 2, 3, 4, 5, 8, 9, 11, 12, 15, 16, 19, 22, 103, 109,
112, 113,115,116, 119, 120, 123, or 127 (hGH, SEQ ID NO: 2 or the corresponding amino acids

in SEQ ID NO: 1 or 3), is substituted with the following non-naturally encoded amino acid as described in Example 3.
■ ■*■ - — *" ■
[617] Once modified, the hGH polypeptide variant comprising the carbonyl-containing
amino acid will be reacted with an aminooxy-containing PEG derivative of the form:
R-PEG(N)-0-(CH2)n-0-NH2
where R is methyl, n is 4 and N is 20,000 MW to generate a hGH polypeptide antagonist comprising a non-naturally encoded amino acid that is modified with a PEG derivative at a single site within the polypeptide. Coupling, purification, and analyses are performed as in Example 3.
Example 12
Generation of a hGH polypeptide homodimer, heterodimer, homomultimer, or heteromultimer in
which the hGH Molecules are Linked Directly
[678J A hGH polypeptide variant comprising the alkyne-containing amino acid can be
directly coupled to another hGH polypeptide variant comprising the azido-containing amino acid,
each of which comprise non-naturally encoded amino acid substitutions at the sites described in, but not limited to, Example 10. This will generate the corresponding hGH polypeptide
homodimer where the two hGH polypeptide variants are physically joined at the site II binding
interface. In an analogous manner a hGH polypeptide polypeptide may be coupled to one or more
other polypeptides to form heterodimers, homomultimers, or heteromultimers. Coupling,
purification, and analyses are performed as in Examples 3, 6, and 7.
Example 13
PEG-OH + Br-CGEfeVCsCR' -» PEG-0-(CH2VCR'
A B
[679] The polyalkylene glycol (P-OH) is reacted with the alkyl halide (A) to form the
ether (B). In these compounds, n is an integer from one to nine and R' can be a straight- or
branched-chain, saturated or unsaturated CI, to C20 alkyl or heteroalkyl group. R' can also be a
C3 to C7 saturated or unsaturated cyclic alkyl or cyclic heteroalkyl, a substituted or unsubstituted

aryl or heteroaryl group, or a substituted or unsubstituted alkaryl (the alkyl is a CI to C20
saturated or unsaturated alkyl) or heteroalkaryl group. Typically, PEG-OH is polyethylene glycol
(PEG) or monomethoxy polyethylene glycol (mPEG) having a molecular weight of 800 to 40,000
Daltons (Da).
Example 14
mPEG-OH + Br-CH2 -C^CH ^ mPEG-0-CH2-CsCH
[680] mPEG-OH with a molecular weigjrt of 20,000 Da (mPEG-OH 20 kDa; 2.0 g, 0.1
mmol, Sunbio) was treated with NaH (12 mg, 0.5 mmol) in THF (35 mL). A solution of propargyl bromide, dissolved as an 80% weight solution in xylene (0.56 mL, 5 mmol, 50 equiv., Aldrich), and a catalytic amount of KI were then added to the solution and the resulting mixture was heated to reflux for 2 hours. Water (1 mL) was then added and the solvent was removed under vacuum. To the residue was added CH2CI2 (25 mL) and the organic layer was separated, dried over anhydrous Na2SC>45 and the volume was reduced to approximately 2 mL. This CH2CI2 solution was added to diethyl ether (150 mL) drop-wise. The resulting precipitate was collected, washed with several portions of cold diethyl ether, and dried to afford propargyl-O-PEG.
Example 15
mPEG-OH + Br-(CH2)3-CsCH ^ mPEG-0-(CH2)3-OCH
[6811 The mPEG-OH with a molecular weight of 20,000 Da (mPEG-OH 20 kDa; 2.0 g,
0.1 mmol, Sunbio) was treated with NaH (12 mg, 0.5 mmol) in THF (35 mL). Fifty equivalents of 5-bromo-l-pentyne (0.53 mL, 5 mmol, Aldrich) and a catalytic amount of KI were then added to the mixture. The resulting mixture was heated to reflux for 16 hours. Water (1 mL) was then added and the solvent was removed under vacuum. To the residue was added CH2CI2 (25 mL) and the organic layer was separated, dried over anhydrous Na2SC>4, and the volume was reduced to approximately 2 mL. This CH2CI2 solution was added to diethyl ether (150 mL) drop-wise. The resulting precipitate was collected, washed with several portions of cold diethyl ether, and dried to afford the corresponding alkyne. 5-chloro-l-pentyne may be used in a similar reaction.
Example 16
(1) m-HOCH2C6H40H + NaOH + Br- CH2-OCH -> m-HOC^C^O-CHs-C^CH

(2) m-HOCH2C6H40-CH2-OCH + MsCl + N(Et) 3 -» m-MsOCHzC^O-CH^C^CH
(3) m-MsOCH2C6H40-CH2-OCH + LiBr -» m-Br-C^C^O-CH^GCH
(4) mPEG-OH + m-Br-CHzCettjO-CHrOCH -> mPEG-O-CHi-C^O-CHrCsCH
[682] To a solution of 3-hydroxybenzylalcohol (2.4 g, 20 mmol) in THF (50 mL) and
water (2.5 mL) was first added powdered sodium hydroxide (1.5 g, 37.5 mmol) and then a
solution of propargyl bromide, dissolved as an 80% weight solution in xylene (3.36 mL, 30
mmol). The reaction mixture was heated at reflux for 6 hours. To the mixture was added 10%
citric acid (2.5 mL) and the solvent was removed under vacuum. The residue was extracted with
ethyl acetate (3 x 15 mL) and the combined organic layers were washed with saturated NaCl
solution (10 mL), dried over MgSC>4 and concentrated to give the 3-propargyloxybenzyl alcohol.
1683] Methanesulfonyl chloride (2.5 g, 15.7 mmol) and triethylamine (2.8 mL, 20 mmol)
were added to a solution of compound 3 (2.0 g, 11.0 mmol) in CH2C12 at 0°C and the reaction was placed in the refrigerator for 16 hours. A usual work-up afforded the mesylate as a pale yellow oil. This oil (2.4 g, 9.2 mmol) was dissolved in THF (20 mL) and LiBr (2.0 g, 23.0 mmol) was added The reaction mixture was heated to reflux for 1 hour and was then cooled to room temperature. To the mixture was added water (2.5 mL) and the solvent was removed under vacuum. The residue was extracted with ethyl acetate (3 x 15 mL) and the combined organic layers were washed with saturated NaCl solution (10 mL), dried over anhydrous Na2SC>4, and concentrated to give the desired bromide.
[684] mPEG-OH 20 kDa (1.0 g, 0.05 mmol, Sunbio) was dissolved in THF (20 mL) and
the solution was cooled in an ice bath. NaH (6 mg, 0.25 mmol) was added with vigorous stirring over a period of several minutes followed by addition of the bromide obtained from above (2.55 g, 11.4 mmol) and a catalytic amount of KI. The cooling bath was removed and the resulting mixture was heated to reflux for 12 hours. Water (1.0 mL) was added to the mixture and the solvent was removed under vacuum. To the residue was added CH2CI2 (25 mL) and the organic layer was separated, dried over anhydrous Na2SC>4, and the volume was reduced to approximately 2 mL. Dropwise addition to an ether solution (150 mL) resulted in a white precipitate, which was collected to yield the PEG derivative.

Example 17
mPEG-NH2 + X-C(OMCM2VGCR' ^ mPEG-NH-C(OMCH2)n-C=CR'
"i"
[685] The terminal alkyne-containing poly(ethylene glycol) polymers can also be
obtained by coupling a poly(ethylene glycol) polymer containing a terminal functional group to a
reactive molecule containing the alkyne functionality as shown above, n is between 1 and 10. R'
can be H or a small alkyl group from CI to C4.
Example 18
(1) H02C-(CH2)2-OCH + NHS +DCC^ NHSO-C(0>(CH2)2-CsCH
(2) mPEG-NH2 +NHSO-C(0>(CH2)2-OCH -» mPEG-NH-C(0)-(CH2)2-OCH
[686] 4-pentynoic acid (2.943 g, 3.0 mmol) was dissolved in CH2C12 (25 mL). N-
hydroxysuccinimide (3.80 g, 3.3 mmol) and DCC (4.66 g, 3.0 mmol) were added and the solution was stirred overnight at room temperature. The resulting crude NHS ester 7 was used in the following reaction without further purification.
[687] mPEG-NH2 with a molecular weight of 5,000 Da (mPEG-NH2> 1 g, Sunbio) was '
dissolved in THF (50 mL) and the mixture was cooled to 4 °C. NHS ester 7 (400 mg, 0.4 mmol) was added portion-wise with vigorous stirring. The mixture was allowed to stir for 3 hours while warming to room temperature. Water (2 mL) was then added and the solvent was removed under ' vacuum. To the residue was added CH2C12 (50 mL) and the organic layer was separated, dried over anhydrous Na2S04, and the volume was reduced to approximately 2,mL. This CH2CI2 solution was added to ether (150 mL) drop-wise. The resulting precipitate was collected and dried in vacuo.
Example 19
[688] This Example represents the preparation of the methane sulfonyl ester of
poly(ethylene glycol), which can also be referred to as the methanesulfonate or mesylate of poly(ethylene glycol). The corresponding tosylate and the halides can be prepared by similar procedures.

mPEG-OH + CH3SO2CI + N(Et) 3 -» mPEG-0-S02CH3 -» mPEG-N3
[689] The mPEG-OH (MW = 3,400, 25 g, 10 mmol) in 150 mL of toluene was
azeotropically distiUed for 2 hours under nitrogen and the solution was cooled to room
temperature. 40 mL of dry CH2CI2 and 2.1 mL of dry triethylamine (15 mmol) were added to the
solution. The solution was cooled in an ice bath and 1.2 mL of distilled methanesulfonyl chloride
(15 mmol) was added dropwise. The solution was stirred at room temperature under nitrogen
overnight, and the reaction was quenched by adding 2 mL of absolute ethanol. The mixture was
evaporated under vacuum to remove solvents, primarily those other than toluene, filtered,
concentrated again under vacuum, and then precipitated into 100 mL of diethyl ether. The filtrate
was washed with several portions of cold diethyl ether and dried in vacuo to afford the mesylate.
[690] The mesylate (20 g, 8 mmol) was dissolved in 75 ml of THF and the solution was
cooled to 4 °C. To the cooled solution was added sodium azide (1.56 g, 24 mmol). The reaction was heated to reflux under nitrogen for 2 hours. The solvents were then evaporated and the residue diluted with CH2CI2 (50 mL). The organic fraction was washed with NaCl solution and dried over anhydrous MgSC>4. The volume was reduced to 20 ml and the product was precipitated by addition to 150 ml of cold dry ether.
Example 20
(1) N3-C6H4-CO2H -» N3-C6H4CH2OH
(2) N3-C6H4CH2OH -> Br-CH2-C6H4-N3
(3) mPEG-OH + Br-CHz-CeBU-Ns -» mPEG-O-CHz-C^-Ns
[691] 4-azidobenzyl alcohol can be produced using the method described in U.S. Patent
5,998,595, which is incorporated by reference herein. Methanesulfonyl chloride (2.5 g, 15.7 mmol) and triethylamine (2.8 mL, 20 mmol) were added to a solution of 4-azidobenzyl alcohol (1.75 g, 11.0 mmol) in CH2CI2 at 0 °C and the reaction was placed in the refrigerator for 16 hours. A usual work-up afforded the mesylate as a pale yellow oil. This oil (9.2 mmol) was dissolved in THF (20 mL) and LiBr (2.0 g, 23.0 mmol) was added. The reaction mixture was heated to reflux for 1 hour and was then cooled to room temperature. To the mixture was added water (2.5 mL)

and the solvent was removed under vacuum. The residue was extracted with ethyl acetate (3x15 mL) and the combined organic layers were washed with saturated NaCl solution (10 mL), dried over anhydrous Na2SC>4, and concentrated to give the desired bromide.
[692] mPEG-OH 20 kDa (2.0 g, 0.1 mmol, Sunbio) was treated with NaH (12 mg, 0.5
mmol) in THF (35 mL) and the bromide (3.32 g, 15 mmol) was added to the mixture along with a catalytic amount of KI. The resulting mixture was heated to reflux for 12 hours. Water (1.0 mL) was added to the mixture and the solvent was removed under vacuum. To the residue was added CH2CI2 (25 mL) and the organic layer was separated, dried over anhydrous Na2SC>4, and the volume was reduced to approximately 2 mL. Dropwise addition to an ether solution (150 mL) resulted in a precipitate, which was collected to yield mPEG-0-CH2-C6H4-N3-
Example 21
NH2-PEG-O-CH2CH2CO2H 4- N3-CH2CH2CO2-NHS -> N3-CH2CH2-C(0)NH-PEG-0-CH2CH2CO2H
[693] NH2-PEG-O-CH2CH2CO2H (MW 3,400 Da, 2.0 g) was dissolved in a saturated
aqueous solution of NaHCOa (10 mL) and the solution was cooled to 0°C. 3-azido-l-N-hydroxysuccinimido propionate (5 equiv.) was added with vigorous stirring. After 3 hours, 20 mL of H2O was added and the mixture was stirred for an additional 45 minutes at room temperature. The pH was adjusted to 3 with 0.5 N H2SO4 and NaCl was added to a concentration of approximately 15 wt%. The reaction mixture was extracted with CH2CI2 (100 mL x 3), dried over Na2SC>4 and concentrated. After precipitation with cold diethyl ether, the product was collected by filtration and dried under vacuum to yield the omega-carboxy-azide PEG derivative.
Example 22
mPEG-OMs + HGCLi -> mPEG-0-CH2-CH2-OC-H
[694] To a solution of lithium acetylide (4 equiv.), prepared as known in the art and
cooled to -78°C in THF, is added dropwise a solution of mPEG-OMs dissolved in THF with vigorous stirring. After 3 hours, the reaction is permitted to warm to room temperature and quenched with the addition of 1 mL of butanol. 20 mL of H2O is then added and the mixture was

stirred for an additional 45 minutes at room temperature. The pH was adjusted to 3 with 0.5 N
H2SO4 and NaCl was added to a concentration of approximately 15 wt%. The reaction mixture
was extracted with CH2CI2 (100 mL x 3), dried over Na2SC>4 and concentrated. After precipitation
with cold diethyl ether, the product was collected hy filtration and dried under vacuum to yield the
l-(but-3-ynyloxy)-methoxypolyethylene glycol (mPEG).
Example 23
[695] The azide- and acetylene-containing amino acids were incorporated site-selectively
into proteins using the methods described in L. Wang, et ah, (2001), Science 292:498-500, J.W.
Chin et al., Science 301:964-7 (2003)), J. W. Chin et aL, (2002), Journal of the American
Chemical Society 124:9026-9027; J. W. Chin, & P. G. Schultz, (2002), Chem Bio Chem
3(11):1135-1137; J. W, Chin, et aL, (2002), PNAS United States of America 99:11020-11024:
and, L. Wang, & P. G. Schultz, (2002), Chem. Comm.. 1:1-11. Once the amino acids were
incorporated, the cycloaddition reaction was carried out with 0.01 mM protein in phosphate buffer
(PB), pH 8, in the presence of 2 mM PEG derivative, 1 mM CUSO4, and ~1 mg Cu-wire for 4
hours at 37 °C.
Example 24
[696] This example describes the synthesis of p-Acetyl-D,L-phenyialanine (pAF) and m-
PEG-hydroxylamine derivatives.
[697] The racemic pAF was synthesized using the previously described procedure in
Zhang, Z., Smith, B. A. C, Wang, L., Brock, A., Cho, C. & Schultz, P. G., Biochemistry, (2003)
42, 6735-6746.
[698] To synthesize the m-PEG-hydroxylamine derivative, the following procedures were
completed. To a solution of (N-t-Boc-aminooxy)acetic acid (0.382 g, 2.0 mmol) and 1,3-
Diisopropylcarbodiimide (0.16 mL, 1.0 mmol) in dichloromethane (DCM, 70mL), which was
stirred at room temperature (RT) for 1 hour, methoxy-polyethylene glycol amine (m-PEG-NH2,
7.5 g, 0.25 mmol, Mt. 30 K, from BioVectra) and Diisopropylethylamine (0.1 mL, 0.5 mmol)
were added. The reaction was stirred at RT for 48 hours, and then was concentrated to about 100
mL. The mixture was added dropwise to cold ether (800 mL). The t-Boc-protected product
precipitated out and was collected by filtering, washed by ether 3xl00mL. It was further purified

by re-dissolving in DCM (100 mL) and precipitating in ether (800 mL) twice. The product was
dried in vacuum yielding 7.2 g (96%), confirmed by NMR and Nihydrin test.
[699] The deBoc of the protected product (7.0 g) obtained above was carried out in 50%
TFA/DCM (40 mL) at 0 °C for 1 hour and then at RT for 1.5 hour. After removing most of TFA in vacuum, fee TFA salt of the hydroxylamine derivative was converted to the HC1 salt by adding 4N HC1 in dioxane (lmL) to the residue. The precipitate was dissolved in DCM (50 mL) and re-precipitated in ether (800 mL). The final product (6.8 g, 97%) was collected by filtering, washed with ether 3x lOOmL, dried in vacuum, stored under nitrogen. Other PEG (5K, 20K) hydroxylamine derivatives were synthesized using the same procedure. Example 25
[700] This example describes expression and purification methods used for hGH
polypeptides comprising a non-natural amino acid. Host cells have been transformed with
orthogonal tRNA, orthogonal aminoacyl tRNA synthetase, and hGH constructs.
[701] A small stab from a frozen glycerol stock of the transformed DH10B(fis3) cells
were first grown in 2 ml defined medium (glucose minimal medium supplemented with leucine, isoleucine, trace metals, and vitamins) with 100 |ig/ml ampicillin at 37 °C. When the OD600 reached 2-5, 60 \xl was transferred to 60 ml fresh defined medium with 100 [ig/ml ampicillin and again grown at 37 °C to an ODeoo of 2-5. 50 ml of the culture was transferred to 2 liters of defined medium with 100 ng/ml ampicillin in a 5 liter fermenter (Sartorius BBI). The fermenter pH was controlled at pH 6.9 with potassium carbonate, the temperature at 37 °C, the air flow rate at 5 1pm, and foam with the polyalkylene defoamer KFO F119 (Lubrizol). Stirrer speeds were automatically adjusted to maintain dissolved oxygen levels >30% and pure oxygen was used to supplement the air sparging if stirrer speeds reached their maximum value. After 8 hours at 37 °C, the culture was fed a 50X concentrate of the defined medium at an exponentially increasing rate to maintain a specific growth rate of 0,15 hour"1. When the OD600 reached approximately 100, a racemic mixture of para-acetyl-phenylalanine was added to a final concentration of 3.3 raM, and the temperature was lowered to 28°C. After 0.75 hour, isopropyl-b-D-thiogalactopyranoside was added to a final concentration of 0.25 mM. Cells were grown an additional 8 hour at 28 °C, pelleted, and frozen at -80 °C until further processing.

[702] The His-tagged mutant hGH proteins were purified using the ProBond Nickel-
Chelating Resin (Invitrogen, Carlsbad, CA) via the standard His-tagged protein purification
procedures provided by Invitrogen's instruction manual, followed by an anion exchange column.
[703] The purified hGH was concentrated to 8 mg/ml and buffer exchanged to the
reaction buffer (20 mM sodium acetate, 150 mM NaCl, 1 mM EDTA, pH 4.0). MPEG-Oxyamine powder was added to the hGH solution at a 20:1 molar ratio of PEG:hGH. The reaction was carried out at 28°C for 2 days with gentle shaking. The PEG-hGH was purified from un-reacted PEG and hGH via an anion exchange column.
[704] The quality of each PEGylated mutant hGH was evaluated by three assays before
entering animal experiments. The purity of the PEG-hGH was examined by running a 4*12% acrylamide NuPAGE Bis-Tris gel with MES SDS running buffer under non-reducing conditions (Invitrogen). The gels were stained with Coomassie blue. The PEG-hGH band was greater than 95% pure based on densitometry scan. The endotoxin level in each PEG-hGH was tested by a kinetic LAL assay using the KTA2 kit from Charles River Laboratories (Wilmington, MA), and it was less than 5 EU per dose. The biological activity of the PEG-hGH was assessed with the IM-9 pSTAT5 bioassay (mentioned in Example 2), and the EC50 value was less than 15 nM. Example 26
[705] This example describes methods for evaluating purification and homogeneity of
hGH polypeptides comprising a non-natural amino acid.
[706] Figure 8 is a SDS-PAGE of hGH polypeptides comprising a non-natural amino.
acid at position 92. Lanes 3,4, and 5 of the gel show hGH comprising a p-acetyl-phenylalanine at position 92 covalently linked to either a 5 kDa, 20kDa, or 30 kDa PEG molecule. Additional hGH polypeptides comprising a non-natural amino acid that is PEGylated are shown Figure 11. Five jig of each PEG-hGH protein was loaded onto each SDS-PAGE. Figure 11, Panel A: Lane 1, molecular weight marker, lane 2, WHO rhGH reference standard (2 p,g); lanes 3 and 7, 30KPEG-F92pAF; lane 4, 30KPEG-Y35pAF; lane 5, 30KPEG-R134pAF; lane 6, 20KPEG-R134pAF; lane 8, WHO rhGH reference standard (20 jig). Figure 11, Panel B: Lane 9, molecular weight marker, lane 10, WHO rhGH reference standard (2 \ig); lane 11, 30KPEG-F92pAF; lane 12, 30KPEG-K145pAF; lane 13, 30KPEG-Y143pAF; lane 14, 30KPEG-G131pAF; lane 15, 30KPEG-F92pAF/G120R, lane 16 WHO rhGH reference standard (20 p.g). Figure 9 shows the biological

activity of PEGylated hGH polypeptides (5 kDa, 20 kDa, or 30 kDa PEG) in M-9 cells; methods were performed as described in Example 2.
[707] The purity of the hGH-PEG conjugate can be assessed by proteolytic degradation
(including but not limited to, trypsin cleavage) followed by mass spectrometry analysis. Pepinsky RB., et a!., /. Pharmcol & Exp. Ther. 297(3): 1059-66 (2001). Methods for performing tryptic digests are also described in the European Pharmacopoeia (2002) 4th Edition, pp. 1938). Modifications to the methods described were performed. Samples are dialyzed overnight in 50 mM TRIS-HC1, pH 7.5. ihGH polypeptides were incubated with trypsin (TPCK-treated trypsin, Worthington) at a mass ratio of 66:1 for 4 hours in a 37°C water bath. The samples were incubated on ice for several minutes to stop the digestion reaction and subsequently maintained at 4°C during HPLC analysis. Digested samples (-200 jig) were loaded onto a 25 x 0.46 cm Vydac C-8 column (5-p.m bead size, 100 A pore sizie) in 0.1% trifluoroacetic acid and eluted with a gradient from 0 to 80% acetonitrile over 70 min at a flow rate of 1 ml/min at 30°C. The elution of tryptic peptides was monitored by absorbance at 214 nm.
[708J Figure 10, Panel A depicts the primary structure of hGH with the trypsin cleavage
sites indicated and the non-natural amino acid substitution, F92pAF, specified with an arrow (Figure modified from Becker et al. Biotechnol Appl Biochem. (1988) 10(4):326-337). Panel B shows superimposed tryptic maps of peptides generated from a hGH polypeptide comprising a non-naturally encoded amino acid that is PEGylated (30K PEG His6-F92pAF rhGH, labeled A), peptides generated from a hGH polypeptide comprising a non-naturally encoded amino acid (Hise-F92pAF rhGH, labeled B), and peptides generated from wild type hGH (WHO rhGH, labeled C). Comparison of the tryptic maps of WHO rhGH and HiS6-F92pAF rhGH reveals only two peak shifts, peptide peak 1 and peptide peak 9, and the remaining peaks are identical. These differences are caused by the addition of the His6 on the N-terminus of the expressed His6-F92pAF rhGH, resulting in peak 1 shifting; whereas the shift in peak 9 is caused by the substitution of phenylalanine at residue 92 with p-acetyl-phenylalanine. Panel C - A magnification of peak 9 from Panel B is shown. Comparison of the His6»F92pAF and the 30K PEG His6-F92pAF rhGH tryptic maps reveals the disappearance of peak 9 upon pegylation of His6-F92pAF rhGH, thus confirming that modification is specific to peptide 9. Example 27

[709J This example describes a homodimer formed from two hGH polypeptides each
comprising a non-natural amino acid.
[710J Figure 12 compares IM-9 assay results from a His-tagged hGH polypeptide
comprising a p-acetyl-phenylalanine substitution at position 92 with a homodimer of this modified
polypeptide joined with a linker that is biftinctional having functional groups and reactivity as
described in Example 25 for PBGylation of hGH.
Example 28
[711] This example describes a monomer and dimer hGH polypeptide that act as a hGH
antagonist.
[712] An hGH mutein in which a G120R substitution has been introduced into site II is
able to bind a single hGH receptor, but is unable to dimerize two receptors. The mutein acts as an
hGH antagonist in vitro, presumably by occupying receptor sites without activating intracellular
signaling pathways (Fuh, G., et al.9 Science 256:1677-1680 (1992)). Figure 13, Panel A shows
IM-9 assay data measuring phosphorylation of pSTAT5 by hGH with the G120R substitution. A
hGH polypeptide with a non-natural amino acid incorporated at the same position (G120) resulted
in a molecule that also acts as an hGH antagonist, as shown in Figure 13, Panel B. A dimer of the
hGH antagonist shown in Figure 13, Panel B was constructed joined with a linker that is
bifunctional having functional groups and reactivity as described in Example 25 for PEGylation of
hGH. Figure 14 shows that this dimer also lacks biological activity in the IM-9 assay.
[713] Additional assays were performed comparing hGH polypeptide comprising a
G120pAF substitution with a dimer of G120pAF modified hGH polypeptides joined by a PEG linker. WHO hGH induced phosphorylation of STAT5 was competed with a dose-response range of the monomer and the dimer joined by a PEG linker. Surface receptor competition studies were also performed showing that the monomer and the dimer compete with GH for cell surface receptor binding on IM-9 and rat GHR (L43R)/BAF3 cells. The dimer acted as a more potent antagonist than the monomer. Table 4 shows the data from these studies.



■ »
Example 29
[714] This example details the measurement of hGH activity and affinity of hGH
polypeptides for the hGH receptor.
[715] Cloninfl and purification of rat GH receptor The extracellular domain of rat GH
receptor (GHR ECD, amino acids S29-T238) was cloned into pET20b vector (Novagen) between Nde I and Hind HI sites in fame with C-terminal 6His tag. A mutation of L43 to R was introduced to further approximate the human GH receptor binding site (Souza et aL, Proc Natl Acad Sci USA. (1995) 92(4): 959-63). Recombinant protein was produced in BL21(DE3) E. coli cells (Novagen) by induction with 0.4 mM IPTG at 30°C for 4-5 hours. After lysing the cells, the pellet was washed four times by resuspendingin a dounce with 30mL of 50 mM Tris, pH 7.6, lOOmM NaCl, 1 mM EDTA, 1% Triton X-100, and twice with the same buffer without Triton X~ 100. At this point inclusion bodies consisted of more than 95% GHR ECD and were solubilized in 0.1M Tris, pH 11.5, 2M urea. Refolding was accomplished by means of passing an aliquot of the inclusion body solution through a SI00 (Sigma) gel filtration column, equilibrated with 50 mM Tris, pH 7.8, 1 M L-arginine, 3.7 mM cystamine, 6.5 mM cysteamine. Fractions containing . soluble protein were combined and dialyzed against 50 mM Tris, pH 7.6, 200 mM NaCl, 10% glycerol. The sample was briefly centrifuged to remove any precipitate and incubated with an aliquot of Talon resin (Clontech), according to manufacturer's instructions. After washing the resin with 20 volumes of dialysis buffer supplemented with 5 mM imidazole, protein was eluted with 120 mM imidazole in dialysis buffo:. Finally, the sample was dialyzed overnight against 50 mM Tris, pH 7.6, 30 mM NaCl, 1 mM EDTA, 10% glycerol, centrifuged briefly to remove any precipitate, adjusted to 20% glycerol final concentration, aliquoted and stored at -80 C. Concentration of the protein was measured by OD(280) using calculated extinction coefficient of s=65,700 M-^cm"1.
Biocore™ Analysis of binding ofGHto GHR

[716] Approximately 600-800 RUs of soluble GHR ECD was immobilized on a
Biacore™ CM5 chip, using a standard amine-coupling procedure, as recommended by the manufacturer. Even though a significant portion of the receptor was inactivated by this technique, it was found experimentally that this level of immobilization was sufficient to produce maximal specific GH binding response of about 100-150 RUs, with no noticeable change in binding kinetics. See, e.g., Cunningham et al. JMol Biol (1993) 234(3): 554-63 and Wells JA. Proc Natl AcadSci USA (1996) 93(1): 1-6).
[717J Various concentrations of wild type or mutant GH (0.1- 300nM) in HBS-EP buffer
(Biacore™, Pharmacia) were injected over the GHR surface at a flow rate of 40 ^1/min for 4-5 minutes* and dissociation was monitored for 15 minutes post-injection. The surface was regenerated by a 15 second pulse of 4.5M MgCk- Only a minimal loss of binding affinity (1-5%) was observed after at least 100 regeneration cycles. Reference cell with no receptor immobilized was used to subtract any buffer bulk effects and non-specific binding.
[718] Kinetic binding data obtained from GH titration experiments was processed with
BiaEvaluation 4.1 software (BIACORE™). "Bivalent analyte" association model provided satisfactory fit (chi values generally below 3), in agreement with proposed sequential 1:2 (GH:GHR) dimerization (Wells JA. Proc Natl Acad Sci USA (1996) 93(1): 1-6). Equilibrium dissociation constants (Kd) were calculated as ratios of individual rate constants (koff/kon)-
[719] Table 5 indicates the binding parameters from Biacore™ using rat GHR ECD
(L43R) immobilized on a CM5 chip.

GHR Stable Cell Lines
[720] The IL-3 dependent mouse cell line, BAF3, was routinely passaged in RPMI1640,
sodium pyruvate, penicillin, streptomycin, 10% heat-inactivated fetal calf serum, 50uM 2-mercaptoethanol and 10% WEHI-3 cell line conditioned medium as source of IL-3. All cell cultures were maintained at 37°C in a humidified atmosphere of 5% CO2-
[721] The BAF3 cell line was used to establish the rat GHR (L43R) stable cell clone,
2E2-2B12-F4. Briefly, 1X107 mid-confluent BAF3 cells were electroporated with 15 ug of linearized pcDNA3.1 plasmid containing the full length rat GHR (L43R) cDNA. Transfected cells were allowed to recover for 48 hours before cloning by limiting dilution in media containing 800 ug/ml G418 and 5 nM WHO hGH. GHR expressing transfectants were identified by surface staining with antibody against human GHR (R&D Systems, Minneapolis, MN) and analyzed on a FACS Array (BD Biosciences, San Diego, CA). Transfectants expressing a good level of GHR

were thai screened for proliferative activity against WHO hGH in a BrdU proliferation assay (as described below). Stably transfected rat GHR (L43R) cell clones were established upon two further rounds of repeated subcloning of desired transfectants in the presence of L2 mg/ml G418 and 5 nM hGH with constant profiling for surface receptor expression and proliferative capability. Cell clone, 2E2-2B12-F4, thus established is routinely maintained in BAF3 media plus 1.2 mg/ml G418 in the absence of hGH. Proliferation by BrdU labeling
[722] Serum starved rat GHR (I43R) expressing BAF3 cell line, 2E2-2B12-F4, were
plated at a density of 5 X 104 cells/well in a 96-well plate. Cells were activated with a 12-point dose range of hGH proteins and labeled at the same time with 50 uM BrdU (Sigma, St. Louis, MO). After 48 hours in culture, cells were fixed/permeabilized with lOOul of BD cytofix/cytoperm solution (BD Biosciences) for 30 min at room temperature. To expose BrdU epitopes, fixed/permeablilized cells were treated with 30 ug/well of DNase (Sigma) for 1 hour at 37°C. hnmunofluorescent staining with APC-conjugated anti-BrdU antibody (BD Biosciences) enabled sample analysis on the FACS Array.
[723] Table 6 shows the bioactivity of PEG hGH mutants as profiled on the pSTAT:
(IM-9) and BrdU proliferation assays. WHO hGH is expressed as unity for comparison betweei assays.











Example 30
[724] This example describes methods to measure in vitro and in vivo activity of
PEGylatedhGH.
Cell Binding Assays
[725] Cells (3X106) axe incubated in duplicate in PBS/1% BSA (100 fil) in the absence or
presence of various concentrations (volume: 10 pi) of unlabeled GH, hGH or GM-CSF and in tile presence of1251-GH (approx. 100,000 cpm or 1 ng) at 0°C for 90 minutes (total volume: 120 jil). Cells are then resuspended and layered over 200 /μ ice cold FCS in a 350 /d plastic centrifuge tube and centrifuged (1000 g; 1 minute). The pellet is collected by cutting off the end of the tube and pellet and supernatant counted separately in a gamma counter (Packard).
[726] Specific binding (cpm) is determined as total binding in the absence of a competitor
(mean of duplicates) minus binding (cpm) in the presence of 100-fold excess of unlabeled GH (non-specific binding). The non-specific binding is measured for each of the cell types used. Experiments are run on separate days using the same preparation of 125I-GH and should display
IOC
internal consistency. I-GH demonstrates binding to the GH receptor-producing cells. The binding is inhibited in a dose dependent manner by unlabeled natural GH or hGH, but not by GM-CSF or other negative control. The ability of hGH to compete for the binding of natural125 I-GH, similar to natural GH, suggests that the receptors recognize both forms equally well.
In Vivo Studies of PEGvlated hGH
[727] PEG-hGH, unmodified hGH and buffer solution are administered to mice or rats.
The results will show superior activity and prolonged half life of the PEGylated hGH of the present invention compared to unmodified hGH which is indicated by significantly increased bodyweight
Measurement of the in vivo Half-life of Conjugated and Non-coniugated hGH and Variants Thereof.

[728] All animal experimentation was conducted in an AAALAC accredited facility and
under protocols approved by the Institutional Animal Care and Use Committee of St Louis University. Rats were housed individually in cages in rooms with a 12-hour light/dark cycle. Animals were provided access to certified Purina rodent.chow 5001 and water ad libitum. For hypophysectomized rats, the drinking water additionally contained 5% glucose. Pharmacokinetic studies
[729] The quality of each PEGylated mutant hGH was evaluated by Ihree assays before
entering animal experiments. The purity of the PEG-hGH was examined by running a 4-12% acrylamide NuPAGE Bis-Tris gel with MES SDS running buffer under non-reducing conditions (Invitrogen, Carlsbad, CA). The gels were stained with Coomassie blue. The PEG-hGH band was greater than 95% pure based on densitometry scan. The endotoxin level in each PEG-hGH was tested by a kinetic LAL assay using the KTA2 kit from Charles River Laboratories (Wilmington, MA), and was less than 5 EU per dose. The biological activity of the PEG-hGH was assessed with the IM-9 pSTAT5 bioassay (described in Example 2), and the EC50 value confirmed to be less
a-
than 15 nM.
[730] Pharmacokinetic properties of PEG-modified growth hormone compounds were :
compared to each other and to nonPEGylated growth hormone in male Sprague-Dawley rats (261- ■" 425g) obtained from Charles River Laboratories. Catheters were surgically installed, into the .' carotid artery for blood collection. Following successful catheter installation, animals were assigned to treatment groups (three to six per group) prior to dosing. Animals were dosed subcutaneously with 1 mg/kg of compound in a dose volume of 0.41-0.55 ml/kg. Blood samples were collected at various time points via the indwelling catheter and into EDTA-coated microfuge tubes- Plasma was collected after centrifugation, and stored at -80°C until analysis. Compound concentrations were measured using antibody sandwich growth hormone ELISA kits from either BioSource International (Camarillo, CA) or Diagnostic Systems Laboratories (Webster, TX). Concentrations were calculated using standards corresponding to the analog that was dosed. Pharmacokinetic parameters were estimated using the modeling program WiriNonlin (Pharsight, version 4.1). Noncompartmental analysis with linear-up/log-down trapezoidal integration was used, and concentration data was uniformly weighted.
[731] Figure 15 shows the mean (+/- S.D.) plasma concentrations following a single
subcutaneous dose in rats. Rats (n=3-4 per group) were given a single bolus dose of 1 mg/kg hGH

wad-type protein (WHO hGH), His-tagged hGH polypeptide (his-hGH), or His-tagged hGH polypeptide comprising non-natural amino acid p-acetyl-phenylalanine at position 92 covalently linked to 30 kDa PEG (30KPEG-pAF92(his)hGH). Plasma samples were taken over the indicated time intervals and assayed for injected compound as described 30KPEG-pAF92 (his)hGH has dramatically extended circulation compared to control hGH.
[732] Figure 16 shows the mean (+/- S.D.) plasma concentrations following a single
subcutaneous dose in rats. Rats (n=3-6 per group) wea^ given a single bolus dose of 1 mg/kg protein. hGH polypeptides comprising non-natural amino acid p-acetyl-phenylalanine covalently linked to 30 kDa PEG at each of six different positions were compared to WHO hGH and (his)-hGH. Plasma samples were taken over the indicated time intervals and assayed for injected compound as described. Table 7 shows the pharmacokinetic parameter values for single-dose administration of hGH polypeptides shown in Figure 16. Concentration vs time curves were evaluated by noncompartmental analysis (Pharsight, version 4.1). Values shown are averages (+/-standard deviation). Cmax: maximum concentration; terminal ti/2- terminal half-life; AUQ>^in£ area under the concentration-time curve extrapolated to infinity; MRT: mean residence time; Cl/f: apparent total, plasma clearance; Vz/f: apparent volume of distribution during terminal phase. Table 7: Pharmacokinetic parameter values for single-dose 1 mg/kg bolus s.c. administration in normal male Sprague-Dawley rats.


Pharmacodynamic studies
[733] Hypophysectomized male Sprague-Dawley rats were obtained from Charles River
Laboratories. Pituitaries were surgically removed at 3-4 weeks of age. Animals were allowed to acclimate for a period of three weeks, during which time bodyweight was monitored. Animals with a bodyweight gain of 0-8g over a period of seven days before the start of the study were included and randomized to treatment groups. Rats were administered either a bolus dose or daily dose subcutaneously. Throughout the study rats were daily and sequentially weighed, anesthetized, bled, and dosed (when applicable). Blood was collected from the orbital sinus using a heparinized capillary tube and placed into an EDTA coated microfuge tube. Plasma was isolated by centrifugation and stored at -80°C until analysis.
[734] Figure 17 shows the mean (+/- S.D.) plasma concentrations following.a single
subcutaneous dose in hypophysectomized rats. Rats (n=5-7 per group) were given a single bolus dose of 2.1 mg/kg protein. Results from hGH polypeptides comprising non-natural amino acid p-acetyl-phenylalanine covalently linked to 30 kDa PEG at each of two different positions (position 35, 92) are shown. Plasma samples were taken over the indicated time intervals and assayed for injected compound as described.
[735] The peptide IGF-1 is a member of the family of somatomedins or insulin-like
growth factors. IGF-1 mediates many of the growth-promoting effects of growth hormone. IGF-1 concentrations were measured using a competitive binding enzyme immunoassay kit against the provided rat/mouse IGF-1 standards (Diagnosic Systems Laboratories). Significant difference was determined by t-test using two-tailed distribution, unpaired, equal variance. Figure 18, Panel A shows the evaluation of compounds in hypophysectomized rats. Rats (n= 5-7 per group) were given either a single dose or daily dose subcutaneously. Animals were sequentially weighed, anesthetized, bled, and dosed (when applicable) daily. Bodyweight results are shown for placebo treatments, wild type hGH (hGH), His-tagged hGH ((his)hGH), and hGH polypeptides comprising p-acetyl-phenylalanine covalently-linked to 30 kDa PEG at positions 35 and 92. Figure 18, Panel B - A diagram is shown of the effect on circulating plasma IGF-1 levels after administration of a single dose of hGH polypeptides comprising a non-naturally encoded amino acid that is PEGylated. Bars represent standard deviation. In Figure 18, Panel A, the bodyweight gain at

day 9 for. 30KPEG-pAF35(his)hGH compound is statistically different (p 30KPEG-pAF92(his)hGH compound, in that greater weight gain was observed.
[736] Figure 18, Panel C shows the evaluation of compounds in hypophysectomized rats.
Rats (n= 11 per group) were given either a single dose or daily dose subcutaneously. Animals were sequentially weighed, anesthetized, bled, and dosed (when applicable) daily. Bodyweight results are shown for placebo treatments, wild type hGH (hGH), and hGH polypeptides comprising p-acetyl-phenylalanine covalently-linked to 30 kDa PEG at positions 92, 134, 145, 131, and 143. Figure 18, Panel D - A diagram is shown of the effect on circulating plasma IGF-1 levels after administration of a single dose of hGH polypeptides comprising a non-naturally encoded amino acid that is PEGylated (position 92, 134, 145, 131, 143) compared to placebo treatments and wild type hGH. Figure 18, Panel E shows the mean (+/- S.D.) plasma concentrations corresponding to hGH polypeptides comprising a non-naturally encoded amino acid-that is PEGylated (position 92, 134, 145, 131, 143). Plasma samples were taken over the indicated time intervals and assayed for injected compound as described. Bars represent standard deviation. Example 31
[7371 Human Clinical Trial of the Safety and/or Efficacy of PEGylated hGH Comprising
a Non-Naturally Encoded Amino Acid.
[738] Objective To compare the safety and pharmacokinetics of subcutaneously
administered PEGylated recombinant human hGH comprising a non-naturally encoded amino acid with one or more of the commercially available hGH products (including, but not limited to Humatrope™ (Eli Lilly & Co.), Nutropin™ (Genentech), Norditropin™ (Novo-Nordisk), Genotropin™ (Pfizer) and Saizen/Serostim™ (Serono)).
[739] Patients Eighteen healthy volunteers ranging between 20-40 years of age and
weighing between 60-90 kg are enrolled in the study. The subjects will have no clinically significant abnormal laboratory values for hematology or serum chemistry, and a negative urine toxicology screen, HIV screen, and hepatitis B surface antigen. They should not have any evidence of the following: hypertension; a history of any primary hematologic disease; history of significant hepatic, renal, cardiovascular, gastrointestinal, genitourinary, metabolic, neurologic

disease; a history of anemia or seizure disorder; a known sensitivity to bacterial or mammalian-derived products, PEG, or human serum albumin; habitual and heavy consumer to beverages containing caffeine; participation in any other clinical trial or had blood transfused or donated within 30 days of study entry; had exposure to hGH within three months of study entry; had an illness within seven days of study entry; and have significant abnormalities on the pre-study physical examination or the clinical laboratory evaluations within 14 days of study entry. All subjects are evaluable for safety and all blood collections for pharmacokinetic analysis are collected as scheduled. All studies are performed with institutional ethics committee approval and patient consent
[740] Study Design This will be a Phase I, single-center, open-label, randomized, two-
period crossover study in healthy male volunteers. Eighteen subjects are randomly assigned to one of two treatment sequence groups (nine subjects/group). GH is administered over two separate dosing periods as a bolus s.c. injection in the upper thigh using equivalent doses of the PEGylated hGH comprising a non-naturally encoded amino acid and the commercially available product chosen. The dose and frequency of administration of the commercially available product is as instructed in the package label. Additional dosing, dosing frequency, or other parameter as desired, using the commercially available products may be added to the study by including additional groups of subjects. Each dosing period is separated by a 14-day washout period. Subjects are confined to the study center at least 12 hours prior to and 72 hours following dosing for each of the two dosing periods, but not between dosing periods. Additional groups of subjects may be added if there are to be additional dosing, frequency, or other parameter, to be tested for the PEGylated hGH as well. Multiple formulations of GH that are approved for human use may be used in this study. Humatrope™ (Eli Lilly & Co.), Nutropiri™ (Genentech), Norditropin™ (Novo-Nordisk), Genotropin™ (Pfizer) and Saizen/Serostim™ (Serono)) are commercially available GH products approved for human use. The experimental formulation of hGH is the PEGylated hGH comprising a non-naturally encoded amino acid.
[741] Blood Sampling Serial blood is drawn by direct vein puncture before and after
administration of hGH. Venous blood samples (5 mL) for determination of serum GH concentrations are obtained at about 30, 20, and 10 minutes prior to dosing (3 baseline samples) and at approximately the following times after dosing: 30 minutes and at 1, 2, 5, 8, 12, 15, 18, 24,

30, 36, 48, 60 and 72 hours. Each serum sample is divided into two aliquots. All serum samples are stored at -20°C. Serum samples are shipped on dry ice. Fasting clinical laboratory tests (hematology, serum chemistry, and urinalysis) are performed immediately prior to the initial dose on day 1, themorning of day 4, immediately prior to dosing on day 16, and the morning of day 19.
[742] Bioanalvtical Methods An ELISA kit procedure (Diagnostic Systems Laboratory
[DSL], Webster TX), is used for the determination of serum GH concentrations.
[743J Safety Determinations Vital signs are recorded immediately prior to each dosing
(Days 1 and 16), and at 6, 24, 48, and 72 hours after each dosing. Safety determinations are based on the incidence and type of adverse events and the changes in clinical laboratory tests from baseline. In addition, changes from pre-study in vital sign measurements, including blood pressure, and physical examination results are evaluated.
[744] Data Analysis Post-dose serum concentration values are corrected for pre-dose
baseline GH concentrations by subtracting from each of the post-dose values the mean baseline GH concentration determined from averaging the GH levels from the three samples collected at -30, 20, and 10 minutes before dosing- Pre-dose serum GH concentrations are not included in the calculation of the mean value if they are below the quantification level of the assay. Pharmacokinetic parameters are determined from serum concentration data corrected for baseline GH concentrations. Pharmacokinetic parameters are calculated by model independent methods on a Digital Equipment Corporation VAX 8600 computer system using the latest version of the BIOAVL software. The following pharmacokinetics parameters are determined: peak serum concentration (Cmax); time to peak serum concentration (tmax); area under the concentration-time curve (AUC) from time zero to the last blood sampling time (AUC0-72) calculated with the use of the linear trapezoidal rule; and terminal elimination half-life (ti/2), computed from the elimination rate constant. The elimination rate constant is estimated by linear regression of consecutive data points in the terminal linear region of the log-linear concentration-time plot The mean, standard deviation (SD)5 and coefficient of variation (CV) of the pharmacokinetic parameters are calculated for each treatment. The ratio of the parameter means (preserved formulation/non-preserved formulation) is calculated.

[745] Safety Results The incidence of adverse events is equally distributed across the
treatment groups. There are no clinically significant changes from baseline or pre-study clinical laboratory tests or blood pressures, and no notable changes from pre-study in physical examination results and vital sign measurements. The safety profiles for the two treatment groups should appear similar.
[746] Pharmacokinetic Results Mean serum GH concentration-time profiles (uncorrected
for baseline GH levels) in all 18 subjects after receiving a single dose of one or more of commercially available hGH products (including, but not limited to Humatrope™ (Eli Lilly & Co.), Nutropin™ (Genentech), Norditropin™ (Novo-Nordisk), Genotropin™ (Pfizer) and Saizen/Serostim™ (Serono)) are compared to the PEGylated hGH comprising a non-naturally encoded amino acid at each time point measured. All subjects should have pre-dose baseline GH concentrations within the normal physiologic range. Pharmacokinetic parameters are determined from serum data corrected for pre-dose mean baseline GH concentrations and the Cma* and tmax are determined. The mean tmax for the clinical comparators) chosen (Humatrope™ (Eli Lilly & Co.), Nutropin™ (Genentech), Norditropin™ (Novo-Nordisk), Genotropin™ (Pfizer), Saizen/Serostim™ (Serono)) is significantly shorter than the W for the PEGylated hGH comprising the non-naturally encoded amino acid. Terminal half-life values are significantly shorter for the commerically available hGH products tested compared with the terminal half-life for the PEGylated hGH comprising a non-naturally encoded amino acid.
747] Although the present study is conducted in healthy male subjects, similar
tbsorption characteristics and safety profiles would be anticipated in other patient populations;
;uch as male or female patients with cancer or chronic renal failure, pediatric renal failure patients,
)atients in autologous predeposit programs, or patients scheduled for elective surgery. In
sonclusion, subcutaneously administered single doses of PEGylated hGH comprising non-
laturally encoded amino acid will be safe and well tolerated by healthy male subjects. Based on a
comparative incidence of adverse events, clinical laboratory values, vital signs, and physical
ixamination results, the safety profiles of the commercially available forms of hGH and
.'EGylated hGH comprising non-naturally encoded amino acid will be equivalent. The PEGylated
hGH comprising non-naturally encoded amino acid potentially provides large clinical utility to
patients and health care providers.

Example 32
[748] In the following Examples, ahGH and PEG-^GH are, respectively, hGH and a
PEGylated hGH of SEQ ID NO:2 with a para-acetylphenylalanine at the 35 position and, in the
PEGylated hGH, the PEG linked via an oxime bond formed with the para-acetylphenylalanine,
where the PEG is a linear 30 kDa PEG.
STAT5 phosphorylation assay
[749] The interaction of hGH with its receptor leads to the tyrosine phosphorylation of a
signal transducer and activator of transcription family member, STAT5, in the human IM-9
lymphocyte cell line. The concentration of ^GH and PEG-^GH (required for 50% maximal
STAT5 phosphorylation (EC50) was determined by activating IM-9 cells with increasing
concentrations of ahGH and PEG-ahGH followed by intra-cellular immunofluorescent staining for
phospho-STAT5. With the EC50 of World Health Organization (WHO) standard hGH as 1.0, the
relative EC50 of ahGH as compared to WHO hGH was determined to be 1.1 while that of PEG-
ahGHwasl0.9.
Example 33:
Proliferation assay
[750] PEG-ahGH activity was determined in vitro by the use of a cell line that proliferates
in response to growth hormone. An example of such a cell line is the rat GHR[L43R]/BAF3 cell clone named 2E2-2B12-F4, a line generated by stably transfecting mouse BAF3 cells with the rat GHR bearing a Leu to Arg substitution at position 43. The conversion of Leu-43 of the rat receptor to Arg-43 renders the rat GHR more 'human-like' and hence enables efficient hGH binding. Bromodeoxyuridine (BrdU)-labeling of actively dividing rat GHR[L43R]/BAF3 cells was employed to provide a high resolution, non-radioactive method for the quantitation of growth hormone induced proliferation. Setting the EC50 for WHO hGH as unity, the relative ECso's of ahGH and PEG-ahGH as compared to WHO hGH were determined to be 1.06 + 0.29 (n=l 1) and 5.37 ± 1.23,(n=9), respectively.
Example 34.
Efficacy studies of PEGylated hGH

[751] Preclinical efficacy studies were conducted in a rat model of growth hormone
deficiency. In this model, the pituitary gland was surgically removed at approximately 4 weeks of
age. The body weights of these hypophysectomized rats were monitored after surgery and animals
showing less than 7.5 grams of bodyweight gain over, a period of 7 days before the study were
deemed successfully hypophysectomized and were randomized amongst the treatment groups.
Animals showing more than 2.5 g of weight-loss were deemed not healthy and were excluded
from the study. Hie study was initiated approximately 3 weeks after the surgery.
[752] Animals were dosed weekly (i.e. dosed on days 0 and 7) with either placebo or
increasing PEG-ahGH dose. An additional treatment group received Genotropin or placebo daily. Bodyweights and blood were collected predose and daily. All animals were sacrificed on day 14. Figure 28 shows the plasma IGF-1 levels throughout the study. A robust, dose-dependent increase in IGF-1 was observed.
[753] A dose-dependent increase in IGF-1 Cmax was observed after each dose interval.
Curve fitting of the Cmax values from the first dose estimated the minimum (Eo) and maximum (Emax) IGF-1 Cmax to be 136.7 and 1,136.2 ng/mL respectively, and determined the ED50 to be 0.136 mg/kg (Table 8).
[754] Plasma IGF-1 levels also showed a clear dose-dependent increase when expressed
as AUC For this parameter, the AUC is expressed as AUC above the efficacious IGF-1 plasma level. Previous work showed that a sustained IGF-1 concentration of 34 ng/mL above baseline resulted in bodyweight gain in hypophysectomized rats. In the current study, the baseline IGF-1 level determined from the placebo group throughout the study was 128 ng/mL. An increase of 34 ng/mL over 128 ng/mL estimates an efficacious IGF-1 level of 162 ng/mL. Thus the AUC above 162 ng/mL was integrated. From this analysis, a dose-dependent increase in AUC above efficacious level was observed after each dose interval. Curve fitting of the AUC values from the first dose estimated the Eo and Emax IGF-1 AUC to be 0 and 5,029.8 ngXhr/mL, respectively, and determined the ED50 for this parameter to be 0.909 mg/kg (Table 8)
[755] The duration of IGF-1 levels induced above the estimated efficacious level after the
first dose was determined. At the higher doses, the IGF-1 levels had not returned to baseline before the second dose, hi these instances, the IGF-1 concentration was extrapolated to the efficacious level using the calculated terminal slopes. From this evaluation, a dose-dependent increase in duration of IGF-1 concentration above the efficacious level was evident. Curve fitting

estimated minimum and maximum durations to be 0 and 8.84 days, respectively, and determined the ED50 for this parameter to be 0.173 mg/kg (Table 8).
[756] Bone growth was used as an additional pharmacodynamic measure to calculate the
PEG-ahGH ED50' Tibias were collected from each animal at the end of the study and immersion fixed in 10% neutral-buffered formalin followed by radiography. The results are shown in Figure 29. There was a clear dose-dependent increase in tibial bone length for the PEG-ahGH treated animals. Moreover, there was a dose sparing effect compared to the daily Genotropin treated animals. The amount of Genotropin administered over a 7-day interval is equivalent to 2.1 mg/kg of PEG-ahGH given weekly (i.e., days 0 and 7). An induction of tibial bone length increase similar to Genotropin is shown for PEG-ahGH at 0.42 to 1.0 mg/kg. This represents a >50% dose-sparing effect for PEG-ahGH when compared to Genotropin.
[757] PEG-ahGH also induced a dose-dependent increase in bodyweight (Figure 30).
Moreover, as with induction of tibial bone length, a dose-sparing effect was evident for PEG-
"hGH over Genotropin. Daily treatment with Genotropin at 0.3 mg/kg/day induced 27.74 (+/-
7.92) % bodyweight change on day 14 from day 0. PEG-ahGH, administered at the equivalent
amount of GH (i.e. 2.1 mg/kg on days 0 and 7), induced greater bodyweight increase over
Genotropin. This dose of PEG-^GH resulted in 33.66 (+/- 7.55) % bodyweight change on day 14
from day 0. The percent bodyweight change induced by PEG-^GH administered at the lower
dose of 1.0 mg/kg on days 0 and 7 induced 27.02 (+/- 3.97) % bodyweight change on day 14.
This result represents a nearly 50% dose-sparing effect for PEG-ahGH. Administration of
unPEGylated GH weekly at 2.1 mg/kg dose failed to induce body weight gain.
[758] Curve fitting of the percent bodyweight change on day 14 estimated the minimum
and maximum percent bodyweight change, induced by PEG-ahGH, to be 7.17 and 50.65, respectively. From this curve, the ED50 for this parameter was determined to be 1.097 mg/kg (Table 8). Table 8. Efficacy study results with PEG-^GH



[759] The same plasma samples collected for IGF-1 concentration determination were
also assayed for PEG~ahGH concentration. The EUSA assay used is specific for hGH, shows a
reduced though still rohust response for PEG-^GH, and does not detect rat GIL The PEG-ahGH
plasma concentration-time profiles are shown in Figure 31. A dose-dependent increase in PEG-
^GH Cmax occurred. The duration of PEG-ahGH persistence in the circulation, as well as the
overall PEG-ahGH AUC, increased in a dose-dependent maimer. Genotropin, administered daily,
was not detectable in plasma likely due to rapid clearance. The PEG-ahGH exposure results
support the dose-dependent efficacy shown above.
[760] The hypophysectomized rat studies described above have shown the following:
1. PEGr-^GH dose-dependently increased IGF-1 plasma concentration. IGF-1 Cmax as well
as IGF-1 AUC and duration above efficacious level were all dose-dependently increased.
2. Tibial bone length and bodyweight were dose-dependently increased.
3. Dose sparing of > 50% over Genotropin administered daily was demonstrated.
4. PEG-ahGH showed dose-dependent increase in Cmax, AUC and persistence in the
circulation that correlated with the above pharmacodynamic effects.
Example 35
Pharmacokinetic Studies
Rat Pharmacokinetics
[761] Plasma concentration versus time profiles for PEG-ahGH administered
jubcutaneously at various doses in the rat disease model are shown in Example 34, above.
Primate Pharmacokinetics
762] The pharmacokinetic properties of the version of PEG-^GH that differs only in
hat the molecule contained a methionine at the N-terminal position (PEG-a(met)hGH), were
evaluated in male cynomolgus monkeys (FIG. 32).

[763] A single injection of PEG-3 (met)hGH was administered either at a subcutaneous or
intravenous dose of 0.75 mg/kg or 0.15 mg/kg, respectively. After subcutaneous administration, a Cmax of 4,977 (+/- 1,286) ng/mL was reached approximately 16 hours after injection. The apparent terminal half-life was 12.23 (+/- 1.72) hours, compared to 7.05 (+/- 0.47) in rat with PEG-ahGH. The half-life after intravenous administration was 6.42 (4-/-0.51) hours. The dose-corrected AUC values were 362,443 and 312,440 ngXhrXkg/mL/mg for the subcutaneous and intravenous doses, respectively. The bioavailability from the subcutaneous administration was calculated to be 116%.
Example 36
Rationale for Dose and Dosing Regimen Proposed in the Clinical Protocol
[764] The optimal regimen for a PEGylated GH in humans is determined from the
following studies in animals.
[765] Rat efficacy study- Dose-sparing (i.e. comparable efficacy to Genotropin but with
less PEG-*hGH dose) observed in preclinical efficacy studies are used in dose estimation required
for biological activity in humans.
[766] Pharmacokinetic evaluation in rat and cynomolgus monkey- Allometric scaling is
used to eslimate pharmacokinetic parameters in human.
[767] Single-dose acute safety studies in rat and cynomolgus monkey are used to evaluate
exposure and determine NOAEL (no observed adverse effect level).
[768] Rat one-month repeat-dose GLP safety study- Safety is evaluated following one
month of exposure from doses that are 2X, 6X, and 20X above the maximum recommended
human dose (MRHD). MRHD = 0.36 mg/kg/week for pediatric GHD.
[769] Cynomolgus monkey one-month repeat-dose GLP safety study- Safety is evaluated
following one month of exposure from doses that are 2X, 10X, and 3 OX above the maximum
recommended human dose (MRHD). MRHD = 0.36 mg/kg/week for pediatric GHD.
[770] Rat six-month repeat-dose GLP safety study. Safety is evaluated following six
months of exposure with dosing such that the exposure in rats is 1-2X and 10X the observed
exposure at the MRHD in humans.


[771] Cynomolgus monkey six-month repeat-dose GLP safety study. Safety is evaluated
following six months of exposure with dosing such that the exposure in monkeys is 1-2X and 10X the observed exposure at the MRHD in humans.
[772] It is understood that the examples and embodiments described herein are for
illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons of ordinary skill in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, patent applications, and/or other documents cited in this application are incorporated by reference in their entirety for all purposes to the same extent as if each individual publication, patent, patent application, and/or other document were individually indicated to be incorporated by reference for all purposes.



WHAT IS CLAIMED IS:
1. A hormone composition comprising a growth hormone (GH) linked to at least one water-soluble polymer by a covalent bond, wherein the covalent bond is an oxime bond.
2. The hormone composition of claim 1 wherein the GH is a human growth hormone (hGH).
3. The hormone composition of claim 2 wherein the hGH comprises a sequence that is at least about 80% identical to SEQ ID NO: 2.
4. The hormone composition of claim 2 wherein the hGH comprises the sequence of SEQ ID NO: 2.
5. The hormone composition of claim 1 or 2 wherein the GH comprises a non-naturally encoded amino acid (NEAA).
6. The hormone composition of claim 5 comprising an oxime bond between the NEAA and the water-soluble polymer.
7. The hormone composition of claim 6 wherein the NEAA comprises a carbonyl group.
8. The hormone composition of claim 7 wherein the NEAA comprises a ketone.
9. The hormone composition of claim 8 wherein the NEAA is para-acetylphenylalanine.

10. The hormone composition of claim 9 wherein the para-acetylphenylalanine is substituted at position corresponding to position 35 of SEQ ID NO: 2.
11. The hormone composition of claim 1 or 2 wherein the water-soluble polymer comprises polyethylene glycol (PEG).

12. The hormone composition of claim 11 wherein the PEG is a linear PEG.
13. The hormone composition of claim 12 wherein the PEG has a molecular weight between about 0.1 and about 100 kDa.
14. The hormone composition of claim 12 wherein the PEG has a molecular weight between about 1 and about 60 kDa.
15. The hormone composition of claim 12 wherein the PEG has a molecular weight between about 20 and about 40 kDa.
16. The hormone composition of claim 12 wherein the PEG has a molecular weight of about 30 kDa.
17. The hormone composition of claim 11 wherein the PEG is a branched PEG.
18. The hormone composition of claim 17 wherein the PEG has a molecular weight between about 1 and about 100 kDa.
19. The hormone composition of claim 17 wherein the PEG has a molecular weight between about 30 and about 50 kDa.
20. The hormone composition of claim 17 wherein the PEG has a molecular weight of about 40 kDa.
21. The hormone composition of claim 7 wherein the water-soluble polymer comprises a PEG.
i.
22. The hormone composition of claim 21 wherein the PEG is a linear PEG.
23. The hormone composition of claim 21 wherein the PEG has a molecular weight between about 0.1 and about 100 kDa.

24. The hormone composition of claim 21 wherein the PEG has a molecular weight between about 1 and about 60 kDa.
25. The hormone composition of claim 21 wherein the PEG has a molecular weight between about 20 and about 40 kDa.
26. The hormone composition of claim 21 wherein the PEG has a molecular weight of about 30
kDa.
27. The hormone composition of claim 7 wherein the PEG is a branched PEG.
28. The hormone composition of claim 28 wherein PEG has a molecular weight between about 1 and about 100 kDa.
29. The hormone composition of claim 28 wherein the PEG has a molecular weight between about 30 and about 50 kDa.
30. The hormone composition of claim 28 wherein the PEG has a molecular weight of about 40 kDa.
31. The hormone composition of claim 10 wherein the water-soluble polymer is a PEG.
32. The hormone composition of claim 31 wherein the PEG is a linear PEG.
33. The hormone composition of claim 32 wherein the PEG has a molecular weight between about 0.1 and about 100 kDa.
34. The hormone composition of claim 32 wherein the PEG has a molecular weight between about 1 and about 60 kDa.

35. The hormone composition of claim 32 wherein the PEG has a molecular weight between about 20 and about 40 kDa.
36. The hormone composition of claim 32 wherein the PEG has a molecular weight of about 30 kDa.
37. The hormone composition of claim 32 wherein the GH is hGH
38. The hormone composition of claim 37 wherein the hGH comprises SEQ ID NO: 2.
39. The hormone composition of claim 1 comprising GH linked by a plurality of covalent bonds
to a plurality of water-soluble polymers, wherein at least one the covalent bonds are oxime bonds. .
40. The hormone composition of claim 39 wherein the GH is a human growth hormone (hGH).
41. The hormone composition of claim 40 wherein the hGH comprises a sequence that is at least about 80% identical to SEQ ID NO: 2.
42. The hormone composition of claim 2 wherein the hGH comprises the sequence of SEQ ID NO: 2.
43. The hormone composition of claim 39 or 41 wherein the GH comprises a plurality of NEAAs.
44. A hormone composition comprising a hGH linked via an oxime bond to at least one linear PEG, wherein the hGH comprises the amino acid sequence of SEQ ID NO: 2 and comprises at least one NEAA substituted at one or more positions selected from the group consisting of residues 1-5,6-33,34-74,75-96,97-105,106-129,130-153,154-183, and 184-191.
45. The hormone composition of claim 44, wherein the NEAA(s) is substituted at one or more positions selected from the group consisting of residues before position 1 (i.e. at theN-terminus), 1,2,3, 4, 5, 8,9,11,12, 15,16,19, 22,29, 30, 32, 33, 34, 35, 36, 37, 38, 39,40,41,42,43, 44,

45,46,47, 48,49, 52, 55, 57, 59, 65, 66,69y 70, 71, 74, 88, 91, 92, 94, 95, 97, 98, 99, 100,101, 102,103,104, 105,106, 107,108,109, 111, 112,113,115,116,119, 120, 122,123,126,127, 129,130,131, 132,133,134, 135,136,137,138,139,140,141,142,143, 144,145,146,147, 148,149,150, 151,152,153,154,155,156,158,159,161, 168,172,183,184,185,186,187, 188,189,190, 191, and 192 (i.e., at the carboxyl terminus of the protein).
46. The hormone composition of claim 44, wherein the NEAA(s) is substituted at one or more positions selected from the group consisting of residues 35, 92,131,134, 143, and 145.
47. The hormone composition of claim 44, wherein the NEAA(s) is substituted at one or more positions selected from the group consisting of residues 30, 35, 74, 92,103, 143, and 145.
48. The hormone composition of claim 44, wherein the NEAA(s) is substituted at one or more positions selected from the group consisting of residues 35, 92, 143, and 145.
49. The hormone composition of claim 44, comprising an NEAA substituted at position 35.
50. The hormone composition of claims 44,45,46, 47,48, or 49 comprising an NEAA that is para-acetylphenylalanine.
51. The hormone composition of claim 50 wherein the PEG has a molecular weight between about 0.1 and about 100 kDa.
52. The hormone composition of claim 50 wherein the PEG has a molecular weight between about 1 and about 60 kDa.
53. The hormone composition of claim 50 wherein the PEG has a molecular weight between about 20 and about 40 kDa.
54. The hormone composition of claim 50 wherein the linear PEG has a MW of about 30 kDa.

55. A method of making a GH linked via an oxime bond to a water-soluble polymer comprising contacting a GH that comprises a NEAA comprising a carbonyl group with a PEG oxyamine under conditions suitable for formation of an oxime bond.
56. The method of claim 55 wherein the NEAA contains a ketone group.
57. The method of claim 56 wherein the NEAA is para-acetylphenylalanine.
58. The method of claim 57 wherein the para-acetylphenylalanine is substituted at a position in the GH, e.g., hGH corresponding to amino acid 35 in SEQ ID NO: 2.
59. The method of claim 55 wherein the PEG oxyamine is a monomethoxyPEG (MPEG) oxyamine.
60. The method of claim 59 wherein the MPEG oxyamine is linear.
61. The method of claim 60 wherein the MW of the PEG is about 20-40 kDa.
62. The method of claim 61 wherein the MW of the PEG is about 30 kDa.
63. The method of claim 62 wherein the MPEG oxyamine is a linear 30kD monomethoxy-PEG-2-aminooxy ethylamine carbamate hydrochloride.
64. The method of claim 55 further comprising making the GH comprising an NEAA by a process comprising introducing
(i) a nucleic acid encoding a GH wherein the nucleic acid has been modified to provide a signal for incorporation of the NEAA; and
(ii) the NEAA; to an organism that is capable of incorporating the NEAA into a protein in response to the signal of the nucleic acid of (i).
65. The method of claim 55 wherein the conditions comprise

(i) mixing the MPEG and GH to produce a MPEG-GH mixture with a MPEG:GH ratio of about 5
to 10,
(ii) a pH of about 4 to 6; and
(iii) gentle stirring of the MPEG-GH mixture for about 10 to 50 hours at room temperature.
66. The method of claim 55 further comprising purifying the GH.
67. The method of claim 56 wherein the GH produced by the process is at least about 99% pure.
68. A pharmaceutical composition comprising
(i) a hormone composition comprising a growth hormone linked by a covalent bond to at least one water-soluble polymer, wherein the covalent bond is an oxime bond; and (ii) a pharmaceutically acceptable excipient.
69. The pharmaceutical composition of claim 68 wherein the GH is hGH.
70. The pbannaeutical composition of claims 68 or 69 wherein the composition comprises a pharmaceutically acceptable formulation liquid for injection. *i
71. The pharmaceutical composition of claim 69 wherein the GH comprises a NEAA.
72. The pharmaceutical composition of claim 71 wherein the water-soluble polymer comprises a PEG.
73. The pharmaceutical composition of claim 71 wherein the PEG is a linear PEG.
74. The pharmaceutical composition of claim 73 wherein the PEG is a linear PEG of about 30 kDa and the GH is hGH substituted at a position corresponding to amino acid 35 of SEQ ID NO: 2 with a para-acetyiphenylalanine, and wherein the oxime bond is formed between the para-acetylphenylalanine and the PEG.

75. A method of treatment comprising administering to an individual in need of treatment an effective amount of a hormone composition comprising a growth hormone (GH) linked by covalent bond(s) to at least one water-soluble polymer, wherein the covalent bond(s) is an oxime bond.
76. The method of claim 75 wherein the individual suffers from a condition selected from the group consisting of pediatric growth hormone deficiency, idiopathic short stature, adult growth hormone deficiency of childhood onset, adult growth hormone deficiency of adult onset, and secondary growth hormone deficiency.
77. A method of treatment comprising administering to an individual in need of treatment an
effective amount of a hormone composition comprising a growth hormone (GH) linked by
covalent bond(s) to at least one water-soluble polymer, wherein the water-soluble polymer is a
linear polymer, and wherein the hormone composition is given at a frequency of no more than
once per week, once per two weeks, or once per month.
78. A hormone composition comprising a GH, wherein the GH has an average serum half-life of
at least about 12 hours when administered to a mammal subcutaneously.
79. A hormone composition comprising a GH linked via an oxime bond to a PEG, wherein the GH
has an average serum half-life of at least about 7-fold the serum half-life of a composition
comprising the GH without the PEG, when administered to a mammal subcutaneously.


Documents:

2737-CHENP-2007 AMENDED CLAIMS 14-02-2011.pdf

2737-CHENP-2007 AMENDED PAGES OF SPECIFICATION 14-02-2011.pdf

2737-CHENP-2007 CORRESPONDENCE OTHERS 25-06-2010.pdf

2737-chenp-2007 form-3 14-02-2011.pdf

2737-CHENP-2007 OTHER PATENT DOCUMENT 14-02-2011.pdf

2737-CHENP-2007 POWER OF ATTORNEY 14-02-2011.pdf

2737-chenp-2007 correspondence others 14-02-2011.pdf

2737-CHENP-2007 CORRESPONDENCE OTHERS.pdf

2737-chenp-2007-abstract.pdf

2737-chenp-2007-claims.pdf

2737-chenp-2007-correspondnece-others.pdf

2737-chenp-2007-description(complete).pdf

2737-chenp-2007-drawings.pdf

2737-chenp-2007-form 1.pdf

2737-chenp-2007-form 3.pdf

2737-chenp-2007-form 5.pdf

2737-chenp-2007-pct.pdf


Patent Number 248485
Indian Patent Application Number 2737/CHENP/2007
PG Journal Number 29/2011
Publication Date 22-Jul-2011
Grant Date 19-Jul-2011
Date of Filing 22-Jun-2007
Name of Patentee AMBRX, INC
Applicant Address 10975 N. Torrey Pines Road, Suite 100, La Jolla, CA 92037 (US)
Inventors:
# Inventor's Name Inventor's Address
1 CHO, Ho, Sung 5225 Fiore Terrace, Apt. 107, San Diego, CA 92122
2 DANIEL, Thomas, O 2201 VIA PRAVIA LA JOLLA CALIFORNIA 92037
3 DIMARCHI, Richard 10890 Wilmington Drive, Carmel, IN 46033
4 PUTNAM, Anna-Maria, A., HAYS 3187 Via Alicante, #251, La Jolla, CA 92037
5 WILSON, Troy 575 Old Mill Road, San Marino, CA 91108
6 SIM, Bee-Cheng 7564 Charmant Drive #18277, San Diego, CA 92122
7 LITZINGER, David 13976 Arbolitos Drive, Poway, CA 92064
PCT International Classification Number C12Q 1/68
PCT International Application Number PCT/US05/46542
PCT International Filing date 2005-12-21
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/727,996 2005-10-17 U.S.A.
2 60/638,616 2004-12-22 U.S.A.