Indian Patents
Title of Invention

MODIFIED BOUGANIN PROTEINS, CYTOTOXINS AND METHODS AND USES THEREOF
Abstract Modified forms of bouganin protein are provided having biological activity and a reduced propensity to activate human T cells as compared to the non-modified bouganin protein. Also provided are T-cell epitope peptides of bouganin, and modified T-cell epitope peptides of bouganin, which have a reduced propensity to activate human T cells as compared to the non-modified T-cell epitope peptide. Also provided are cytotoxins that comprise a ligand which binds to cancer cells, and is attached to modified bouganin proteins. Also provided are methods of inhibiting or destroying mammalian cancer cells using the cytotoxins and pharmaceutical compositions for treating human cancer.
Full Text TITLE: Modified Bouganin Proteins, Cytotoxins and Methods and Uses Thereof
FIELD OF THE INVENTION
The invention relates to modified bouganin proteins and cytotoxins containing the modified proteins useful as therapeutics against cancer. Specifically, T-cell epitopes are removed .or altered to reduce immunogenicity of the bouganin toxins.
BACKGROUND OF THE INVENTION
There are many instances whereby the efficacy of a therapeutic protein is limited by an unwanted immune reaction to the therapeutic protein. Several mouse monoclonal antibodies have shown promise as therapies in a number of human disease settings but in certain cases have failed due to the induction of significant degrees of a human anti-murine antibody (HAMA) response [Schraff, R. W. et al (1985) Cancer Res. 45: 879-885; Shawler, D.L et al (1985) J. Immunol. 135: 1530-1535]. For monoclonal antibodies, a number of techniques have been developed in attempt to reduce the HAMA response [WO 89/09622; EP 0239400; EP 0438310; WO 91/06667]. These recombinant DNA approaches have generally reduced the mouse genetic information in the final antibody construct whilst increasing the human genetic information in the final construct. Notwithstanding, the resultant "humanised" antibodies have, in several cases, still elicited an immune response in patients [Issacs J.D. (1990) Sem. Immunol. 2: 449, 456; Rebello, P.R. et al (1999) Transplantation 68:1417-1420].
The key to the induction of an immune response is the presence within the protein of peptides that can stimulate the activity of T-cells via presentation on MHC class II molecules, so-called "T-cell epitopes". Such T-cell epitopes are commonly defined as any amino acid residue sequence with the ability to bind to MHC Class II molecules. Implicitly, a "T-cell epitope" means an epitope which when bound to MHC molecules can be recognized by a T-cell receptor (TCR), and which can, at least in principle, cause the activation of these T-cells by engaging a TCR to promote a T-cell response.

MHC Class II molecules are a group of highly polymorphic proteins which play a central role in helper T-cell selection and activation. The human leukocyte antigen group DR (HLA-DR) are the predominant isotype of this group of proteins; however, isotypes HLA-DQ and HLA-DP perform similar functions. In the human population, individuals bear two to four DR alleles, two DQ and two DP alleles. The structure of a number of DR molecules has been solved and these appear as an open-ended peptide binding groove with a number of hydrophobic pockets which engage hydrophobic residues (pocket residues) of the peptide [Brown et al (1993) Nature 364: 33; Stern et al (1994) Nature 368: 215]. Polymorphism identifying the different allotypes of class II molecule contributes to a wide diversity of different binding surfaces for peptides within the peptide binding groove and at the population level ensures maximal flexibility with regard to the ability to recognize foreign proteins and mount an immune response to pathogenic organisms.
An immune response to a therapeutic protein proceeds via the MHC class II peptide presentation pathway. Here exogenous proteins are engulfed and processed for presentation in association with MHC class II molecules of the DR, DQ or DP type. MHC Class II molecules are expressed by professional antigen presenting cells (APCs), such as macrophages and dendritic cells amongst others. Engagement of a MHC class II peptide complex by a cognate T-cell receptor on the surface of the T-cell, together with the cross-binding of certain other co-receptors such as the CD4 molecule, can induce an activated state within the T-cell. Activation leads to the release of cytokines further activating other lymphocytes such as B cells to produce antibodies or activating T-killer cells as a full cellular immune response.
T-cell epitope identification is the first step to epitope elimination as recognized in WO98/52976; WOOO/34317; WO02/069232; WO02/079232; and WO02/079415. In these teachings, predicted T-cell epitopes are removed by the use of judicious .amino acid substitution within the protein of interest. Besides computational techniques, there are in vitro methods for measuring the ability of synthetic peptides to bind MHC class II molecules.

An exemplary method uses B-ce!l lines of defined MHC aitotype as a source of MHC class II binding surface and may be applied to MHC class II ligand identification [Marshall K.W. et al. (1994) J. Immunol. 152:4946-4956; O'Sullivan et al (1990) J. Immunol. 145: 1799-1808; Robadey C. et al (1997) J. Immunol 159: 3238-3246]. However, such techniques are not adapted for the screening of multiple potential epitopes to a wide diversity of MHC allotypes, nor can they confirm the ability of a binding peptide to function as a T-cell epitope.
Techniques exploiting soluble complexes of recombinant MHC molecules in combination with synthetic peptides have also come into use [Kern, F. et al (1998) Nature Medicine 4:975-978; Kwok, W.W. et al (2001) TRENDS in tmtnunol. 22:583-588]. These reagents and procedures are used to identify the presence of T-cell clones from peripheral blood samples from human or experimental animal subjects that are able to bind particular MHC-peptide complexes and are not adapted for screening multiple potential epitopes to a wide diversity of MHC allotypes.
Biological assays of T-cell activation offer a practical option to providing a reading of the ability of a test peptide/protein sequence to evoke an immune response. Examples of this kind of approach include the work of Petra et al using T-cell proliferation assays to the bacterial protein staphylokinase, followed by epitope mapping using synthetic peptides to stimulate T-cell lines [Petra, A.M. et al (2002) J. Immunol. 168: 155-161]. Similarly, T-cell proliferation assays using synthetic peptides of the tetanus toxin protein have resulted in definition of immunodominant epitope regions of the toxin [Reece J.C. et al (1993) J. Immunol. 151: 6175-6184]. WO99/53038 discloses an approach whereby T-cell epitopes in a test protein may be determined using isolated sub-sets of human immune cells, promoting their differentiation in vitro and culture of the cells in the presence of synthetic peptides of interest and measurement of any induced proliferation in the cultured T-cells. The same technique is also described by Stickler et al. [Stickler, M.M. et al (2000) J. Immunotherapy 23:654-660], where in both instances the method is applied to the detection of T-cell epitopes within bacterial subtilisin. Such a technique

requires careful application of cell isolation techniques and cell cuttufle w'rth multiple cytokine supplements to obtain the desired immune cell sub-sets (dendritic cells, CD4+ and or CD8+ T-cells) and is not conducive to rapid through-put screening using multiple donor samples.
Recently a combination approach using population based T-cell proliferation assays and in silico simulation of peptide MHC binding in the design of epitope depleted proteins has also been advanced [WO 03/104803].
As depicted above and as consequence thereof, it would be desirable to identify and to remove or at least to reduce T-cell epitopes from a principal therapeutically valuable but originally immunogenic peptide, polypeptide or protein.
SUMMARY OF THE INVENTION
The invention is conceived to overcome the practical reality that soluble proteins introduced with therapeutic intent in humans can trigger an immune response resulting in development of host antibodies that bind to the soluble protein. The present invention seeks to address this by providing bouganin proteins with reduced propensity to elicit an immune response. According to the methods described herein, the inventors have identified the regions of the bouganin molecule comprising the critical T-cell epitopes driving the immune responses to this protein.
The present invention relates to a modified bouganin protein wherein the modified bouganin has a reduced propensity to elicit an immune response. In a preferred embodiment, the modified bouganin has a reduced propensity to activate T-cells and the modified bouganin is modified at one or more amino acid residues in a T-cell epitope. The T-cell epitopes are selected preferably from the group consisting of:
a) AKVDRKDLELGVYKL (epitope region R1, SEQ ID NO: 2),
b) LGVYKLEFSIEAIHG (epitope region R2, SEQ ID NO: 3); and
c) NGQEIAKFFLMQM (epitope region R3, SEQ ID NO: 4).
The present invention also relates to a cytotoxin comprising a targeting moiety attached to a modified bouganin protein of the invention. In one

embodiment, the targeting moiety is a ligand that binds to a cancer cell. In a further embodiment, the ligand is an antibody or antibody fragment that binds to a cancer cell. In a particular embodiment, the antibody recognizes Ep-CAM or tumor-associated antigen. In a most particular embodiment, the present invention provides a cytotoxin comprising VB6-845 or VB6-011.
In another aspect, the invention provides a method of inhibiting or destroying cancer cells comprising administering a cytotoxin of the invention to the cancer cells.
The present invention also relates to a method of treating cancer by administering a cytotoxin of the invention to an animal in need thereof.
Still further, a process .is provided for preparing a pharmaceutical for treating an animal with cancer comprising the steps of identifying T-cell epitopes of bouganin, modifying one or more amino acid residues in a T-cell epitope to prepare a modified bouganin having reduced propensity to activate T-cells; preparing a cytotoxin have a cancer-binding ligand attached to a modified bouganin; and suspending the cytotoxin in a pharmaceutically acceptable carrier, diluent or excipient.
In a further aspect, the invention provides a pharmaceutical composition for treating an animal with cancer comprising the cytotoxin of the invention and a pharmaceutically acceptable carrier, diluent or excipient.
The cytotoxins, compositions and methods of the present invention may be used to treat various forms of cancer such as colorectal cancer, breast cancer, ovarian cancer, pancreatic cancer, head and neck cancer, bladder cancer, gastrointestinal cancer, prostate cancer, small cell and non small cell lung cancer, sarcomas, gliomas, T- and B-cell lymphomas.
The invention also provides the T-cell epitope peptides of the bouganin protein and the modified T-cell epitope peptides of the invention.
Other features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples while indicating preferred embodiments of the invention are given by way of illustration only, since various changes and modifications within the spirit and

scope of the invention will become apparent to those skilled in the art from this detailed description.
BRIEF DESCRIPTION OF THE DRAWINGS
The invention will now be described in relation to the drawings in which:
Figure 1 shows results of activity assays of the T-cell epitope depleted modified bouganin proteins Bou156 (panel A) and Bou157 (panel B). Bou156 comprises the substitutions V123A, D127A, Y133N and I152A. Sou 157 comprises the substitutions V123A, D127A, Y133Q and I152A. Both assay sets are conducted using wild type protein and a disabled modified bouganin (Y70A) as controls. Activity is expressed as % measured luciferase activity versus concentration of bouganin protein in the assay.
Figure 2 shows T-cell proliferation assay results for three synthetic peptides and 2 different PBMC donor samples. The peptides designated Del-41, Del-44 and Del-50 were tested at I^M final concentration (panel A) and 5\M final concentration (panel B). These peptides are derived from the immunogenic regions of the bouganin molecule and contain substitutions designed to eliminate their immunogenicity.
Figure 3 illustrates VB6-845, a modified bouganin cytotoxin having a Fab anti-Ep-CAM, wherein the de-bouganin (Bou156) is linked to the C-terrninus of the CH domain via a furin linker. Figure 3A illustrates the dicistronic unit encoding the pro-sequences, Figure 3B illustrates the nucleic acid coding sequence (SEQ ID N0:15) and the amino acid sequence (SEQ ID NO: 16) of the pro-sequences and Figure 3C illustrates the assembled VB6-845 protein without the pelB sequences.
Figure 4 illustrates the map of the expression vector plNG3302. Inserts of the examples were ligated in 3302 vector using EcoRI and Xhol restriction sites.
Figure 5 illustrates the control Fab anti-Ep-CAM construct without the plant toxin, de-bouganin (VB5-845). Figure 5A illustrates the dicistronic unit encoding the pro-sequences, Figure 5B illustrates the nucleic acid coding

sequence (SEQ ID NO:17) and the amino acid sequence (SEQ ID NO:18) of the pro-sequences and Figure 5C illustrates the assembled VB5-845 protein without the pelB sequences.
Figure 6 illustrates the Fab anti-Ep-CAM de-bouganin construct VB6-845-CL-de-bouganin, wherein the Bou156 is linked at the C-terminus of the CL domain. Figure 6A illustrates the dicistronic units encoding the pro-sequences, Figure 6B illustrates the nucleic acid coding sequence (SEQ ID N0:19) and the amino acid sequence (SEQ ID N0:20) of the pro-sequences and Figure 6C illustrates the assembled VB6-845-C|_-de-bouganin protein without the pelB sequences.
Figure 7 illustrates the Fab anti Ep-CAM, de-bouganin construct, VB6-845-NVH-de-bouganin, wherein Bou156 is linked to the N-terminus of the VH domain. Figure 7A illustrates the dicistronic units encoding the pro-sequences, Figure 7B illustrates the nucleic acid coding sequence (SEQ ID N0:21) and the amino acid sequence (SEQ ID NO:22) of the pro-sequences and Figure 7C illustrates the assembled VB6-845-NVH-de-bouganin protein without the pelB sequences.
Figure 8 illustrates the Fab anti-Ep-CAM de-bouganin construct, VB6-845-NV|_-de-bouganin, wherein Bou156 is linked to the N-terminus of the VL domain. Figure 8A illustrates the dicistronic units encoding the pro-sequences, Figure 8B illustrates the nucleic acid coding sequence (SEQ ID N0:23) and the amino acid sequence (SEQ ID NO:24) of the pro-sequences and Figure 8C illustrates the assembled VB6-845-NVi_-de-bouganin protein without the pelB sequences.
Figure 9 is a Western Blot illustrating the expression of VB6-845 (construct of Figure 3) and VB6-845-CL-de-bouganin (Bou156) (construct of Figure 6) in the supernatant of induced E104 cells at lab-scale.
Figure 10 illustrates the results of the flow cytometry reactivity studies. Figure 10A illustrates the reactivity of VB6-845 (construct of Figure 3) and VB6-845-Ci_-de-bouganin (construct of Figure 6) in Ep-CAM-positive cell lines CAL 27 and OVCAR-3 and Ep-CAM-negative cell line A-375, while Figure 10

B, illustrates the results of the same tests conducted with VB6-845 (construct >f Figure 3) and VB6-845-gelonin (construct of Figure 14C) and control (PBS).
Figure 11 is a graph illustrating the results of the competition assay-/B6-845 and Proxinium™ in NIH:OVCAR-3 cells and as described in Example 7.
Figure 12 is a graph illustrating the results of the cell free assay of Example 7.
Figure 13 illustrates the results of the MTS cytotoxicity assay of Example 8 comparing the cytoxocity of VB6-845 (construct of Figure 3), VB6-345-CL-de-bouganin (construct of Figure 6) and de-bouganin (Bou156) in DAL 27 (Figure 13A) and NIH:OVCAR3 (Figure 13B) cells.
Figures 14A and B illustrate the results of the MTS cytotoxicity assay Df Example 8 comparing the cytoxocity of VB6-845 (construct of Figure 3), \/B6-845-gelonin (construct of Figure 14C) and gelonin in CAL 27 (Figure 14A) and NIH:OVCAR3 (Figure 14B) cells. Figure 14C illustrates the nucleic acid coding sequence (SEQ ID N0:25) and the amino acid sequence (SEQ ID N0:26) of the VB6-845-gelonin construct.
Figure 15 illustrates the nucleic acid coding sequence (SEQ ID NO: 27) and the amino acid sequence (SEQ ID N0:28) of the pro-sequences of VB6-011.
Figure 16 illustrates the results of the MTS cytotoxicity assay of Example 9 showing the cytotoxicity of VB6-011 in MB-435S cells.
DETAILED DESCRIPTION OF THE INVENTION
The inventors have identified T-cell epitopes in bouganin, and have designed and made modified bouganin proteins that have reduced propensity to activate human T cells compared to the non-modified bouganin protein.
(A) Modified Bouganin Proteins
The present invention relates to a modified bouganin protein wherein bouganin has been modified in order to have a reduced propensity to elicit an immune response, preferably a T-cell response, as compared to a non-

modified bouganin protein. Mature bouganin protein is a single polypeptide of 250 amino acids with a molecular weight of approximately 26,200 Da [Den Hartog et al (2002) Eur. J. Biochem. 269: 1772-1779; US Patent No. 6,680,296]. Bouganin is a type 1 ribosome inactivating protein (RIP) originally isolated from the plant Bougainvillea spectabilis Willd [Bolognesi et al (1997) Planta 203: 422-429]. The RIPs from plants are RNA N-glycosidases that depurinate the major ribosomal RNA of cells, thereby damaging the ribosornes and leading to a cessation of protein synthesis and cell death.
The amino acid sequence of the mature bouganin protein (depicted in single-letter code) is:
YNTVSFNLGEAYEYPTFIQDLRNELAKGTPVCQLPVTLQTIADDKRFV LVDITTTSKKTVKVAIDVTDVYWGYQDKWDGKDRAVFLDKVPTVAT SKLFPGVTNRVTLTFDGSYQKLVNAAKVDRKDLELGVYKLEFSIEAIH GKTINGQEIAKFFLIVIQMVSEAARFKYIETEWDRGLYGSFKPNFKVL NLENNWGDISDAIHKSSPQCTTINPALQLISPSNDPWWNKVSQISPD MGILKFKSSK [SEQ ID NO. 1].
The term "non-modified bouganin protein" means a bouganin protein that has not been modified in order to reduce its propensity to elicit an immune response. The sequence of wild-type or a non-modified bouganin is shown in SEQ ID NO:1. However, one of skill in the art will appreciate that the term "non-modified bouganin" also includes modifications to SEQ ID NO:1 as long as such modifications do not reduce the propensity to elicit an immune response. Examples of modifications that can be made to SEQ ID N0:1 include peptide fragments and conservative amino acid substitutions that do not reduce the immunogenicity of the protein.
The term "modified bouganin protein" means a bouganin protein that has been modified as compared to the non-modified bouganin protein (described above) wherein said modification reduces the propensity of the bouganin to elicit an immune response. Modified bouganin protein can also be referred to as deimmunized bouganin. The "modified bouganin protein" can be a modified full length sequence or a modified fragment of the non-modified bouganin protein. The "modified bouganin protein" may also contain

other changes as compared to the wild-type bouganin sequence which do not alter immunogenicity of the peptide. The modified bouganin protein will preferably have the same biological activity as the non-modified bouganin.
The term "reduced propensity to elicit an immune response" as used herein means that the modified bouganin protein is less immunogenic than non-modified bouganin.
The term "immune response" includes both cellular and humoral immune responses. In a preferred embodiment, the modified bouganin has a reduced propensity to activate T-cells.
The term "reduced propensity to activate human T-cells" as used herein means the modified bouganin protein has a reduced propensity to activate human T-cells as compared to the non-modified bouganin protein. One of skill in the art can test whether or not a modified bouganin has a reduced propensity to activate T-cells using assays known in the art including assessing the stimulation index of the protein.
The term "stimulation index" as used herein refers to the measure of the ability of the modified or non-modified bouganin protein to activate h uman T cells. For example, the modified or non-modified bouganin protein, or peptides thereof, can be tested for their ability to evoke a prolife native response in human T-cells cultured in vitro. Where this type of approach is conducted using naTve human T-cells taken from healthy donors, the inventors have established that in the operation of such an assay, a stimulation index equal to or greater than 2.0 is a useful measure of induced proliferation. The stimulation index is conventionally derived by division of the proliferation score (e.g. counts per minute of radioactivity if using 3H-thymidine incorporation) measured to the test peptide by the score measured in cells not contacted with a test peptide.
In one embodiment, the invention provides a modified bouganin protein, wherein the modified bouganin protein has biological activity and has reduced propensity to activate human T cells compared to a non-modified bouganin protein.

In another embodiment, the invention provides a modified bouganin protein, wherein the modified bouganin protein has reduced propensity to activate human T cells compared to a non-modified bouganin protein and has biological activity that is lower than the non-modified bouganin protein. In yet another embodiment, the invention provides a modified bouganin protein wherein the modified bouganin protein has reduced propensity to activate human T cells and no biological activity. Such modified proteins could, for instance, be used as controls, in assays or to tolerize subjects.
The term "biological activity" as used herein is the ability of the modified or non-modified bouganin pn>tein to inhibit protein synthesis on ribosomes, which can be assessed in a number of ways. It should be noted that a modified bouganin protein will still have biological activity even if such activity is lower than that of the non-modified protein, however it would need to have some level of detectable activity. For example, the biological activity of the modified or non-modified bouganin protein can be assessed by identifying their N-glycosidase activity, and in particular with sufficient activity to provide significant inhibition of protein translation. One such suitable assay involves testing the activity of the variant bouganin proteins in comparison to non-modified bouganin in a cell-free protein synthesis assay. A coupled transcription/translation mix containing methionine, DNA encoding the reporter protein luciferase and serial dilutions of non-modified and modified bouganin protein are co-incubated. The levels of translated luciferase are readily detected using a luminescence counter following addition of a substrate reagent. The measured luminescence is inversely proportional to the bouganin N-glycosidase activity present in the reaction. It is usual to provide a negative control such as an in-active bouganin protein, for example containing a Y70A substitution.
In a preferred embodiment, the modified bouganin peptide is modified at one or more T-cell epitopes in the bouganin protein sequence.
The term 'T-cell epitope" means an amino acid sequence which is able to bind major histocompatibllity complex: (MHC) class II, able to stimulate T-

cells and/or also able to bind (without necessarily measurably activating) T-cells in complex with MHC class II.
In one aspect, a general method that can be used in the present invention leading to the modified bouganin proteins comprising modified T-cell epitopes comprises the following steps:
(i) determining the amino acid sequence of the protein or part
thereof;
(ii) identifying one or more potential T-cell epitopes within the amino acid sequence of the protein by methods such as determination of the binding of the peptides to MHC molecules using in vitro or in silico techniques or biological assays;
(Hi) designing new sequence variants with one or more amino acids within the identified potential T-cell epitopes modified in such a way to substantially reduce or eliminate the activity of the T-cell epitope as determined by the binding of the peptides to MHC molecules using in vitro or in silico techniques or biological assays. Such sequence variants are created in such a way to avoid creation of new potential T-cell epitopes by the sequence variations unless such new potential T-cell epitopes are, in turn, modified in such a way to substantially reduce or eliminate the activity of the T-cell epitope;
(iv) constructing such sequence variants by recombinant DMA techniques and testing said variants in order to identify one or more variants with desirable properties according to well known recombinant techniques; and (v) optionally repeating steps (ii) to (iv).
In an example, step (iii) is carried out by substitution, addition or deletion of amino acid residues in any of the T-cell epitopes in the non-modified bouganin protein. In another example, the method to make the modified bouganin protein is made with reference to the homologous protein sequence and/or in silico modeling.

The identification of potential T-cell epitopes according to step (ii) can be carried out according to methods described previ ously in the art. Suitable methods are disclosed in WO 98/59244; WO 98/52976; WO 00/34317; WO 02/069232 and may be used to identify binding propensity of bouganin derived peptides to an MHC class II molecule. In order to identify biologically relevant peptides, the inventors have developed an approach exploiting ex vivo human T-cell proliferation assays. This approach has proven to be a particularly effective method and has involved the testing of overlapping bouganin derived peptide sequences in a scheme so as to scan and test the entire bouganin sequence. The synthetic peptides are tested for their ability to evoke a proliferative response in human T-cells cultured in vitro. Where this type of approach is conducted using naTve human T-cells taken from healthy donors, the inventors have established that in the operation of such an assay, a stimulation index equal to or greater than 2.0 is a useful measure of induced proliferation. The stimulation index is conventionally derived by division of the proliferation score (e.g. counts per minute of radioactivity if using 3H-thymidine incorporation) measured to the "test peptide by the score measured in cells not contacted with a test peptide.
Accordingly, in the present studies, 89 synthetic 15-mer peptides (as listed in Table 1) were used in T-cell proliferation assays with PBMCs (peripheral blood . mononuclear cells) from naTve donors (i.e. no known sens'rtization to bouganin). 20 donor PBMC samples were selected to achieve an optimal coverage of MHC class II allotypes. PBIVICs were stimulated with individual peptides in triplicate cultures for 7 days, before proliferation was assessed by 3H-thymidine incorporation. All peptides were diluted at two different concentrations: 1nM and 5piM. The stimulation indices (SI) were calculated as the amount of 3H incorporated into the cells, divided by the amount of 3H incorporated in mock-stimulated controls.
This method has identified the most immunogenic regions of the bouganin molecule in humans. Accordingly, in a specific embodiment, the modified bouganin protein is modified at one or more amino acid residues in a T-cell epitope selected from the group consisting of:

a) AKVDRKDLELGVYKL, termed herein epitope region R1 (SEQ ID
N0:2);
b) LGVYKLEFSIEAIHG, termed herein epitope region R2 (SEQ ID
NO:3); and
c) NGQEIAKFFLIVIQM, termed herein epitope region R3 (SEQ ID
NO:4).
These T-cell epitopes have been identified on the basis of giving SI > 2 in two or more donor PBMC samples. The above disclosed peptide sequences represent the critical information required for the construction of modified bouganin proteins in which one or more of these epitopes is compromised.
In an embodiment of the invention, the modified bouganin protein of the invention has at least one T-cell epitope removed. In another embodiment, the modified bouganin protein of the invention has one, two or three T-cell epitopes removed. The invention also contemplates a modified bouganin protein wherein 1 to 9 amino acid residues are modified, preferably in the T-cell epitope. In another embodiment, 1 to 5 amino acid residues are modified. The term "modified" as used herein means the amino acid residues are modified by substitution, addition or deletion, preferably by substitution, but the bouganin protein has reduced propensity to activate human T cells. In another embodiment the modified protein has biological activity. More preferably the modified bouganin protein of the invention is modified by substitution at a position corresponding to any of the amino acids specified within sequences (a), (b) or (c) above.
One embodiment of the present invention comprises bouganin proteins for which the MHC class II ligands identified within any of the epitopes R1 -R3 are modified such as to eliminate binding or otherwise reduce the numbers of MHC allotypes to which the peptide can bind. Amino acids in the R1 to R3 regions to eliminate binding or otherwise reduce the numbers of MHC allotypes to which the peptide can bind can be modified by substitution, addition or deletion.

For the elimination of T-cell epitopes, amino acid substitutions are made at appropriate points within the peptide sequence predicted to achieve substantial reduction or elimination of the activity of the T-cell epitope. In practice an appropriate point will in one embodiment equate to an amino acid residue binding within one of the pockets provided within the MHC class II binding groove.
In one embodiment, the binding within the first pocket of the cleft at the so-called P1 or P1 anchor position of the peptide is modified. The quality of binding interaction between the P1 anchor residue of the peptide and the first pocket of the MHC class II binding groove is recognized as being a major determinant of overall binding affinity for the whole peptide. An appropriate substitution at this position of the peptide will be for a residue less readily accommodated within the pocket, for example, substitution to a more hydrophilic residue. Amino acid residues in the peptide at positions equating to binding within other pocket regions within the MHC binding cleft are also considered and fall under the scope of the present.
It is understood that single amino acid substitutions, deletions or additions within a given potential T-cell epitope are a preferred route by which the epitope may be eliminated. Combinations of modifications (i.e. substitutions, deletions and additions) within a single epitope may be contemplated and for example can be particularly appropriate where individually defined epitopes are in overlap with each other as is the present case where epitope regions R1 and R2 overlap by 5 residues. Moreover, either single amino acid modifications within a given epitope or in combination within a single epitope may be made at positions not equating to the "pocket residues" with respect to the MHC class II binding groove, but at any point within the peptide sequence. Modifications may be made with reference to an homologue-structure or structural method produced using in silico techniques known in the art and may be based on known structural features of the molecule according to this invention. All such modifications fall within the scope of the present invention.

The epitope regions R1 - R3 of bouganin were analyzed for indication of MHC class II ligands encompassed within their respective sequences. A software tool exploiting the schemes outlined in WO 98/59244 and WO 02/069232 was used for this analysis. The software simulates the process of antigen presentation at the level of the peptide MHC class II binding interaction to provide a binding score for any given peptide sequence. Such a score is determined for many of the predominant MHC class II allotypes existent in the population. As this scheme is able to test any peptide sequence, the consequences of amino acid substitutions, additions or deletions with respect to the ability of a peptide to interact with a MHC class II binding groove can be predicted. Consequently new sequence compositions can be designed which contain reduced numbers of peptides able to interact with the MHC class II and thereby function as immunogenic T-cell epitopes.
Under this scheme in one embodiment of the invention substitutions within epitope region R1 comprise changes at positions V123, D127 and/or E129. Similarly for epitope region R2, in one embodiment the substitution is at position Y133. This residue falls into the region of overlap between R1 and R2 but substitution at Y133 is sufficient to eliminate the R2 related MHC class II ligand and is not sufficient of itself to eliminate R1 related MHC class II ligands. For epitope region R3, in one embodiment of the invention substitutions are to residues E151, and/or 1152.
In all instances the substitutions are to one or more alternative amino> acid residues. Analysis of R1 with the MHC II stimulation software indicated that amino acid residues 123, 127, 129 and 131 were key residues in this-epitope for binding to MHC II molecules. Residue 123 is a preferred site for mutation of the R1 region because it is at the surface of the molecule, away from the active site and is variable in RIP sequence alignment Nevertheless, not all substitution yield an active molecule hence the need to validates mutations in the bioactivity assay. Thus for example within R1, substitutions V123T, V123A and V123Q are examples of preferred alternative substitutions. Residue 131 was found to be absolutely conserved in RIP and hence is unlikely suitable for mutation. Residue 127 and 129 are not highly conserved

but only a restricted number of residues were found to have an impact on MHC II binding. The substitution sets: D127G, D127A, E129Q and E129G are also preferred substitutions. For R2, residue 133 was shown to be a likely candidate to abolish MHC II binding and its apparent surface localization (as determined by modeling) combined to the fact that it is not highly conserved across RIP make it a good candidate for mutation. Preferred alternative substitutions were found to be Y133N, Y133T, Y133A, Y133R, Y133D, Y133E, Y133Q, Y133G, Y133K, Y133H and Y133S. For R3, amino acid residues 152,155 and 158 were identified as key residues for MHC II binding. However, residues 155 and 158 are part of a highly conserved hydrophobic stretch thus suggesting that their mutation would not yield bioactive molecules. Residue poorly conserved was found to be a more likely candidate. For R3, the substitution sets: I152Q and I152A are also preferred substitutions.
Accordingly, the invention provides a modified bouganin protein wherein the bouganin is modified at one or more of X1, X2, X3, X4 or X5 as follows:
a) AKX1DRKX2LX3LGVX4KL (epitope region R1, SEQ ID NO:5);
b) LGVX4KLEFSlEAIHG (epitope region R2, SEQ ID NO:6); and
c) NGQEX5AKFFLIVIQM (epitope region R3, SEQ ID NO:7)
wherein X1 through X5 can be any amino acid.
In a specific embodiment, X1 is T or A or Q; X2 is G or A; X3 is Q or G; X4 is N or D or T or A or R or Q or E or G or H or K or S; and X5 Is Q or A (epitope region R1, SEQ ID NO:8; epitope region R2, SEQ ID NO:9; epitope region R3, SEQ ID N0:10).
Taken together a most preferred substitution set may be compiled based on immunogenic epitope mapping studies using ex vivo T-cell assays, in silico MHC peptide binding simulations and structural considerations from sequence homology analysis. Finally, if a bioactive protein is preferred, in vitro activity assay can then be performed on the modified protein that may comprise one or multiple mutations.

Accordingly, in another embodiment, the invention provides a modified
bouganin peptide, comprising the amino acid sequence:
YNTVSFNLGEAYEYPTFIQDLRNELAKGTPVCQLPVTLQTIADDKRFV
LVDITTTSKKTVKVAIDVTDVYWGYQDKWDGKDRAVFLDKVPTVAT
SKLFPGVTNRVTLTFDGSYQKLVNAAKX1DRKX2LX3LGVX4KLEFSIEA
IHGKTINGQEX5AKFFLMQMVSEAARFKYIETEWDRGLYGSFKPNF
KVLNLENNWGDISDAIHKSSPQCTTINPALQLISPSNDPWWNKVSQI
SPDMGILKFKSSK
wherein X1 through X5 can be any amino acid (SEQ ID N0:11).
In a preferred embodiment, X1 is T or A or Q; X2 is G or A; X3 is Q or G;
X4 is N or D or T or A or R or Q or E or G or H or K or S; and X5 is Q or A
(SEQ ID NO: 12).
In a specific embodiment, the modified bouganin protein comprises the
amino acid sequence:
YNTVSFNLGEAYEYPTFIQDLRNELAKGTPVCQLPVTLQTIADDKRFV
LVDITTTSKKTVKVAIDVrDVYWGYQDKWDGKDRAVFLDKVPTVAT
SKLFPGVTNRVTLTFDGSYQKLVNAAKADRKALELGVNKLEFSIEAIH
GKTINGQEAAKFFLIVIQMVSEAARFKYIETENA/DRGLYGSFKPNFKVL
NLENNWGDISDAIHKSSPQCTTINPALQLISPSNDPVWVNKVSQISPD
MGILKFKSSK (SEQ ID NO: 13).
In yet another embodiment, the- modified bouganin protein comprises.
the amino acid sequence:
YNTVSFNLGEAYEYPTFIQDLRNELAKGTPVCQLPVTLQTIADDKRFV
LVDITTTSKKTVKVAIDVTDVYVVGYQDKWDGKDRAVFLDKVPTVAT
SKLFPGVTNRVTLTFDGSYQKLVNAAKADRKALELGVQKLEFSIEAIH
GKTINGQEAAKFFLIVIQMVSEAARFKYIETEWDRGLYGSFKPNFKVL
NLENNWGDISDAIHKSSPQCTTINPALQUSPSNDPWWNKVSQISPD
MGILKFKSSK (SEQ ID N0:14).
Underlined residues are substituted residues different from the non-modified
bouganin protein.
As will be clear to the person skilled in the art, multiple alternative sets
of modifications could be arrived at which achieve the objective of removing

undesired epitopes. The resulting sequences would however remain broadly homologous with the specific proteins disclosed herein and therefore fall under the scope of the present invention. Obvious chemical equivalents to the sequences disclosed by the present invention are also contemplated to fall within the scope of the present invention. Such equivalents include proteins that perform substantially the same function in substantially the same way.
In another embodiment the modified bouganin protein of the invention has 1, 2, 3, 4, 5 or more amino acid modifications in the T-cell epitopes of the protein.
In an additional embodiment, the modified bouganin protein of the invention when tested in a T-cell assay evokes a reduced stimulation index in comparison to the non-modified bouganin protein.
In a further embodiment of the invention, the T-cell epitopes of the bouganin protein are mapped using a T-cell assay and then modified such that upon re-testing in the T-cell assay the modified bouganin protein evokes a stimulation index less than the non-modified bouganin protein, preferably the stimulation index is less than 2.0.
It will be clear to a person skilled in the art that if the modified bouganin protein has substantially reduced or no biological activity, it may need further modification by substitution, addition or deletion of amino acid residues to restore the biological activity of the modified bouganin protein. However, such modified bouganin proteins that have substantially reduced or no biological activity are still encompassed within the scope of the invention and have utility as controls in assays, or for tolerization.
In one embodiment, the modified bouganin is mutated at the tyrbsine residue at position 70 to yield an inactive bouganin. In a specific embodiment, the tyrosine at position 70 is replaced with alanine. In a preferred embodiment, the modified bouganin has the sequence:
YNTVSFNLGEAYEYPTFIQDLRNELAKGTPVCQLPVTLQTIADDKRFV LVDITTTSKKTVKVAIDVTDVAVVGYQDKWDGKDRAVFLDKVPTVAT SKLFPGVTNRVTLTFDGSYQKLVNAAKVDRKDLELGVYKLEFSIEAIH GKTINGQEIAKFFLIVIQMVSEAARFKYIETEWDRGLYGSFKPNFKVL

NLENNWGDISDAIHKSSPQCTTINPALQLISPSNDPWWNKVSQISPD
MGILKFKSSK [SEQ ID NO. 129].
Under the scheme of the present invention, the epitopes are compromised by mutation to result in sequences no longer able to function as T-cell epitopes. It is possible to use recombinant DNA methods to achieve directed mutagenesis of the target sequences and many such techniques are available and well known in the art. In practice a number of modified bouganin proteins will be produced and tested for the desired immune and functional characteristic. It is particularly important when conducting modifications to the protein sequence that the contemplated changes do not introduce new immunogenic epitopes. This event is avoided in practice by re-testing the contemplated sequence for the presence of epitopes and/or of MHC class II ligands by any suitable means.
The modified bouganin proteins of the invention may also contain or be used to obtain or design "peptide mimetics". "Peptide mimetics" are structures which serve as substitutes for peptides in interactions between molecules (See Morgan et al (1989), Ann. Reports Med. Chem. 24:243-252 for a review), Peptide mimetics include synthetic structures which may or may not contain amino acids and/or peptide bonds but retain the structural and functional features protein of the invention, including biological activity and a reduced propensity to activate human T cells. Peptide mimetics also include peptoids, oligopeptoids (Simon et al (1972) Proc. Natl. Acad, Sci USA 89:9367).
Peptide mimetics may be designed based on information obtained by systematic replacement of L-amino acids by D-amino acids, replacement of side chains with groups having different electronic properties, and by systematic replacement of peptide bonds with amide bond replacements. Local conformational constraints can also be introduced to determine conformational requirements for activity of a candidate peptide mimetic. The mimetics may include isosteric amide bonds, or D-amino acids to stabilize or promote reverse turn conformations and to help stabilize the molecule. Cyclic amino acid analogues may be used to constrain amino acid residues to

particular conformational states. The mimetics can also include mimics of the secondary structures of the proteins of the invention. These structures can. model the 3-dimensbnal orientation of amino acid residues into the known secondary conformations of proteins. Peptoids may also be used which are oligomers of N-substituted amino acids and can be used as motifs for the generation of chemically diverse libraries of novel molecules.
The molecules of this invention can be prepared in any of several ways but is most preferably conducted exploiting routine recombinant methods. It is a relatively straightforward procedure to use the protein sequences and information provided herein to deduce a polynucleotide (DNA) encoding any of the preferred protein sequences. This can be achieved for example using computer software tools such as the DNSstar software suite [DNAstar Inc, Madison, Wl, USA] or similar. Any such DNA sequence with the capability of encoding the preferred polypeptides of the present or significant homologues thereof, should be considered as embodiments of this invention.
As a general scheme, genes encoding any of the preferred modified bouganin protein sequences can be made using gene synthesis and cloned into a suitable expression vector. In turn the expression vector is introduced into a host cell and cells selected and cultured. The proteins of the invention are purified from the culture medium and formulated into a preparation for therapeutic administration. Alternatively, a wild-type bouganin gene sequence can be obtained for example following a cDNA cloning strategy using RNA prepared from the root tissues of the Bougainvillea spectabilis Willd plant. The wild-type gene can be used as a template for mutagenesis and construction preferred variant sequences. • In this regard it is particularly convenient to use the strategy of "overlap extension PCR" as described by Higuchi et al [Higuchi et al (1988) Nucleic Acids Res. 16: 7351] although other methodologies and systems could be readily applied.
The biological activity of the proteins of the invention can equally be assessed in many ways. In one embodiment, modified bouganin molecules are identified with N-glycosidase activity, and in particular with sufficient activity to provide significant inhibition of protein translation. One such

suitable assay involves testing the activity of the modified bouganin proteins in comparison to non-modified bouganin in a cell-free protein synthesis assay. A coupled transcription/translation mix containing methionine, DNA encoding the reporter protein luciferase and serial dilutions of non-modified and modified bouganin proteins are co-incubated. The levels of translated luciferase are readily detected using a luminescence counter following addition of a substrate reagent. The measured luminescence is inversely proportional to the bouganin N-glycosidase activity present in the reaction. It is usual to provide a negative control such as an in-active bouganin protein for example containing a Y70A substitution.
Constitution of the preferred and active bouganin molecules may be achieved by recombinant DNA techniques and this includes bouganin molecules fused with desired antibody or other targeting moieties. Methods for purifying and manipulating recombinant proteins including fusion proteins are well known in the art. Necessary techniques are explained fully in the literature, such as, "Molecular Cloning: A Laboratory Manual", second edition (Sambrook et al., 1989); "Oligonucleotide Synthesis" (M. J. Gait, ed., 1984); "Animal Cell Culture" (R. I. Freshney, ed., 1987); "Methods in Enzymology" (Academic Press, Inc.); "Handbook of Experimental Immunology" (D. M. Weir & C. C. Blackwell, eds.); "Gene Transfer Vectors for Mammalian Cells" (J. M. Miller & M. P. Calos, eds., 1987); "Current Protocols in Molecular Biology" (F. M. Ausubel et al., eds., 1987); "PCR: The Polymerase Chain Reaction", (Mullis et al., eds., 1994); "Current Protocols in Immunology" (J. E. Coligan et al., eds., 1991).
The proteins and peptides of the invention can be prepared using recombinant DNA methods. The proteins of the invention may also be prepared by chemical synthesis using techniques well known in the chemistry of proteins such as solid phase synthesis (Merrifield, 1964, J. Am. Chem. Assoc. 85:2149-2154) or synthesis in homogenous solution (Houbenweyl, 1987, Methods of Organic Chemistry, ed. E. Wansch, Vol. 15 I and II, Thieme, Stuttgart).

The present invention also provides a purified and isolated nucleic acid molecule comprising a sequence encoding the modified bouganin proteins or peptides of the invention, preferably a sequence encoding the protein described herein as SEQ ID NO:13 or SEQ ID NO:14.
The term "isolated and purified" as used herein refers to a nucleic acid substantially free of cellular material or culture medium when produced by recombinant DNA techniques, or chemical precursors, or other chemicals when chemically synthesized. An "isolated and purified" nucleic acid is also substantially free of sequences which naturally flank the nucleic acid (i.e. sequences located at the 5' and 3' ends of the nucleic acid) from which the nucleic acid is derived.
The term "nucleic acid" as used herein refers to a sequence of nucleotide or nucleoside monomers consisting of naturally occurring bases, sugars and intersugar (backbone) linkages. The term also includes modified or substituted sequences comprising non-naturally occurring monomers or portions thereof, which function similarly. The nucleic acid sequences of the present invention may be ribonucleic (RNA) or deoxyribonucleic acids (DNA) and may contain naturally occurring bases including adenine, guanine, cytosine, thymidine and uracil. The sequences may also contain modified bases such as xanthine, hypoxanthine, 2-aminoadenine, 6-methyl, 2-propyl, and other alkyl adenines, 5-halo uracil, 5-halo cytosine, 6-aza uracil, 6-aza cytosine and 6-aza thymine, pseudo uracil, 4-thiouracil, 8-halo adenine, 8-amino adenine, 8-thiol adenine, 8-thio-alkyl adenines, 8-hydroxy! adenine and other 8-substituted adenines, 8-halo guanines, 8-amino guanine, 8-thiol guanine, 8-thioalkyl guanines, 8-hydroxyl guanine and other 8-substituted guanines, other aza and deaza uracils, thymidines, cytosines, adenines, or guanines, 5-trifluoromethyl uracil and 5-trifluoro cytosine.
In one embodiment, the purified and isolated nucleic acid molecule comprises a sequence encoding the proteins or peptides, preferably SEQ ID NO: 13 or SEQ ID NO: 14, of the invention, comprising
(a) the nucleic acid sequence, wherein T can also be U;
(b) nucleic acid sequences complementary to (a);

(c) nucleic acid sequences which are homologous to (a) or (b);
(d) a fragment of (a) to (c) that is at least 15 bases, preferably 20 to 30 .
bases, and which will hybridize to (a) to (c) under stringent
hybridization conditions; or
(e) a nucleic acid molecule differing from any of the nucleic acids of (a)
to (c)' in codon sequences due to the degeneracy of the genetic
code.
Further, it will be appreciated that the invention includes nucleic acid molecules comprising nucleic acid sequences having substantial sequence homology with the nucleic acid sequences encoding the proteins and peptides of the invention, and fragments thereof. The term "sequences having substantial sequence homology" means those nucleic acid sequences which have slight or inconsequential sequence variations from these sequences, i.e., the sequences function in substantially the same manner to produce functionally equivalent proteins. The variations may be attributable to local mutations or structural modifications.
Nucleic acid sequences having substantial homology include nucleic acid sequences having at least 80%, preferably 90% identity with the nucleic acid sequence encoding the proteins and peptides of the invention.
Another aspect of the invention provides a nucleic acid molecule, and fragments thereof having at least 15 bases, which hybridize to nucleic acid molecules of the invention under hybridization conditions, preferably stringent hybridization conditions. Appropriate stringency conditions which promote DNA hybridization are known to those skilled in the art, or may be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. For example, the following may be employed: 6.0 x sodium chloride/sodium citrate (SSC) at about 45°C, followed by a wash of 2.0 x SSC at 50°C. The stringency may be selected based on the conditions used in the wash step. For example, the salt concentration in the wash step can be selected from a high stringency of about 0.2 x SSC at 50°C. In addition, the temperature in the wash step can be at high stringency conditions, at about 65'C.

Accordingly, nucleic acid molecules of the present invention having a sequence which encodes a protein or peptide of the invention may be incorporated according to procedures known in the art into an appropriate expression vector which ensures good expression of the protein or peptide. Possible expression vectors include but are not limited to cosmids, plasmids, or modified viruses (e.g., replication defective retroviruses, adenoviruses and adeno associated viruses), so long as the vector is compatible with the host cell used. The expression "vectors suitable for transformation of a host cell", means that the expression vectors contain a nucleic acid molecule of the invention and regulatory sequences, selected on the basis of the host cells to be used for expression, which are operatively linked to the nucleic acid molecule. "Operatively linked" is intended to mean that the nucleic acid is linked to regulatory sequences in a manner which allows expression of the nucleic acid.
The invention therefore contemplates a recombinant expression vector of the invention containing a nucleic acid molecule of the invention, or a fragment thereof, and the necessary regulatory sequences for the transcription and translation of the inserted protein-sequence. Suitable regulatory sequences may be derived from a variety of sources, including bacterial, fungal, or viral genes (For example, see the regulatory sequences > described in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990). Selection of appropriate regulatory sequences is dependent on the host cell chosen, and may be readily accomplished by one of ordinary skill in the art. Examples of such regulatory sequences include: a transcriptional promoter and enhancer or RNA polymerase binding sequence, a ribosomal binding sequence, including a translation initiation signal. Additionally, depending on the host cell chosen and the vector employed, other sequences, such as an origin of replication, additional DNA restriction sites, enhancers, and sequences conferring inducibility of transcription may be incorporated into the expression vector. It will also be appreciated that the necessary regulatory sequences may be supplied by the native protein and/or its flanking regions.

The recombinant expression vectors of the invention may also contain a selectable marker gene which facilitates the selection of host cells transformed or transfected with a recombinant molecule of the invention. Examples of selectable marker genes are genes encoding a protein such as G418 and hygromycin which confer resistance to certain drugs, B-galactosidase, chloramphenicol acetyltransferase, or firefly luciferase. Transcription of the selectable marker gene is monitored by changes in the concentration of the selectable marker protein such as S-galactosidase, chloramphenicol acetyltransferase, or firefly luciferase. If the selectable marker gene encodes a protein conferring antibiotic resistance such as neomycin resistance transformant cells can be selected with G418. Cells that have incorporated the selectable marker gene will survive, while the other cells die. This makes it possible to visualize and assay for expression of recombinant expression vectors of the invention and in particular to determine the effect of a mutation on expression and phenotype. It will be appreciated that selectable markers can be introduced on a separate vector from the nucleic acid of interest.
The recombinant expression vectors may also contain genes which encode a fusion moiety which provides increased expression of the recombinant protein; increased solubility of the recombinant protein; and aid in the purification of a target recombinant protein by acting as a ligand in affinity purification. For example, a proteolytic cleavage site may be added to the target recombinant protein to allow separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein.
Recombinant expression vectors can be introduced into host cells to produce a transformed host cell. The term "transformed host cell" is intended to include prokaryotic and eukaryotic cells which have been transformed or transfected with a recombinant expression vector of the invention. The terms "transformed with", "transfected with", "transformation" and "transfection" are intended to encompass introduction of nucleic acid (e.g. a vector) into a cell by one of many possible techniques known in the art. Prokaryotic cells can be transformed with nucleic acid by, for example, electroporation or calcium-

chloride mediated transformation. Nucleic acid can be introduced into mammalian cells via conventional techniques such'as calcium phosphate or calcium chloride co-precipitation, DEAE-dextran mediated transfection, lipofectin, electroporation or microinjection. Suitable methods for transforming and transfecting host cells can be found in Sambrook et al. (Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory press (1989)), and other such laboratory textbooks.
Suitable host cells include a wide variety of prokaryotic and eukaryotic host cells. For example, the proteins of the invention may be expressed in bacterial cells such as E. coli, insect cells (using baculovirus), yeast cells or mammalian cells. Other suitable host cells can be found in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1991).
Nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, "operably linked" means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading frame. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
In some embodiments the expression vector comprises a nucleic acid sequence encoding a modified bouganin with a reduced number of potential T cell epitopes, operably linked to an expression control sequence. In various embodiments the expression vector comprises a nucleic acid sequence encoding the proteins or peptides of the invention, or a degenerate variant thereof and will comprise at least the RIP encoding domain of the said nucleic

acids operably linked with suitable expression control and selection sequences. Degeneracy in relation to polynucleotides refers to the fact well recognized that in the genetic code many amino acids are specified by more than one codon. The degeneracy of the code accounts for 20 different amino acids encoded by 64 possible triplet sequences of the four different bases comprising DNA.
The term "RIP encoding domain" or "Ribosome Inactivating Protein encoding domain" as used here in means the functional domain which gives bouganin its biological activity.
The nucleic acid molecules of the invention may also be chemically synthesized using standard techniques. Various methods of chemically synthesizing polydeoxynucleotides are known, including solid-phase synthesis which, like peptide synthesis, has been fully automated in commercially available DNA synthesizers (See e.g., Itakura et al. U.S. Patent No. 4,598,049; Caruthers et al. U.S. Patent No. 4,458,066; and Itakura U.S. Patent Nos. 4,401,796 and 4,373,071).
The invention also provides nucleic acids encoding fusion proteins comprising a novel protein of the invention and a selected protein, or a selectable marker protein
Another aspect of the present invention is a cultured cell comprising at least one of the above-mentioned vectors.
A further aspect of the present invention is a method for preparing the modified bouganin comprising culturing the above mentioned cell under conditions permitting expression of the modified bouganin from the expression vector and purifying the bouganin from the cell.
(B) Modified Bouqanin Cvtotoxins:
As mentioned previously, bouganin is a type 1 ribosome inactivating protein (RIP) that depurinates the major ribosomal RNA of cells leading to cessation of protein synthesis and cell death. As such, the modified bouganins of the invention can be used to prepare cytotoxins. Cytotoxins containing a modified bouganin protein are preferred over cytotoxins

containing a non-modified bouganin protein as the former is less immunogenic and will be less likely to be destroyed by the immune system before it reaches its target.
Accordingly, the present invention also provides a cytotoxin comprising (a) a targeting moiety attached to (b) a modified bouganin protein of the invention.
The term "modified bouganin protein of the invention" is used for ease of referral and includes any and all of the modified bouganin proteins described herein such as the modified bouganin proteins described above in Section (A) as well as in the figures and examples.
The term "targeting moiety" as used herein refers to a substance, means, or technique of delivering the modified bouganin protein to a target cell. In one 'embodiment the targeting moiety is an antibody. In one embodiment the targeting moiety could be a liposome. In one embodiment the liposome can be linked to an antibody. In another embodiment the targeting moiety is a protein able to direct a specific binding interaction to a particular target cell. Such protein moieties include a variety of polypeptide ligands for which there are specific cell surface receptors and include therefore numerous cytokines, peptide and polypeptide hormones and other biological response modifiers. Prominent examples include such proteins as vascular epithelial growth factor, epidermal growth factor, heregulin, the interleukins, interferons, tumour necrosis factor and other protein and glycoprotein molecules. Fusion proteins of these and other molecules with bouganin of the present invention may be contemplated and may comprise the modified bouganin moiety in either the N-terminal or C-terminal orientation with respect to the protein ligand domain. The targeting moiety may be jointed directly to the proteins of the invention or through a linker. In one embodiment, the linker is a peptide linker or a chemical linker. Equally, chemical cross-linking of the purified ligand to the modified bouganin protein may be contemplated and within the scope of the present invention.

In a preferred embodiment, the present invention provides a cytotoxin comprising (a) a ligand that binds to a cancer cell attached to; (b) a modified bouganin protein of the invention.
The ligand can be any molecule that can bind to a cancer cell including, but not limited to, proteins. In one embodiment, the ligand is an antibody or antibody fragment that recognizes the surface of a cancer cell.
Accordingly, the cytotoxins of the present invention may be used to treat various forms of cancer such as colorectal cancer, breast cancer, ovarian cancer, pancreatic cancer, head and neck cancer, bladder cancer, gastrointestinal cancer, prostate cancer, small cell and non small cell lung cancer, sarcomas, gliomas, T- and B- cell lymphomas.
In one embodiment, the cancer cell binding ligand comprises a complete immunoglobulin molecule that binds to the cancer cell. When a cancer cell binding ligand is an antibody or fragment thereof, cytotoxin can be referred to as immunotoxin. In another embodiment, the cancer cell-binding ligand is a dimer of Fab, Fab1, scFv, single-domain antibody fragments, or disulfide stabilized Fv fragments. In another embodiment, the cancer antibody comprises a variable heavy chain, variable light chain, Fab, Fab1, scFv, single-domain antibody fragment, or disulfide-stabilized Fv fragment Portions of the cancer cell-binding ligand may be derived from one or more species, preferably comprising portions derived from the human species, and most preferably are completely human or humanized. Regions designed to facilitate purification or for conjugation to toxin may also be included in or added to the cancer cell-binding portion.
In a particular embodiment, the cancer cell binding ligand recognizes Ep-CAM. Ep-CAM (for Epithelial Cell Adhesion Molecule, which is also known as 17-1A, KSA, EGP-2 and GA733-2) is a transmembrane protein that is highly expressed in many solid tumors, including carcinomas of the lung, breast, ovary, colorectum, and squamous cell carcinoma of the head and neck, but weakly expressed in most normal epithelial tissues.
Accordingly, in one embodiment, the invention provides an Ep-CAM-targeted-modified bouganin cytotoxin comprising (a) a ligand (such as an

antibody or antibody fragment) that binds to Ep-CAM on the cancer cell attached to; (b) a modified bouganin protein having a reduced propensity to activate T-cells as compared to a non-modified bouganin protein.
In a specific embodiment, the cytotoxin comprises (a) a humanized antibody or antibody fragment that binds to the extracellular domain of human Ep-CAM and comprises complementarity determining region (CDR) sequences derived from a MOC-31 antibody attached to: (b) a modified bouganin protein having a reduced propensity to activate T-cells as compared to a non-modified bouganin protein.
Suitable Ep-CAM-targeted-modified bouganins according to the invention include, without limitation, VB6-845 and variants thereof, other cytotoxins that comprises other single or double chain immunoglobulins that selectively bind Ep-CAM, or variants thereof. The term "VB6-845" as used herein means a cytotoxin that comprises a Fab version of an anti-Ep-CAM scFv antibody linked to a modified form of bouganin, Bou 156 (SEQ ID NO: 13). The amino acid sequence and nucleotide sequence of VB6-845 Is shown in Figure 3B (SEQ ID NO:16 and SEQ ID NO:15, respectively).
In another embodiment, the cancer cell binding ligand recognizes a tumor-associated antigen that is found specifically on neoplastic cells and not on normal cells. In a preferred embodiment, the ligand is an antibody that binds tumor-associated antigen. The anti-tumor-associated-antigen antibody specifically recognizes cancer cells from a wide variety of cancers but does not recognize normal, non-cancerous cells.
Accordingly in another embodiment, the invention provides a cytotoxin comprising (a) ligand (such as an antibody or antibody fragment) that binds to tumor-associated antigen on the cancer cell attached to; (b) a modified bouganin protein having a reduced propensity to activate T-cells as compared to a non-modified bouganin protein.
Suitable tumor-associated-antigen-targeted-modified bouganins according to the invention include, without limitation, VB6-011 and variants thereof, other cytotoxins that comprises other single or double chain immunoglobulins that selectively bind tumor-associated-antigen, or variants

thereof. The term "VB6-011" as used herein means a cytotoxin that comprises a Fab version of the H11 human monoclonal antibody genetically linked to a modified form of bouganin, BOU 156 (SEQ ID No. 13). The H11 antibody was obtained by the fusion of peripheral blood lymphocytes of a 64 year old male cancer patient fused with a human myeloma cell line to produce hybridomas. The hybridoma NBGM1/H11 produces an IgMk that was re-engineered into a Fab format to make VB6-011 (see US 6,207,153 or WO 97/44461 for detail on the preparation of the H11 antibody-secreting hybridoma). The amino acid sequence and nucleotide sequence of VB6-011 is shown in Figure 15 (SEQ ID NO:28 and SEQ ID NO:27, respectively).
In a specific, non-limiting embodiment, the cytotoxin comprises VB6-845 (Figure 3B, SEQ ID No.16) or VB6-011 (Figure 15, SEQ ID NO: 28). In other non-limiting embodiments, the cytotoxin comprises a variant of VB6-845 orVB6-011.
A VB6-845 variant binds to the same Ep-CAM epitope or to a substantially similar Ep-CAM epitope that is bound by VB6-845, and the variant may competitively inhibit VB6-845 binding to Ep-CAM, under physiologic conditions, by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%. A VB6-845 variant may comprise the same modified bouganin as VB6-845, or may comprise a different modified bouganin of the invention. In another non-limiting embodiment, the cytotoxin comprises an Ep-CAM-binding portion comprising the variable region of MOC31, or a variant thereof. In yet another embodiment, the cytotoxin comprises an Ep-CAM-binding portion comprising 4D5MOCB, or a variant thereof. Binding of any of these cytotoxins to Ep-CAM may be reduced by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% by competition with the reference MOC31 or 4D5MOCB antibody under physiologic conditions.
A VB6-011 variant binds to the same tumor-associated-antigen epitope or to a substantially similar tumor-associated-antigen epitope that is bound by VB6-011, and the variant may competitively inhibit VB6-01.1 binding to tumor-

associated-antigen, under physiologic conditions, by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%. A VB6-011 variant may comprise the same modified bouganin as VB6-011, or may comprise a different modified bouganin of the invention. In another non-limiting embodiment, the cytotoxin comprises a tumor-associated-antigen binding portion comprising the H11 monoclonal antibody, H11 antigen binding fragments, or variants thereof. Binding of any of these cytotoxins to VB6-011 may be reduced by at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% by competition with the reference H11 antibody under physiologic conditions.
In a preferred embodiment, the binding affinity of the Ep-CAK/l-binding portion or the tumor-associated-antigen-binding portion is at least four orders of magnitude, preferably at least three orders of magnitude, more preferably less than two orders of magnitude of the binding affinity of VB6-845 or VB6-011 respectively as measured by standard laboratory techniques. In non-limiting embodiments, the Ep-CAM-binding portion may competitively block the binding of a known anti-Ep-CAM antibody, such as, but not limited to, PANOREX® or MT201, to Ep-CAM, under physiologic conditions, by at least 0.1%, 1%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%. In non-limiting embodiments, the tumor-associated-antigen-binding portion may competitively block the binding of a known anti-tumor-associated-antigen antibody, such as, but not limited to, H11, to tumor-associated antigen, under physiologic conditions, by at least 0.1%, 1%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%.
The skilled artisan would appreciate that specificity determining residues can be identified. The term "specificity determining residue," also known as "SDR," refers to a residue that forms part of the paratope of an antibody, particularly CDR residues, the individual substitution of which by alanine, independently of any other mutations, diminishes the affinity of the antibody for the epitope by at least 10 fold, preferably by at least 100 fold,

more preferably by at least 1000 fold. This loss in affinity underscores that residue's importance in the ability of the antibody to bind the epitope. See, e.g., Tamura et al., 2000, "Structural correlates of an anticarcinoma antibody: identification of specificity-determining residues (SDRs) and development of a minimally immunogenic antibody variant by retention of SDRs only," J. Immunol. 164(3): 1432-1441.
The effect of single or multiple mutations on binding activity, particularly on binding affinity, may be evaluated contemporaneously to assess the importance of a particular series of amino acids on the binding interaction (e.g., the contribution of the light or heavy chain CDR2 to binding). Effects of an amino acid mutation may also be evaluated sequentially to assess the contribution of a single amino acid when assessed individually. Such evaluations can be performed, for example, by in vitro saturation scanning (see, e.g., U.S. Patent No. 6,180,341; Hilton et al., 1996, "Saturation mutagenesis of the WSXWS motif of the erythropoietin receptor," J Biol Chem. 271:4699-4708) and site-directed mutagenesis (see, e.g., Cunningham and Wells, 1989, "High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis," Science 244:1081-1085; Bass et al., 1991, "A systematic mutational analysis of hormone-binding determinants in the human growth hormone receptor," Proc Natl Acad Sei. USA 88:4498-4502). In the alanine-scanning mutagenesis technique, single alanine mutations are introduced at multiple residues in the molecule, and the resultant mutant molecules are tested for biological activity to identify amin o acid residues that are critical to the activity of the molecule.
Sites of ligand-receptor or other biological interaction can also be identified by physical analysis of structure as determined by, for example, nuclear magnetic resonance, crystallography, electron diffraction, or photoaffinity labeling, in conjunction with mutation of putative contact site amino acids (see, e.g., de Vos et al., 1992, "Human growth hormone and extracellular domain of its receptor: crystal structure of the complex," Science 255:306-312; Smith et al., 1992, "Human interleukin 4. The solution structure of a four-helix bundle protein," J Mol Biol. 224:899-904; Wlodaver et al., 1992,

"Crystal structure of human recombinant interleukin-4 at 2.25 A resolution," FEBS Lett. 309:59-64). Additionally, the importance of particular individual amino acids, or series of amino acids, may be evaluated by comparison with the amino acid sequence of related polypeptides or analogous binding sites.
Furthermore, the skilled artisan would appreciate that increased avidity may compensate for lower binding affinity. The avidity of a cytotoxin for a cancer cell receptor is a measure of the strength of the Ep-CAM-binding portion's binding of Ep-CAM, which has multiple binding sites. The functional binding strength between Ep-CAM and the Ep-CAM-binding portion represents the sum strength of all the affinity bonds, and thus an individual component may bind with relatively low affinity, but a miiltimer of such components may demonstrate potent biological effect. In fact, the multiple interactions between Ep-CAM-binding sites and Ep-CAM epitopes may demonstrate much greater than additive biological effect, i.e., the advantage of multivalence can be many orders of magnitude with respect to the equilibrium constant.
Similarly, the avidity of a cytotoxin for a cancer cell receptor is a measure of the strength of the tumor-associated antigen-binding portion's binding of tumor-associated antigen, which may have multiple binding sites. The functional binding strength between tumor-associated antigen and the tumor-associated antigen-binding portion represents the sum strength of all the affinity bonds, and thus an individual component may bind with relatively low affinity, but a multimer of such components may demonstrate potent biological effect. In fact, the multiple interactions between tumor-associated antigen-binding sites and tumor-associated antigen epitopes may demonstrate much greater than additive biological effect, i.e., the advantage of multivalence can be many orders of magnitude with respect to the equilibrium constant.
In one non-limiting embodiment, the Ep-CAM-binding portion has a structure substantially similar to that of 4D5MOCB. The substantially similar structure can be characterized by reference to epitope maps that reflect the binding points of the cytotoxin's Ep-CAM-binding portion to an Ep-CAM

molecule. In another non-limiting embodiment, epitope maps can be generated for the tumor-associated antigen binding portion and a substantially similar structure can be characterized by reference to epitope maps that reflect the binding points of the cytotoxin's tumor-associated antigen binding portion to a tumor-associated antigen molecule.
The cytotoxins of the present invention may be prepared by chemical synthesis using techniques well known in the chemistry of proteins such as solid phase synthesis (Merrifield, J. Am. Chem. Assoc. 85:2149-2154 (1964)) or synthesis in homogenous solution (Houbenweyl, Methods of Organic Chemistry, ed. E. Wansch, Vol. 15 I and II, Thieme, Stuttgart (1987)). In one embodiment, the cancer-binding ligand and modified bouganin are both proteins and can be conjugated using techniques well known in the art. There are several hundred crosslinkers available that can conjugate two proteins. (See for example "Chemistry of Protein Conjugation and Crosslinking". 1991, Shans Wong, CRC Press, Ann Arbor). The crosslinker is generally chosen based on the reactive functional groups available or inserted on the ligand or toxin. In addition, if there are no reactive groups a photoactivatible crosslinker
*
can be used. In certain instances, it may be desirable to include a spacer between the ligand and the toxin. Crosslinking agents known to the art include the homobifunctional agents: glutaraldehyde, dimethyladipimidate and Bis(diazobenzidine) and the heterobifunctional agents: m Maleimidobenzoyl-N-Hydroxysuccinimide and Sulfo-m Maleimidobenzoyl-N-Hydroxysuccinimide.
A ligand-bouganin toxin fusion protein may also be prepared using recombinant DMA techniques. In such a case a DMA sequence encoding the cancer-binding ligand is fused to a DNA sequence encoding the modified bouganin protein, resulting in a chimeric DNA molecule. The chimeric DNA sequence is transfected into a host cell that expresses the ligand-bouganin fusion protein. The fusion protein can be recovered from the cell culture and purified using techniques known in the art.
Antibodies having specificity for cell surface proteins such as Ep-CAM and tumor-associated antigen may be prepared by conventional methods. A

mammal, (e.g. a mouse, hamster, or rabbit) can be immunized with an immunogenic form of the peptide which elicits an antibody response in the mammal. Techniques for conferring immunogenicity on a peptide include conjugation to carriers or other techniques well known in the art. For example, the peptide can be administered in the presence of adjuvant. The progress of immunization can be monitored by detection of antibody titers in plasma or serum. Standard ELISA or other immunoassay procedures can be used with the immunogen as antigen to assess the levels of antibodies. Following immunization, antisera can be obtained and, if desired, polyclonal antibodies isolated from the sera.
To produce monoclonal antibodies, antibody-producing cells (lymphocytes) can be harvested from an immunized animal and fused with myeloma cells by standard somatic cell fusion procedures thus immortalizing these cells and yielding hybridoma cells. Such techniques are well known in the art, (e.g. the hybridoma technique originally developed by Kohler and Milstein (Nature 256:495-497 (1975)) as well as other techniques such as the human B-cell hybridoma technique (Kozbor et al., Immunol. Today 4:72 (1983)), the EBV-hybridoma technique to produce human monoclonal antibodies (Cole et al., Monoclonal Antibodies in Cancer Therapy Allen R., Bliss, Inc., pages 77-96 (1985)), and screening of combinatorial antibody libraries (Huse et al., Science 246:1275 (1989)). Hybridoma cells can be screened immunochemically for production of antibodies specifically reactive with the peptide and the monoclonal antibodies can be isolated .
The term "antibody" as used herein is intended to include monoclonal antibodies and polyclonal antibodies, antibody fragments
antibody on a single stably folded polypeptide chain. Single chain antibodies can be generated by recombinant technology.
Chimeric antibody derivatives, i.e., antibody molecules that combine a non-human animal variable region and a human constant region are also contemplated within the scope of the invention. Chimeric antibody molecules can include, for example, the antigen binding domain from an antibody of a mouse, rat, or other species, with human constant regions. Conventional methods may be used to make chimeric antibodies containing the immunoglobulin variable region which recognizes a cell surface antigen (See, for example, Morrison et al., Proc. Nail Acad. Sci. U.S.A. 81:6851 (1985); Takeda et al., Nature 314:452 (1985), Cabilly et al., U.S. Patent No. 4,816,567; Boss et al., U.S. Patent No. 4,816,397; Tanaguchi et al., E.P. Patent No. 171,496; European Patent No. 173,494, United Kingdom Patent No. GB 2177096B). It is expected that chimeric antibodies would be less immunogenic in a human subject than the corresponding non-chimeric antibody. Chimeric antibodies can be stabilized by the method described in Pluckthun et al., WO 00/61635.
Monoclonal or chimeric antibodies specifically reactive against cell surface components can be further humanized by producing human constant region chimeras, in which parts of the variable regions, particularly the conserved framework regions of the antigen-binding domain, are of human origin and only the hypervariable regions are of non-human origin. Such immunoglobulin molecules may be made by techniques known in the art, (e.g. Teng et al., Proc. Natl. Acad Sci. U.S.A., 80:7308-7312 (1983); Kozbor et al., Immunology Today 4:7279 (1983); Olsson et al., Meth. Enzymol., 92:3-16 (1982), and PCT Publication WO92/06193 or EP 239,400). Humanized antibodies can also be commercially produced (Scotgen Limited, 2 Holly Road, Twickenham, Middlesex, Great Britain.) In addition, monoclonal or chimeric antibodies specifically reactive against cell surface components can be made less immunogenic by reducing their number of potential T-cell epitopes.

Specific antibodies, or antibody fragments, reactive against cell surface components may also be generated by screening expression libraries encoding immunoglobulin genes, or portions thereof, expressed in bacteria with cell surface components. For example, complete Fab fragments, VH regions and Fv regions can be expressed in bacteria using phage expression libraries (See for example Ward et al., Nature 341:544-546 (1989); Huse-et al., Science 246:1275-1281 (1989); and McCafferty et a!., Nature 348:552-554 (1990)). Alternatively, a SClD-hu mouse, for example the model developed by Genpharm, can be used to produce antibodies, or fragments thereof.
In all instances where a modified bouganin protein is made in fusion with an antibody sequence it is most desired to use antibody sequences in which T cell epitopes or sequences able to bind MHC class II molecules or stimulate T cells or bind to T cells in association with MHC class II molecules have been removed.
A further embodiment of the present invention, the modified bouganin protein may be linked to a non-antibody protein yet a protein able to direct a specific binding interaction to a particular target cell. Such protein moieties include a variety of polypeptide ligands for which there are specific cell surface receptors and include therefore numerous cytokines, peptide and polypeptide hormones and other biological response modifiers. Prominent examples include such proteins as vascular epithelial growth factor, epidermal growth factor, heregulin, the interleukins, interferons, tumour necrosis factor and other protein and glycoprotein molecules. Fusion proteins of these and other molecules with bouganin of the present invention may be contemplated and may comprise the modified bouganin moiety in either the N-terminal or C-terminal orientation with respect to the protein ligand domain. Equally, chemical cross-linking of the purified ligand to the modified bouganin protein may be contemplated and within the scope of the present invention.
In a further embodiment the modified bouganin protein of the present invention may be used as a complex containing a water soluble polymer such as hydroxypropylmethacrylamide or other polymers where the modified bouganin protein is in covalent attachment to the polymer or in a non-covalent

binding interaction with the polymer. Such an embodiment may additionafly include an antigen binding domain such as an antibody or a fragment of an antibody in combination with the polymer bouganin complex.
(C) Uses of the Cvtotoxins
The modified bouganin proteins of the invention may be used to specifically inhibit or destroy mammalian cells affected by cancer. It is an advantage of the cytotoxins of the invention that they have less immunogenicity, allowing the RIP to enter the cell and effectively kill the cancer cell. Thus, the cytotoxin may be used to specifically target cancer cells. The bouganin, once in the cancer cell, depurinates the major ribosomal RNA, thereby damaging the ribosomes and leading to a cessation of protein synthesis and cell death.
Accordingly, in one embodiment, the invention provides a method of inhibiting or destroying a cancer cell comprising administering a cytotoxin of the invention to an animal in need thereof. The present invention also includes a use of a cytotoxin of the invention to inhibit or destroy a cancer cell. The present invention further includes a use of a cytotoxin of the invention in the manufacture of a medicament to inhibit or destroy a cancer cell. The type of cancer cells that are inhibited or destroyed by a cytotoxin will be determined by the antigen specificity of its antibody portion.
In another embodiment, the invention provides a method of inhibiting or destroying cancer cells comprising the steps of preparing a cytotoxin of the invention and administering the cytotoxin to the cells. The cancer can be any type of cancer, including, but not limited to, colorectal cancer, breast cancer, ovarian cancer, pancreatic cancer, head and neck cancer, bladder cancer, liver cancer, renal cancer, melanomas, gastrointestinal cancer, prostate cancer, small cell and non small cell lung cancer, sarcomas, gliomas, T- and B-cell lymphomas.
The ability of the cytotoxins of the invention to selectively inhibit or destroy animal cancer cells may be readily tested in vitro using animal cancer cell lines. The selective inhibitory effect of the cytotoxins of the invention may

be determined, for example, by demonstrating the selective inhibition of cellular proliferation in cancer cells.
Toxicity may be measured based on cell viability, for example the viability of normal and cancerous cell cultures exposed to the cytotoxins may be compared. Cell viability may be assessed by known techniques, such as trypan blue exclusion assays.
In another example, a number of models may be used to test the cytotoxicity of cytotoxins. Thompson, E.W. et al. (Breast Cancer Res. Treatment 31:357-370 (1994)) has described a model for the determination of invasiveness of human breast cancer cells in vitro by measuring tumour cell-mediated proteolysis of extracellular matrix and tumour cell invasion of reconstituted basement membrane (collagen, laminin, fibronectin, Matrigel or gelatin). Other applicable cancer cell models include cultured ovarian adenocarcinoma cells (Young, T.N. et al. Gynecol. Oncol. 62:89-99 (1996); Moore, D.H. et al. Gynecol. Oncol. 65:78-82 (1997)), human follicular thyroid cancer cells (Demeure, M.J. et al., World J. Surg. 16:770-776 (1992)), human melanoma (A-2058) and fibrosarcoma (HT-1080) cell lines (Mackay, A.R. et al. Lab. Invest. 70:781-783 (1994)), and lung squamous (HS-24) and adenocarcinoma (SB-3) cell lines (Spiess, E. et al. J. Histochem. Cytochem. 42:917-929 (1994)). An in vivo test system involving the implantation of tumours and measurement of tumour growth and metastasis in athymic nude mice has also been described (Thompson, E.W. et al., Breast Cancer Res. Treatment 31:357-370 (1994); Shi, Y.E. et al., Cancer Res. 53:1409-1415 (1993)).
The present invention also relates to a method of treating cancer comprising administering an effective amount of one or more cytotoxins of the present invention to an animal in need thereof. The invention includes a use of a cytotoxin of the invention to treat cancer. The invention further includes a use of a cytotoxin of the invention in the manufacture of a medicament for treating cancer.
The term "animal" includes all members of the animal kingdom, including humans.

The term "treating cancer" or "treat cancer" refers to inhibition of cancer cell replication, inhibition of cancer spread (metastasis), inhibition of tumor growth, reduction of cancer cell number or tumor growth, decrease in the malignant grade of a cancer or improvement of cancer related symptoms.
In a preferred embodiment, the animal is human. In another embodiment, the cancer is selected from the group consisting of colorectal cancer, breast cancer, ovarian cancer, pancreatic cancer, head and neck cancer, bladder cancer, liver cancer, renal cancer, melanomas, gastrointestinal cancer, prostate cancer, small cell and non small cell lung cancer, sarcomas, gliomas and T- and B-cell lymphomas.
Clinical outcomes of cancer treatments using a cytotoxin of the invention are readily discernible by one of skill in the relevant art, such as a physician. For example, standard medical tests to measure clinical markers of cancer may be strong indicators of the treatment's efficacy. Such tests may include, without limitation, physical examination, performance scales, disease markers, 12-lead EGG, tumor measurements, tissue biopsy, cytoscopy, cytology, longest diameter of tumor calculations, radiography, digital imaging of the tumor, vital signs, weight, recordation of adverse events, assessment of infectious episodes, assessment of concomitant medications, pain assessment, blood or serum chemistry, urinalysis, CT scan, and pharmacokinetic analysis. Furthermore, synergistic effects of a combination therapy comprising the cytotoxin and another cancer therapeutic may be determined by comparative studies with patients undergoing monotherapy.
Remission malignant tumors may be evaluated using criteria accepted by the skilled artisan. See, e.g., Therasse et al., 2000, "New guidelines to evaluate the response to treatment in solid tumors. European Organization for Research and Treatment of Cancer, National Cancer Institute of the United States, National Cancer Institute of Canada," J Natl Cancer Inst. Feb 2;92(3):205-16.
The effective dose of a specific cytotoxin construct may depend on various factors, including the type of cancer, the size of the tumour, the stage

of the cancer, the cytotoxin's toxicity to the patient, the specificity of targeting to cancer cells, as well as the age, weight, and health of the patient.
Cytotoxins comprising the modified bouganin can be administered by i.v. infusion over a period of minutes to hours, depending on the dose and the concentration of the cytotoxin in the infusate.
In one embodiment, the cytotoxin is infused over a period of 3 hours.
In one embodiment, the effective dose by i.v. administration of cytotoxin may range from about 1 to 100 mg/kg/dose. In other embodiments, the dose may range from approximately 2 to 50 mg/kg/dose. In specific embodiments, the dose may be at least approximately 2, 4, 8, 13, 20, 28, 40, 50 mg/kg/dose.
In one embodiment, the single dose is administered approximately every week for approximately 1, 2, 3,4, 5, or 6 weeks. The single dose can be administered in consecutive weeks or, alternatively, one or more weeks can be skipped. After this cycle, a subsequent cycle may begin approximately 1, 2,4, 6, or 12 weeks later. The treatment regime may include 1, 2, 3,4, 5, 6 or more cycles, each cycle being spaced apart by approximately 1, 2,4, 6, or 12 weeks.
In another embodiment the single dose is administered every month for
V
approximately 1,2, 3, 4, 5, or 6 consecutive months. After this cycle, a subsequent cycle may begin approximately 1,2,4, 6, or 12 months later. The treatment regime may include 1, 2, 3, 4, 5, 6 or more cycles, each cycle being spaced apart by approximately 1, 2, 4, 6, or 12 months.
In a particular non-limiting embodiment, the effective dose of the cytotoxin is between about 1 and 50 mg/kg/tumor/day, wherein the patient is administered a single dose per day. The single dose is administered approximately every day (one or more days may optionally be skipped) for approximately 1, 2, 3, 4, 5, 6 or 7 consecutive days. After this cycle, a subsequent cycle may begin approximately 1,2, 3, 4, 5, or 6 weeks later. The treatment regime may include 1, 2, 3, 4, 5, 6 or more cycles, each cycle being spaced apart by approximately 1, 2, 3, 4, 5, or 6 weeks.

The injection volume preferably is at least an effective amount, which is appropriate to the type and/or location of the tumor. The maximum injection volume in a single dose may be between about 25% and 75% of tumor volume, for example approximately one-quarter, one-third, or three-quarters of the estimated target tumor volume. In a specific, non-limiting embodiment, the maximum injection volume in a single dose is approximately 30% of the tumor volume.
In another embodiment, the cytotoxin is infused for 3 hours at a rate of 100cc per hour with a solution containing from 1 to 10 mg cytotoxin/mL. The cytotoxin will be diluted in a suitable physiologically compatible solution.
The effective dose of another cancer therapeutic to be administered together with a cytotoxin during a cycle also varies according to the mode of administration. The one or more cancer therapeutics may be delivered intratumorally, or by other modes of administration. Typically, chemotherapeutic agents are administered systemically. Standard dosage and treatment regimens are known in the art (see, e.g., the latest editions of the Merck Index and the Physician's Desk Reference; NCCN Practice Guidelines in Oncology)).
Combination therapy with a cytotoxin may sensitize the cancer or tumor to administration of an additional cancer therapeutic. Accordingly, the present invention contemplates combination therapies for preventing, treating, and/or preventing recurrence of cancer comprising administering an effective amount of a cytotoxin prior to, subsequently, or concurrently with a reduced dose of a cancer therapeutic. For example, initial treatment with a cytotoxin may increase the sensitivity of a cancer or tumor to subsequent challenge with a dose of cancer therapeutic. This dose is near, or below, the low range of standard dosages when the cancer therapeutic is administered alone, or in the absence of a cytotoxin. When concurrently administered, the cytotoxin may be administered separately from the cancer therapeutic, and optionally, via a different mode of administration.
In another embodiment, a cytotoxih is administered in combination with at least one other immunotherapeutic.

In another embodiment, a cytotoxin is administered in combination with a regimen of radiation therapy. The therapy may also comprise surgery and/or chemotherapy. For example, the cytotoxin may be administered in combination with radiation therapy and cisplatin (Platinol), fluorouracil (5-FU, Adrucil), carboplatin (Paraplatin), and/or paclitaxel (Taxol). Treatment with the cytotoxin may allow use of lower doses of radiation and/or less frequent radiation treatments, which may for example, reduce the incidence of severe sore throat that impedes swallowing function potentially resulting in undesired weight loss or dehydration.
In another embodiment, a cytotoxin is administered in combination with one or more cytokines which include, without limitation, a lymphokine, tumor necrosis factors, tumor necrosis factor-like cytokine, lymphotoxin, interferon, macrophage inflammatory protein, granulocyte monocyte colony stimulating factor, interleukin (including, without limitation, interleukin-1, interleukin-2, interieukin-6, interleukin-12, interleukin-15, interleukin-18), and a variant thereof, including a pharmaceutically acceptable salt thereof.
In yet another embodiment, a cytotoxin is administered in combination with a cancer vaccine including, without limitation, autologous cells or tissues, non-autologous cells or tissues, carcinoembryonic antigen, alpha-fetoprotein, human chorionic gonadotropin, BCG live vaccine, melanocyte lineage proteins, and mutated, tumor-specific antigens.
In yet another embodiment, a cytotoxin is administered in association with hormonal therapy. Hormonal therapeutics include, without limitation, a hormonal agonist, hormonal antagonist (e.g., flutamide, tamoxifen, leuprolide acetate (LUPRON)), and steroid (e.g., dexamethasone, retinoid, betamethasone, cortisol, cortisone, prednisone, dehydrotestosterone, glucocorticoid, mineralocorticoid, estrogen, testosterone, progestin).
In yet another embodiment, a cytotoxin is administered in association with a gene therapy program to treat or prevent cancer.
In yet another embodiment, an Ep-CAM-targeted cytotoxin is administered in combination with one or more agents that increase expression of Ep-CAM in the tumor cells of interest. Ep-CAM expression preferably is

increased so that a greater number of Ep-CAM molecules are expressed on the tumor cell surface. For example, the agent may inhibit the normal cycles of Ep-CAM antigen endocytosis. Such combination treatment may improve the clinical efficacy of the Ep-CAM-targeted cytotoxin alone, or with other cancer therapeutics or radiation therapy. In specific, nonlimiting embodiments, the agent which increases Ep-CAM expression in the tumor cells is vinorelbine tartrate (Navelbine) and/or paclitax (Taxol). See, e.g., Thurmond et al., 2003, "Adenocarcinoma cells exposed in vitro to Navelbine or Taxol increase Ep-CAM expression through a novel mechanism." Cancer Immunol Immunother. Jul;52(7):429-37.
Combination therapy may thus increase the sensitivity of the cancer or tumor to the administered cytotoxin and/or additional cancer therapeutic. In this manner, shorter treatment cycles may be possible thereby reducing toxic events. Accordingly, the invention provides a method for treating or preventing cancer comprising administering to a patient in need thereof an effective amount of a cytotoxin and at least one other cancer therapeutic for a short treatment cycle.The cycle duration may vary according to the specific cancer therapeutic in use. The invention also contemplates continuous or discontinuous administration, or daily doses divided into several partial administrations. An appropriate cycle duration for a specific cancer therapeutic will be appreciated by the skilled artisan, and the invention contemplates the continued assessment of optimal treatment schedules for each cancer therapeutic. Specific guidelines for the skilled artisan are known in the art. See, e.g., Therasse et al., 2000, "New guidelines to evaluate the response to treatment in solid tumors. European Organization for Research and Treatment of Cancer, National Cancer Institute of the United States, National Cancer Institute of Canada," J Natl Cancer Inst. Feb 2;92(3):205-16.
Alternatively, longer treatment cycles may be desired. Accordingly, the cycle duration may range from approximately 10 to 56, 12 to 48,14 to 28, 16 to 24, or 18 to 20 days. The cycle duration may vary according to the specific cancer therapeutic in use.

The present invention contemplates at least one cycle, preferably more than one cycle during which a single cancer therapeutic or series of therapeutics is administered. An appropriate total number of cycles, and the interval between cycles, will be appreciated by the skilled artisan. The number of cycles may be 1,2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, or 21 cycles. The interval between cycles may be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, or 21 days. The invention contemplates the continued assessment of optimal treatment schedules for each cytotoxin and additional cancer therapeutic.
In another embodiment, a process is provided for preparing a pharmaceutical for treating a mammal with cancer comprising the steps of identifying T-cell epitopes of bouganin having reduced propensity for activated T-cells; preparing a cytotoxin of the invention having one or more of the T-cell epitopes and suspending the protein in a pharmaceutically acceptable carrier, diluent or excipient.
The invention also provides a pharmaceutical composition for treating a mammal with cancer comprising a cytotoxin of the invention and a pharmaceutically acceptable carrier, diluent or excipient.
The cytotoxins of the invention may be formulated into pharmaceutical compositions for administration to subjects in a biologically compatible form suitable for administration in vivo. By "biologically compatible form suitable for administration in vivo" is meant a form of the substance to be administered in which any toxic effects are outweighed by the therapeutic effects. The substances may be administered to living organisms including humans, and animals. Administration of a therapeutically active amount of the pharmaceutical compositions of the present invention is defined as an amount effective, at dosages and for periods of time necessary to achieve the desired result: For example, a therapeutically active amount of a substance may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of antibody to elicit a desired response in the individual. Dosage regime may be adjusted to provide the optimum therapeutic response. For example, several divided doses .may be

administered daily or the dose may be proportionally reduced as indicated by the exigencies of the therapeutic situation.
The active substance may be administered in a convenient manner such as by injection (subcutaneous, intravenous, intramuscular, etc.), oral administration, inhalation, transdermal administration (such as topical cream or ointment, etc.), or suppository applications. Depending on the route of administration, the active substance may be coated in a material to protect the compound from the action of enzymes, acids and other natural conditions which may inactivate the compound.
The compositions described herein can be prepared by per se known methods for the preparation of pharmaceutically acceptable compositions which can be administered to subjects, such that an effective quantity of the active substance is combined in a mixture with a pharmaceutically acceptable vehicle. Suitable vehicles are described, for example, in Remington's Pharmaceutical Sciences (Remington's Pharmaceutical Sciences, Mack Publishing Company, Easton, Pa., USA 1985). On this basis, the compositions include, albeit not exclusively, solutions of the substances in association with one or more pharmaceutically acceptable vehicles or diluents, and contained in buffered solutions with a suitable pH and iso-osmotic with the physiological fluids.
The pharmaceutical compositions may be used in methods for treating animals, including mammals, preferably humans, with cancer. It is anticipated that the compositions will be particularly useful for treating patients with colorectal cancer, breast cancer, ovarian cancer, pancreatic cancer, head and neck cancer, bladder cancer, gastrointestinal cancer, prostate cancer, small cell and non small cell lung cancer, sarcomas, gliomas, T- and B-cell lymphomas. The dosage and type of cytotoxin to be administered will depend on a variety of factors which may be readily monitored in human subjects. Such factors include the etiology and severity (grade and stage) of neoplasia.
Pharmaceutical compositions adapted for direct administration include, without limitation, lyophilized powders or aqueous or non-aqueous sterile injectable solutions or suspensions, which may further contain antioxidants,

buffers, bacteriostats and solutes that render the compositions substantially isotonic with the blood of an intended recipient. Other components that may be present in such compositions include water, alcohols, polyols, glycerin and vegetable oils, for example. Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets. Cytotoxin may be supplied, for example but not by way of limitation, as a lyophilized powder which is reconstituted with sterile water or saline prior to administration to the patient.
Pharmaceutical compositions of the invention may comprise a pharmaceutically acceptable carrier. Suitable pharmaceutically acceptable earners include essentially chemically inert and nontoxic compositions that do not interfere with the effectiveness of the biological activity of the pharmaceutical composition. Examples of suitable pharmaceutical carriers include, but are not limited to, water, saline solutions, glycerol solutions, ethanol, N-(1 (2,3-dioleyloxy)propyI)N,N,N-trimethylammonium chloride (DOTMA), diolesylphosphotidyl-ethanolamine (DOPE), and Hposomes. Such compositions should contain a therapeutically effective amount of the compound, together with a suitable amount of carrier so as to provide the form for direct administration to the patient.
In another embodiment, a pharmaceutical composition comprises a cytotoxin and one or more additional cancer therapeutics, optionally in a pharmaceutically acceptable carrier.
The composition may be in the form of a pharmaceutically acceptable salt which includes, without limitation, those formed with free amino groups such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with free carboxyl groups such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylarnino ethanol, histidine, procaine, etc.
In as far as this invention relates to modified bouganin, compositions containing such modified bouganin proteins or fragments of modified bouganin proteins and related compositions should be considered within the scope of the invention. A pertinent example in this respect could be

development of peptide mediated toterance induction strategies wherein one or more of the disclosed peptides is administered to a patient with immunotherapeutic intent. Accordingly, synthetic peptides molecules, for example one of more of comprising all or part of any of the epitope regions R1 - R3 as defined above. Such peptides are considered embodiments of the invention.
In a further aspect of the present invention relates to methods for therapeutic treatment of humans using the modified bouganin compositions. For administration to an individual, any of the modified compositions would be produced to be preferably at least 80% pure and free of pyrogens and other contaminants.
The present invention also provides a kit comprising an effective amount of a cytotoxin, optionally, in combination with one or more other cancer therapeutics, together with instructions for the use thereof to treat the cancer.
(D) T-cell epitope peptides
An additional embodiment of the invention is a T-cell epitope peptide. In an example, the T-cell epitope peptide is able to evoke a stimulation index of greater than 1.8 in a T-cell assay, more preferably greater than 2.0. The T-cell epitope peptide of the invention is able to bind MHC class II.
In an embodiment of the invention the T-cell epitope peptide comprises at least 9 consecutive amino acid residues from any of the sequences of R1, R2 or R3 (above). In another embodiment, the T-cell epitope peptide sequence has greater than 90% amino acid identity with any one of the peptide sequences R1, R2 or R3; more preferably the T-cell epitope peptide has greater than 80% amino acid identity with any one of the peptide sequences R1, R2 or R3.
The term "peptide" as used herein is a compound that includes two or more amino acids. The amino acids are linked together by a peptide bond (defined herein below). There are 20 different naturally occurring amino acids involved in the biological production of peptides, and any number of them may

be linked in any order to form a peptide chain or ring. The naturally occurring amino acids employed in the biological production of peptides all have the L-configuration. Synthetic peptides can be prepared employing conventional synthetic methods, utilizing L-amino acids, D-amino acids, or various combinations of amino acids of the two different configurations. Some peptides contain only a few amino acid units. Short peptides, e.g., having less than ten amino acid units, are sometimes referred to as "oligopeptides". Other peptides contain a large number of amino acid residues, e.g. up to 100 or more, and are referred to as "polypeptides". By convention, a "polypeptide" may be considered as any peptide chain containing three or more amino acids, whereas an "oligopeptide" is usually considered as a particular type of "short" polypeptide. Thus, as used herein, it is understood that any reference to a "polypeptide" also includes an oligopeptide. Further, any reference to a "peptide" includes polypeptides, oligopeptides, and proteins. Each different arrangement of amino acids forms different polypeptides or proteins. The number of polypeptides-and hence the number of different proteins-that can be formed is practically unlimited.
Another embodiment of the invention is the use of the T-cell epitope peptides of the invention to make the modified bouganin proteins of the invention and modified T-cell epitope peptides.
A further embodiment of the invention is a modified T-cell epitope peptide that is modified such that the modified T-cell epitope peptide has reduced propensity to activate human T cells than the non-modified T-cell epitope peptide. In an example, the modified T-cell epitope peptides of the invention contains modifications such that when tested in a T-cell assay evokes a reduced stimulation index in comparison to the non-modified T-cell epitope peptide.
In an embodiment of the invention the modified T-cell epitope peptide has the following sequence:
AKX1 DRKX2LX3LGVX4KL
wherein at least one of X1, X2, X3, and X4 is modified from the non-modified sequence, as follows:

X1 is T or A or Q;
X2isGorA;
X3 is Q or G; and
X4 is N or D or T or A or R or Q or E or G or H or K or S (SEQ ID N0:8).
In another embodiment of the invention the modified T-cell epitope peptide has the following sequence: LGVX4KLEFSIEAIHG
wherein X4 is N or D or T or A or R or Q or E or G or H or K or S (SEQ ID NO:9).
In a further embodiment of the invention the modified T-cell epitope peptide has the following sequence: NGQEX5AKFFLIVIQM
whereirvX6is Q or A (SEQ ID NO:10).
The invention also provides nucleic acid molecules encoding the T-cell epitope peptides or modified T-cell epitope peptides of the invention.
The following figures, sequence listings and examples are provided to aid the understanding of the present invention. It is understood that modifications can be made in the procedures set forth without departing from the spirit of the invention.
The following non-limiting examples are illustrative of the present invention:
EXAMPLES
Example 1: Method of mapping epitopes in bouganin using naive human
T-cell proliferation assays
Peptides covering the sequence of the mature bouganin protein, as described by Den Hartog et al [ibid\ were synthesized. The length of each peptide is 15 amino acids, and successive peptides overlap by 12 residues. The sequence of these peptides and their numbering is indicated in TABLE 1.
The peptides were used in T-cell proliferation assays with PBMCs (peripheral blood mononuclear cells) from naive donors (i.e. no known

sensitization to bouganin). 20 donor PBMC were selected to get an optimal coverage of MHC class II allotypes. The allotypic coverage is in excess of 85%. The HLA-DR allotypes are shown in TABLE 2.
PBMCs were stimulated with individual peptides in triplicate cultures for 7 days before proliferation was assessed by 3H-thymidine (3H-Thy) incorporation. All peptides were tested at two different concentrations (I^M and SyM). Stimulation indices (S.I.) were calculated as the amount of 3H incorporated, divided by the amount of 3H incorporated in mock-stimulated control cells.
Buffy coats from human blood stored for less than 12 hours were obtained from the National Blood Service (Addenbrooks Hospital, Cambridge, UK). Ficoll-paque was obtained from Arnersham Pharmacia Biotech (Amersham, UK). Serum free AIM V media for the culture of primary human lymphocytes and containing L-glutamine, 50p.g/ml streptomycin, lO^g/ml gentomycin and 0.1% human serum albumin was from Gibco-BRL (Paisley, UK). Synthetic peptides were obtained from Eurosequence (Groningen, The Netherlands) and Babraham Technix (Cambridge, UK).
Erythrocytes and leukocytes were separated from plasma and platelets by gentle centrifugation of buffy coats. The top phase (containing plasma and platelets) was removed and discarded. Erythrocytes and leukocytes were diluted 1:1 in phosphate buffered saline (PBS) before layering onto 15ml ficoll-paque (Amersham Pharmacia, Amersham UK). Centrifugation was done according to the manufacturers recommended conditions and PBMCs were harvested from the serum+PBS/ficoll paque interface. PBMCs were mixed with PBS (1:1) and collected by centrifugation. The supernatant was removed and discarded and the PBMC pellet resuspended in 50ml PBS. Cells were again pelleted by centrifugation and the PBS supernatant discarded. Cells were resuspended using 50ml AIM V media and at this point counted and viability assessed using trypan blue dye exclusion. Cells were again collected by centrifugation and the supernatant discarded. Cells were resuspended for cryogenic storage at a density of 3x107 per ml. The storage medium was 90%(v/v) heat inactivated AB human serum (Sigma, Poole, UK) and 10%(v/v)

DMSO (Sigma, Poole, UK). Cells were transferred to a regulated freezing container (Sigma) and placed at -70°C overnight. When required for use, cells were thawed rapidly in a water bath at 37°C before transferring to 10ml pre-warmed AIM V medium.
PBMC were stimulated with protein and peptide antigens in a 96 well flat bottom plate at a density of 2x10s PBMC per well. PBMC were incubated for 7 days at 37°C before pulsing with 3H-Thy (Amersham-Pharmacia, Amersham, UK). Two control peptides termed C-32 and C-49 that have previously been shown to be immunogenic and a potent whole protein non-recall antigen Keyhole Limpet Hemocyanin (KLH) were used in each donor assay. C-32 = sequence PKYVKQNTLKLAT from Flu haemagglutinin residues 307-319 (SEQ ID NO: 127). C-49 = sequence KWDQIKKISKPVQH from Chlamydia HSP 60 (SEQ ID NO:12B).
Peptides were dissolved in DMSO to a final concentration of 10mM, these stock solutions were then diluted 1/500 in AIM V media (final concentration 20|j-M). Peptides were added to a flat bottom 96 well plate to give a final concentration of 1 and 5^M in 100^,1. The viability of thawed PBMC's was assessed by trypan blue dye exclusion, cells were then resuspended at a density of 2x106 cells/ml, and 100^1 (2x105 PBMC/well) was transferred to each well containing peptides. Triplicate well cultures were assayed at each peptide concentration. Plates were incubated for 7 days in a humidified atmosphere of 5% CO2 at 37°C. Cells were pulsed for 18-21 hours with 1 piCi 3H-Thy/welI before harvesting onto filter mats. CPM values were determined using a Wallac microplate beta top plate counter (Perkin Elmer). Results were expressed as stimulation indices, derived by division of the proliferation score (e.g. counts per minute of radioactivity) measured to the test peptide by the score measured in cells not contacted with a test peptide.
Compilation of the results of the above assay indicates the presence of four T cell epitopes, corresponding to peptides 41, 44 and 50 in the mature, processed region of the protein and peptide 88 in the unprocessed form. Since the epitope in peptide 88 is not part of the mature protein, it is ignored under the scheme of the present invention.

For peptide 41 (termed epitope region R1) there were four responsive donors to this peptide; donors 4, 5, 10 and 11. The S.l.s for these at 5|j,M are 3.6, 4.9, 2.1 and 2.0 respectively.
For peptide 44 (termed epitope region R2). There are two responsive donors to this peptide; donors 4 (S.l.=3.5) and 11 (S.I.=2.3). Neighboring peptides 43 and 45 induced lower level T cell proliferation since both these peptides overlap by 12 amino acids with peptide 44.
For peptide 50 there were 2 responsive donors to this peptide; donors 4 (S.l.=2.9) and 14 (S.l.=2.0). Peptide 51 induced lower level T cell proliferation in donor 14 (S.l.>1.9).
The tissue types for all PBMC samples were assayed using a commercially available reagent system (Dynal, Wirral, UK). Assays were conducted in accordance with the suppliers recommended protocols and standard ancillary reagents and agarose electrophoresis systems. The allotypic specificities of each of the responsive donor samples is given in TABLE 2.
Example 2: Cloning of bouganin from Bougainvillea spectabilis
Total RNA was extracted from the leaves of Bougainvillea spectabilis using the 'SV Total RNA Isolation System and protocols provided by the supplier (Promega, Southampton, UK). Fresh leaf tissue was ground to a fine powder under liquid nitrogen, and approximately 50 mg of ground tissue was used for the RNA isolation. RNA quality and quantity was checked by visualization on a 1% agarose gel, and the bouganin gene was amplified from the total RNA using the 'Access RT-PCR System' (Promega) using approximately Ip-g of RNA per reaction and with the gene specific primers OL1032 and OL1033. Primer sequences are given in TABLE 3 below. This reaction generated a 1242 bp fragment encompassing the native leader sequence and the full-length bouganin sequence. This fragment was cloned into the pGEM-T Easy vector (Promega), following kit instructions, and designated pBoul The sequence was confirmed by DMA sequencing.

The bouganin gene was transferred into the pET21a (Novagen, Nottingham.UK) by PCR cloning using the pBoul plasmid as a template. A pelB (pectate lyase) leader sequence was added to the 5' end, and a sequence encoding a 6x histidine tag was added to the 3' end of the bouganin coding sequence. The pelB leader was amplified from vector pPMI-his [Molloy, P. et al, (1995) J. Applied Bacteriology, 78: 359-365] using primer OL1322 (incorporating an Nde1 site) and primer OL1067. The bouganin-his fragment was amplified from pBoul using OL1068 and OL1323 (incorporating a Not1 site). The pelB leader was fused in frame to the bouganin-his fragment using overlap PCR, and the resulting fragment cloned into pGEM-T Easy (Promega). Following sequence confirmation the pelB-bouganin-his fragment was cloned as a Nde1-Not1 fragment into Nde1-Not1 digested pET21a. This clone was designated pBou32.
Example 3: Construction of mutant bouganin proteins
A number of modified (mutant) bouganin proteins were designed using data provided by the T-cell epitope mapping procedure and use of software able to simulate the binding of peptides with human MHC class 11 binding groove. This latter approach is described in detail elsewhere [WO 02/069232]. Variant genes were constructed and the mutant proteins tested for functional activity. In general, "single mutant" proteins containing one amino acid substitution each were first constructed and tested, then genes for active modified proteins combined to produce multiply substituted modified proteins.
Mutant genes were constructed using an overlap PCR procedure in which the mutant amino acid codon becomes introduced into the gene by use of a mutant in "overlap primer". The scheme is well understood in the art and is described in detail elsewhere [Higuchi, et al (1900) Nucl. Adds Res. 16:7351]. A total of 37 single mutant modified proteins were constructed and tested for retained functional activity. In addition, a negative control modified protein containing a substitution Y70A was also constructed and tested in all assays. One of the 37 "single mutant" modified proteins in fact contained two

directly adjacent substitutions (E151T and I152E) and is counted herein as a single mutant. The substitutions tested and the corresponding activity values are given in TABLE 4.
A total of 11 multiple substitution modified proteins were constructed and tested for retained activity. The substitutions tested and the corresponding activity values are given in TABLE 5.
TABLE .6 describes the sequences of the substitution modified proteins. TABLE 7 lists some specific sequences.
In all instances, proteins were purified and tested according to the procedures outlined in examples 4 and 5 below.
Example 4: Expression of and purification of bouganin protein
The plasmid pBou32 was transformed into BL21(DE3) (Novagen) competent cells following manufacturers instructions, and selected on 1_B (Invitrogen, Paisley, UK) plates containing 50|j,g/ml carbenicillin. A fresh colony from this transformation was used to inoculate 5 ml 2xYT (Invitrogen) broth, without antibiotic, and this was grown with shaking at 250rpm at 37°C until OD600 = 1.5-2.0. The culture was then centrifuged at 2500 rpm for 15 minutes at room temperature, and the cells resuspended in 5 ml fresh 2xYT plus 1mM IPTG. This culture was incubated at 30°C with shaking at SOOrpm for 1.5 hours and the cells collected by centrifugation and the supernatant discarded.
The cell pellet was resuspended in 1 ml of PEB2 (50mM Tris-HCI pH8, 20% sucrose, 1 mg/ml lysozyme, 1x Complete Protease Inhibitor Tablet (Roche, Lewes, UK), and incubated on ice for 1 hour with gentle mixing. The cell debris was centrifuged at 14,000 rpm at 4°C and the pellet discarded. The resulting supernatant is now referred to as the 'periplasmic fraction'. Bouganin protein was purified from the periplasmic fraction by nickel affinity column chromatography using commercially available "spin column" and the manufacturer's instructions (Qiagen, Crawley, UK). The resulting material was dialyzed against 4 liters of phosphate buffered saline (0.138M NaCI, 0.0027M KCI , pH 7.4) overnight at4°C using a 10000 molecular weight cut-

off 'Slide-A-Lyzer' (Pierce, Chester, UK). Following dialysis, the protein concentration was estimated using the Micro BCA Assay Kit (Pierce), and samples stored at -20°C.
Bouganin protein concentration was further determined using an ELISA based assay system. Briefly, antiserum against bouganin was generated (Genovac, Freiburg, Germany), through the genetic immunization of two rats with a plasmid expressing bouganin. For the ELISA, recombinant bouganin is captured onto Ni-agarose coated plates via its His-tag and subsequently detected with the rat antiserum and a seconda ry HRP-conjugated anti-rat Fc antibody (Sigma, Poole, UK). As a standard, a large preparation of the wild-type bouganin expressed in E.coli and quantitated using the total protein assay was used in each determination.
Example 5: Assay of bouganin activity
The activity of the wild-type and modified (mutant) bouganin proteins was tested by measuring their ability to inhibit protein synthesis In a cell-free protein synthesis assay.
A mixture of 10 jxl TNT Coupled Transcription/Translation mix (Promega), 20fj,M methionine, 120 ng pT7 luciferase DMA (Promega) and serial dilutions of WT and mutant bouganin protein in a final volume of 12.5 \i\ were incubated at 30°C for one hour, after which the reaction was stopped by addition of 100 \i\ 'SteadyGlow' luciferase assay reagent (Promega). The luciferase activity was measured using a Wallac luminescence counter. Active bouganin protein is detected as a decrease in measured luciferase activity. Each modified bouganin protein was tested in at least 5 concentrations, with each data point in duplicate. Positive and negative controls were included in each experiment.
Results for single mutant proteins are shown in TABLE 4. Results for multiple mutant modified bouganin proteins are shown in TABLE 5. In each instance results are expressed relative to wild-type protein activity. All assays were conducted with the inclusion of an inactive mutant bouganin protein with a Y70A substitution.

In addition, luciferase assay results may be plotted showing % luciferase activity relative to control versus protein concentration of added bouganin. Examples of such plots are shown in Figure 1 depicting the results as determined for two different multiple mutant bouganin proteins.
Example 6: Assay of variant bouganin sequences for loss of T-cell epitopes.
The multiple modified protein designated Bou156 was selected for further testing using an immunogenicity assay. This variant contains the substitutions V123A, D127A, Y133N and I152A. Immunogenicity testing involves use of live cells that may be damaged by testing using whole bouganin protein, therefore these assays were conducted using synthetic peptides comprising the substitutions incorporated into variant Bou156. The peptides tested are listed in TABLE 8. The assays were conducted according to the procedures described in example 1 (above) using a PBMC donor pool of 20 individuals. Peptides were tested in triplicate for each donor sample at a two different final peptide concentrations (1[xM and 5fiM).
The results are expressed as SI per peptide per donor sample and are shown in Figure 2. Del-41 is peptide sequence AKADRKALELGVNKL (SEQ ID N0:29). Del-44 is peptide sequence LGVNKLEFSIEAIHG (SEQ ID NO:30). Del-50 is peptide sequence NGQEAAKFFLIVIQM (SEQ ID NO:31). None of the modified peptides induced a T cell response in any of the donors (S.l. Example 7: VB6-845: recombinant engineering of an Ep-CAM-specific Fab antibody for optimal delivery of de-immunized bouganin (De-bouganin).
For this example and Example 8, the de-immunized bouganin used is Bou156.
Tumor-targeting cytotoxins are composed of the variable region of an antibody linked to a bacterial, fungal or plant toxin. The present study illustrates that the deimmunized bouganin constructs of the invention,

comprising deimmunized bouganin linked to a targeting moiety have reduced immunogenicity, while still retaining their biological activity. TABLE 12 demonstrates the binding of the Ep-CAM antibody to sevesral types of tumours and thus shows that it can be used to treat these types of cancers.
De-immunized Bouqanin Construct: Ep-CAM directed targeting moietv linked to de-bouganin
VB5-845, a Fab version of an anti-Ep-CAM stcFv antibody, was genetically linked to a de-immunized form of bouganin (de-bouganin), Bou 156, a potent, plant-derived, type I ribosome-inactivating protein (RIP), to create the antibody-toxin construct VB6-845. Figure 3 illustrates the construct VB6-845. Figure 3A illustrates dicistronic unit of the pro-VB6-845, with pelB leader sequences. The amino acid sequence (SEQ ID NO: 16) and nucleic acid coding sequence (SEQ ID NO: 15) are provided in Figure 3B. Figure 3C illustrates the assembled VB6-845 protein, which is described below in more detail. Testing of this construct, illustrate that the construct retained its biological activity (cytoxicity) and the specificity of the targeting moiety (Ep-CAM antibody).
Orientation of the de-immunized bouqanin construct
To determine the optimal antibody-de-bouganin orientation, several forms of a dicistronic expression unit were generated, expressed and tested for potency.
In each case, the dicistronic unit was cloned into the plNG3302 vector (Figure 4) under the control of the arabinose-inducible araBAD promoter and transformed in E104 E.coli. Upon induction, the presen&e of the pelB leader sequence directed the secretion of the Fab-de-bouganin fusion protein into the culture supernatant. The cleavable linker enabled the de-bouganin to cleave from the targeting moiety and exert its biological activity. In one embodiment the linker is a furin linker, although a person skilled in the art would appreciate that other cleavable linkers could be suitable. Preferred

linkers could be selected based on target specificity, and environment. A sample of the constructs made and tested are as follows:
Figure 3: VB6-845, wherein the de-bouganin (Bou156) is linked to the C-terminus of the CH domain via a furin linker. Figure 3A illustrates the dicistronic unit of the pro-sequences, Figure 3B illustrates trie nucleic acid coding sequence (SEQ ID NO:.15) and the. amino acid sequence of the pro-sequences (SEQ ID NO:16) and Figure 3C illustrates the assembled VB6-845 protein without the pelB sequences.
Figure 5 illustrates the control Fab anti-Ep-CAM construct without the plant toxin, de-bouganin (VB5-845). Figure 5A illustrates the dicistronic unit of the pro-sequences, Figure 5B illustrates the nucleic acid coding sequence (SEQ ID N0:17) and the amino acid sequence of the pro-sequences (SEQ ID NO:18) and Figure 5C illustrates the assembled VB6-845 protein without the pelB sequences.
Figure 6 illustrates the Fab anti-Ep-CAM de-bouganin construct, VB6-845-Ci_-de-bouganin, wherein the Bou156 is linked at the C-terrninus of the CL domain. Figure 6A illustrates the dicistronic unit of the pro-seq uences, Figure 6B illustrates the nucleic acid coding sequence (SEQ ID NO:19) and the amino acid sequence of the pro-sequences (SEQ ID NO:20) and Figure 6C illustrates the assembled VB6-845-CL-de-bouganin protein without the pelB sequences.
Figure 7 illustrates the Fab anti Ep-CAM, de-bouganin construct, VB6-845-NVH-de-bouganin, wherein Bou156 is linked to the N terminus of the VH domain. Figure 7A illustrates the dicistronic units of the pro-sequences, Figure 7B illustrates the nucleic acid coding sequence (SEQ ID MO:21) and the amino acid sequence of the pro-sequences (SEQ ID NO:22) and Figure 7C illustrates the assembled VB6-845-NVH-de-bouganin protein without the pelB sequences.
Figure 8 illustrates the Fab anti-Ep-CAM construct VB6-845-NVi.-de-bouganin, wherein Bou156 is linked to the IM-terminus of the VL domain. Figure 8A illustrates the dicistronic unit of the pro-sequences, Figure 8B illustrates the nucleic acid coding sequence (SEQ ID NO:23) and the amino

acid sequence of the pro-sequences (SEQ ID N0:24) and Figure 8C illustrates the assembled VB6-845-NVi_-de-bouganin protein without the pelB sequences.
In one embodiment, the de-bouganin molecule is linked to the C-terminal end of the heavy or light chains. The optimal configuration comprised a pelB leader sequence adjacent to VH-CH domain with an N-terminal histidine affinity tag as the first unit. Immediately following was the second unit comprising the pelB-Vi_-Ci_ domain linked to de-bouganin by a protease-sensitive linker. (Figure 6) For constructs where de-bouganin was re-positioned to the N-terminal end, Western-blot analysis showed no detectable product and only C-terminal linked de-bouganin (constructs of Figures 3 and 6) yielded an intact soluble protein (Figure 9), with good binding properties to Ep-CAM-positive cell lines, as illustrated in the reactivity tests detected by flow cytometry. In the Western Blot analysis, Figure 9 illustrates the expression of VB6-B45 and VB6-845 CL-de-bouganin in the supernatant of induced E104 cells at lab scale. An aliquot of the supernatant, 16 microlitres, under non-reducing conditions, was loaded on a SDS-PAGE acrylamide gel and analysed by Western Blot using either a rabbit polyclonal anti-4D5 antibody, followed by a goat anti-rabbit (1/2000), or a goat anti-human Kappa-light chain-HRP antibody (1/1000), to confirm the identity and size of the recombinant protein. The arrow indicates the full-length VB6-845 (construct of Figure 3) and VB6-845-CL-de-bouganin (construct of Figure 6). Western blotting of non-induced E104 culture supernatant revealed no corresponding bands demonstrating the specificity of the antibodies (not shown).
The results of the reactivity tests with VB6-845 (Figure 3) and VB6-845-CL-de-bouganin (Figure 6) to Ep-CAM positive cell lines CAL 27 and "NIH:OVCAR-3 as compared to a control (Ep-CAM-negative cell line, A-375) is illustrated in Figure 10A. The results were comparable to the same reactivity tests conducted with another anti-Ep-CAM construct, VB6-845-gelonin, wherein the de-bouganin is replaced with another plant toxin, gelonin (See Figure 14C showing its amino acid sequence (SEQ ID NO:26) and nucleic acid sequence(SEQ ID NO:25) The results of the reactivity test with the

gelonin construct are illustrated in Figure 10B. The addition of a second de-bouganin domain in the molecule with the optimal orientation did not yield product.
The flow cytometry tests were conducted by incubating the constructs or control with 0.45 x 1D6 cells for an hour on ice. After washing, cell surface bound constructs were detected with a rabbit anti-bouganin (for Figure 10A) or mouse anti-His tag (Figure 10B) for an hour on ice. The cells were washed and incubated with FITC-conjugated sheep anti-rabbit IgG (Figure 10A) and FITC-conjugated sheep anti-mouse (IgG) (Figure 10B) for 30 minutes on ice. Subsequently the cells were washed, resuspended in PBS 5% FCS containing propidium iodide for assessment of antibody binding by flow cytometry. No shift in median fluorescence was detected following incubation with VB6-845 and VB6-845-CL-de-bouganin with A-375. In contrast, a marked shift in median fluorescence was observed with Ep-CAM positive cell lines, CAL 27 and NIH:OVCAR-3 (Figure 10A). As stated above, the results with VB6-845 were similar with the gelonin construct (Figure 10B).
Ep-CAM Specificity
A competition assay of VB6-845 (construct of Figure 3) with Proxinium™, a scFv format of VB6-845, but containing Pseudomonas exotoxin A, demonstrated that the Ep-CAM specificity of VB6-845 was unaltered when engineered into a Fab format. (Figure 11)
Figure 11 illustrates the flow cytometry results of the competition assay, with VB6-845 at 1 and 10 ng/mL and increased concentration of Proxinium™, ranging from 0 to 100 ng/mL, were incubated with NIHrOVCAR-3 cells (Ep-CAM positive tumour cell line). After 1 hour incubation at 4°C, cells were washed and bound VB6-845 was detected with a biotinylated rabbit anti-bouganin followed by streptavidin-cychrome. The same experiment was performed with 4B5-PE which is used as a negative control. The reaction conditions were as indicated on Figure 11.
Potency (biological activity)

In addition, cell-free (Figure 12) and MTS (Figure 13 A and B) assays demonstrated that de-bouganin retained its potency when conjugated to the Fab fragment. The MTS assay used to measure potency was conducted using standard technique known in the art, and as more fully described below in Example 8. Using the Ep-CAM-positive cell lines, CAL 27 and NIH:OVCAR-3, the IC5o of VB6-845 was 3 to 4 nM and 2 to 3 nM, respectively. In the case of VB6-845-C|_-de-bouganin, the potency was measured at 1 to 2 nM for CAL 27 and 0.6 to 0.7 nM versus NIH:OVCAR-3. The development of Fab anti-Ep-CAM construct, comprising a human tumor targeting antibody fragment linked to a de-immunized bouganin should permit repeat systemic administration of this drug and hence yield greater clinical benefit.
Harvesting of the constructs
The constructs can be isolated from the cell cultures by techniques known in the art. For instance, if a His tag is placed at the N-terminal of the peptide construct, the Fab-bouganin protein can be purified using a Ni 2+-chelating capture method. As an example the following protocol can be used.
Conducting fed batch fermentation of VB6-845 variants performed in a 15L CHEMAP fermenter using TB medium. At an ODeoo of 20 (mid-log), the culture is induced with a mixture of feed and inducer containing 50% glycerol and 200 g/l L-arabinose. At 30 hours post induction, the culture is harvested, centrifuged at 8000 rpm for 30 min and VB6-845 variants purified using CM sepharose and Metal-Charged Cheiating sepharose columns followed by a size exclusion column. Briefly, the supernatant is concentrated and diafiltered against 20 mM sodium phosphate pH 6.9 ± 0.1. The diafiltered concentrated supernatant is then applied onto a CM sepharose column equilibrated with 20 mM sodium phosphate, 25 mM NaCI pH 6.9 ± 0.1. The column is washed with 20 mM sodium phosphate, 25 mM NaCI pH 6.9 ± 0.1, bound VB6-845 is subsequently eluted with 20 mM sodium phosphate, 150 mM NaCI pH 7.5± 0.1. The CM sepharose eluate is adjusted to contain a final concentration of 0.25% Triton-X100 and applied to a charged chelating sepharose column.

The chelating sepharose- column is then washed with 3 different wash buffers starting with 20 mM sodium phosphate, 150 mM NaCI, 0.25% triton-X100 pH 7.5 ± 0.1 followed by 20 mM sodium phosphate, 150 mM NaCI pH 7.5 ± 0.1 and followed by 20 mM sodium phosphate, 150 mM NaCI, 10 mM imidazole pH 7.5 ±0.1. The bound VB6-845 is then eluted with 20 mM sodium phosphate, 150 mM NaCI, 250 mM imidazole pH 7.5 ±0.1 and collected in 2 ml fractions. The absorbance at A2eo is determined for each fraction and the fractions with material pooled are applied onto a size exclusion column S200 in order to obtain a purity of >80%. In one embodiment, to increase the protein purity and remove endotoxin, the pooled SEC fraction is diluted 5-fold with 20mM NaPO4, pH 7.5 and passed though a Q-sepharose 15 ml fast flow column equilibrated with 20 mM NaPCU, 25 mM NaCI pH 7.5 at a flow rate of about 5 ml/min. After application of the sample through the column, the column is washed with 10CV of equilibration buffer and the wash is pooled with the initial Q-sepharose flow through. The effluent is concentrated to ~10-fold through the use of a SOkDa MWCO membrane (Sartorius hydrosart membrane] to achieve a final concentration of 7.5 mg/ml. Tween-80 is then added to a final concentration of 0.1%. The final product is sterile filtered and stored at -80°C. Samples at each steps of the process are analyzed by Western blot after immunoblotting with the anti-4D5 antibody. Purity is confirmed by colloidal blue staining. The level of expression of VB6-845 variants is determined by Western Blot analysis and ELISA.
Example 8: Functional and biological characterization of VB6-845, a recombinant Ep-CAM-specific Fab antibody genetically-linked with de-immunized Bouganin (de-bouganin).
Chemotherapeutics are highly cytotoxic agents that often represent the standard of care in the treatment of many of the solid tumor cancers. The cytotoxic action of these, drugs targets rapidly dividing cells, both normal and tumor, thus creating a variety of adverse clinical side-effects. VB6-845 is a Fab antibody linked to a de-immunized form of the plant-derived toxin bouganin. Unlike Chemotherapeutics which lack defined tumor-target

specificity, VB6-845 restricts its cytolytic effect to Ep-CAM-posftive tumor targets alone. In this study, flow cytometry analysis and cytotoxicity were measured to assess the potency and selectivity of VB6-845.
Flow Cvtometrv
The tumour cell lines used in this study were purchase from ATCC and were propagated following ATCC's recommendations except for the cell lines C-41, TOV-112D which were grown in RPMI 1640 or DMEM supplemented with 10% PCS, respectively. Tumor cells were harvested at 60-70% confluence with viability over 90%. The human normal mammary epithelial cells (HMEC) were purchased from CAMBREX and maintained in specified media according to the procedure provided by CAMBREX. The cells were harvested at 70% confluence with viability over 90%.
The gynaecological cell lines from endometrial ovarian and cervical cancer indications were tested for VB6-845 binding on flow cytometry (Table 9). Ten microgram/mL of VB6-845 was added to each cell line (3 x 105 cells) and incubated for 2h at 4°C. A-375 and CAL 27 were used as negative and positive cell line controls, respectively. After washing off the unbound material, a mouse monoclonal anti-Histidine antibody (Amersham Pharmacia, Cat # 27471001) diluted 1/800 in PBS containing 10% PCS was added and incubated for a further 1 hr at 4°C. Subsequently, FITC-labeled anti-mouse IgG (The Binding Site, Cat# AF271) diluted 1/100 in PBS-10% PCS was added and incubated for 30 min. at 4°C. Finally, the cells were analyzed on a FACS Calibur following propidium iodide staining to gate out the dead cells.
Cvtotoxicitv
The level of killing for VB6-845 in the cells listed in the flow cytometry study is as indicated in Table 10, indicated that the construct retained its de-bouganin cytotoxicity activity against Ep-CAM-positive cell lines. The cytoxicity was comparable to another Fab VB6-845 variant containing a different plant-derived toxin, gelonin. (Figure 14) Figure 14 A compares the cytotoxicity of gelonin, Fab anti-Ep-CAM-gelonin construct (VB6-845-GeIonin)

and the Fab anti-Ep-CAM-de-bouganin (Bou156) construct (VB6-845) in CAL 27 (Figure 14A) and NIH:OVCAR-3 cells (Figure 14B). The nucleic acid and amino acid sequence of the VB6-845-gelonin construct is illustrate in Figure 14C.
To study the specificity and selectivity of VB6-845 (Construct of Figure 3), the cytotoxic activity of VB6-845 (90% pure) was tested against Ep-CAM-positive (NIH:OVCAR-3) and Ep-CAM-negative (HMEC, DAUDl, A-375) cell lines (Table 11) along with 17 chemotherapeutic drugs (LKB Laboratories Inc.).'
The MTS assay was preformed using standard techniques known in the art. More particularly, 50 microlitres of cells (2 x 104 cells/ml) were seeded per well and plates were incubated at 37°C under 5% CO2 for 2 hr. Then 50 microlitres of spiked drug (i.e. construct to be tested or control) was added to the culture medium at increasing concentrations. Culture medium, with or without cells, was used as positive and negative controls, respectively. The plates were left at 37°C under 5% CO2 for 5 days. At day 5, the inhibition of cell proliferation was evaluated by adding 20 microlitres of MTS reagent (Promega, Cat# G5430). The plates were further incubated at 37°C under 5% COa for 2 hr and ODs were read at 490nm using the plate reader spetrophotometer. Background values were subtracted from the sample values obtained for each concentration and the results were expressed as a percent of viable cells. The ICso values for each drug were calculated for each cell line.
When assayed for cytotoxicity against NIH:OVCAR-3, an Ep-CAM-positive ovarian carcinoma, using a panel of standard chemotherapeutic agents, VB6-845 was shown to be more potent than 12 of the 17 drugs tested. (Table 11) Though 5 chemotherapeutics were more cytotoxic, they were also shown to be far more toxic in that they lacked any cell-specific killing. Of the five recommended chemotherapeutic agents for the treatment of ovarian cancer (Paclitaxel, Carboplatin, Cisplatin, Doxorubicin and Topotecan), only two (Paclitaxel and Topotecan) were more cytotoxic. While

VB6-845 demonstrated highly potent cytolytic activity in the range of of 1 to 2 nM, the potent killing was restricted exclusively to the Ep-CAM-positive tumor cell line NIH:OVCAR-3. Although some killing of Ep-CAM-negative cell lines was exhibited with VB6-845, the cytotoxic effect was at least 220-fold and at most >1000-fold less toxic. VB6-845 thus represents a potent antibody-directed treatment alternative to chemotherapeutics that when combined with the lower toxicity profile, holds much promise in the treatment of many different types of solid tumors.
Example 9; VB6-011: recombinant engineering of a tumor-associated antigen-specific Fab antibody for optimal delivery of de-immunized bouganin (De-bouganin).
Tumor-targeting cytotoxins are composed of the variable region of an antibody linked to a bacterial, fungal or plant toxin. The present study illustrates that the deimmunized bouganin constructs of the invention, comprising deimmunized bouganin linked to a targeting moiety have reduced immunogenicity, while still retaining their biological activity. TABLE 13 demonstrates the binding of the tumor-associated antigen antibody to several types of tumours and thus shows that it can be used to treat these types of cancers.
De-immunized Bouqanin Construct: Tumor-associated antigen directed targeting moiety linked to de-bouqanin
The H11 antibody, a monoclonal antibody recognizing tumor-associated antigen, was genetically linked to a de-immunized form of bouganin (de-bouganin), Bou 156, a potent, plant-derived, type I ribosome-inactivating protein (RIP), to create the antibody-toxin construct VB6-011. Figure 15 illustrates the nucleic acid coding sequence and amino acid sequence. Testing of this construct, illustrates that the construct retained its biological activity (cytoxicity).
Potency (biological activity)

MTS assay demonstrated that de-bouganin retained rts potency when conjugated to the Fab fragment (Figure 16). The MTS assay used to measure potency was conducted using standard technique known in the art, and as more fully described in Example 8.
Cvtotoxicitv
To study the specificity and selectivity of VB6-011, the cytotoxic activity was tested against MB-435S cells. The MTS assay was performed using standard techniques known in the art. More particularly, 50 microlitres of cells (2 x 104 cells/ml) were seeded per well and plates were incubated at 37°C under 5% COz for 2 hr. Then 50 microlitres of spiked drug (i.e. construct to be tested or control) was added to the culture medium at increasing concentrations. Culture medium, with or without cells, was used as positive and negative controls, respectively. The plates were left at 37°C under 5% CC>2 for 5 days. At day 5, the inhibition of cell proliferation was evaluated by adding 20 microlitres of MTS reagent (Promega, Cat# G5430). The plates were further incubated at 37°C under 5% C02 for 2 hr and ODs were read at 490nm using the plate reader spectrophotometer. Background values were subtracted from the sample values obtained for each concentration and the results were expressed as a percent of viable cells. Results show that the IC50 value ofVB6-011 is 350nM.
While the present invention has been described with reference to what are presently considered to be the preferred examples, it is to be understood that the invention is not limited to the disclosed examples. To the contrary, the invention is intended to cover various modifications and equivalent arrangements included within the spirit and scope of the appended claims.
AH publications, patents and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety.

Table Remove

Bouganin sequence peptides. The underlined residues are not present in the mature protein

Table 2

Table Remove
MHC Allotypes ofPBMC donors

Table Remove
Sequences of primers used in the construction of the WT bouganin gene

Table 4
Single substitution bouganin variants constructed and tested.

Table Remove
* Activity in Luciferase assay:
++ = same or higher than WT protein. 4 = within 2-fold of WT activity. +/- = within 3-fold of
WT activity. - = less than one-third of WT activity. WT = Wild-type protein.
** Clone ED. Designations for functionally active variants only.

Table 5
Multiple substitution bouganin variants constructed and tested.

Table Remove

Table 6

Table Remove
* The numbering commences from residue 1 of the bouganin reading frame and therefore excludes a PelB leader sequence included in most constructs.

Table 7
SEQ ID No 1
Protein
YNTVSFNLGEAYEYPTFIQDLRNELAKGTPVCQLPVTLQTIADDKRFVLVDITTTSKKTVKVAIDVTDVY WGYQDKWDGKDRAVFLDKVPTVATSKLFPGVTNRVTLTFD'GSYQKLVNAAKVDRKDLELGVYKLEFSIE AIHGKTINGQEIAKFFLIVIQMVSEARRFKYIETEWDRGLYGSFKPNFKVLNLENNWGDISDAIHKSSP
QCTTINPALQLISPSNDPWWNKVSQISPDMGILKFKSSK
SEQ ID No 13
Protein
YNTVSFNLGEAYEYPTFIQD1RNELAKGTPVCQLPVTLQTIADDKRFVLVDITTTSKKTVKVAIDVTDVY
WGYQDKWDGKDRAVFLDKVPTVATSKLFPGVTNRVTLTFDGSYQKLVNAAKADRKALELGVNKLEFSIE
AIHGKTINGQEAAKFFLIVIQMVSEAARFKYIETEWDRGLYGSFKPNFKVLNLENNWGDISDAIHKSSP
QCTTINPALQLISPSNDPWWNKVSQISPDMGILKFKSSK

Table 8
Modified and WT peptides ofBouganin further tested in Tee// assays.

Table Remove
'Substituted (mutant) residue underlined.

Table 9 VB6-845 binding to gynecological cell lines by flow cytometry
Results are expressed as fold-increase in MF±SEM.
Table Remove
Table 10 VB6-845-mediated Cytotoxicity by MTS assay

Table Remove

Table 11 Specificity and selectivity of VB6-845 Versus Chemotherapeutics

Table Remove

Table 12: VB6-845 Tumor Cell Indications

Table Remove
N indicates the number of cell lines tested per indication. 2 Mean fold-increase in median fluorescence over the control antibody from all cell lines in each indication.

Table 13: VB6-011 Tumor Cell Indications

Table Remove
N indicates the number of cell lines tested per indication. 2 Values indicate the mean calculated from the sum of the mean fold increase in median fluorescence over the control antibody from all cell lines in each indication. A zero value would mean no measurable reactivity relative to the control activity


WE CLAIM:
1. A modified bouganin protein wherein said modified bouganin has a
reduced propensity to activate an immune response.
2. A modified bouganin according to claim 1 wherein said bouganin has a
reduced propensity to activate T-cells and is modified at one or more
amino acid residues in a T-cell epitope.
3. A modified bouganin according to claim 2 wherein said bouganin is
modified at one or more amino acid residues in a T-cell epitope
selected from the group consisting of:

d) AKVDRKDLELGVYKL (epitope region R1, SEQ ID NO:2),
e) LGVYKLEFSIEAIHG (epitope region R2, SEQ ID NO:3); and
f) NGQEIAKFFLIVIQM (epitope region R3, SEQ ID NO:4)).
4. A modified bouganin according to claim 3 wherein said bouganin is
modified at one or more of X1, X2, X3, X4 or X5 as follows:
a) AKX1DRKX2LX3LGVX4KL (epitope region R1, SEQ ID NO:5)
b) LGVX4KLEFSIEAIHG (epitope region R2, SEQ ID NO:6); and
c) NGQEX5AKFFLIVIQM (epitope region R3, SEQ ID NO:7)
wherein X1 through X5 can be any amino acid.
5. A modified bouganin according to claim 4 wherein:
X1 is T or A or Q;
X2isGorA;
X3isQorG;
X4 is N or D or T or A or R or Q or E or G or H or K or S; and
Xs is Q or A (SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10).
6. A modified bouganin protein of claim 1, wherein the amino acid
sequence of the modified bouganin protein comprises:
YNTVSFNLGEAYEYPTFIQDLRNELAKGTPVCQLPVTLQTIADDKRFV LVDITTTSKKTVKVAIDVTDVYWGYQDKWDGKDRAVFLDKVPTVAT

SKLFPQVTNRVTLTFDGSYQKLVNAAKX1DRKX21JC3LGVX4KLEFSIE AIHGKTINGQEXSAKFFLIVIQMVSEAARFKYIETEWDRGLYGSFKPN FKVLNLENNWGDISDAIHKSSPQCTTINPALQLISPSNDPWWNKVSQ ISPDMGILKFKSSK (SEQ ID N0:11)
wherein X1 through X5 can be any amino acid.
7. A modified bouganin according to claim 6 wherein:
X1 is T or A or Q;
X2isGorA;
X3 is Q or G;
X4 is N or D or T or A or R or Q or E or G or H or K or S; and
X5isQorA(SEQIDNO:12).
8. A modified bouganin protein according to claim 1 wherein the modified
bouganin comprises the following sequence:
YNTVSFNLGEAYEYPTFIQDLRNELAKGTPVCQLPVTLQTIADDKRFV LVDITTTSKKTVKVAIDVTDVYWGYQDKWDGKDRAVFLDKVPTVAT SKLFPGVTNRVTLTFDGSYQLVNAAKADRKALELGVNKLEFSIEAIH GKTINGQEAAKFFLMQMVSEAARFKYIETEWDRGLYGSFKPNF KVL NLENNWGDISDAIHKSSPQCTTINPALQLISPSNDPWWNKVSQISPD MGILKFKSSK (SEQ ID NO:13)
9. A cytotoxin comprising
(a) a targeting moiety attached to;
(b) a modified bouganin protein according to any one of claims 1-8.
10. A cytotoxin comprising
(a) a ligand that binds to a cancer cell attached to;
(b) a modified bouganin protein according to any one of claims 1-8.

11. The cytotoxin of claim 10, wherein the ligand is an antibody or antibody
fragment that binds to a cancer cell.
12. The cytotoxin of claim 11, wherein the antibody or antibody fragment
binds to Ep-CAM on the surface of the cancer cell.
13. The cytotoxin of claim 12, wherein the antibody or antibody fragment

that binds to Ep-CAM is a humanized antibody or antibody fragment that binds to the extracellular domain of human Ep-CAM and comprises complementarity determining region sequences derived from a MOC-31 antibody.
14. The cytotoxin of claim 12, wherein the variable region of the cancer-
binding ligand attached to the modified bouganin protein is 4D5MOCB.
15. The cytotoxin of claim 14, com prising the amino acid sequence shown
in SEQ ID NO:16.
16. The cytotoxin of claim 11, wherein the antibody or antibody fragment
binds to a tumor-associated antigen on the surface of the cancer cell.
17. The cytotoxin of claim 16, comprising the amino acid sequence shown
in SEQ. ID. NO:28.
18. A use of a cytotoxin according to any one of claims 9-17 in the
manufacture of a medicament for inhibiting or destroying a cancer cell.
19. The use of claim 18, wherein the cancer cell is selected from the group
consisting of colorectal cancer, breast cancer, ovarian cancer,
pancreatic cancer, head and neck cancer, bladder cancer, liver cancer,
renal cancer, melanomas, gastrointestinal cancer, prostate cancer,
small cell and non small cell lung cancer, sarcomas, gliomas, T- and B-
cell lymphomas.
20. A use of a cytotoxin according to any one of claims 9-17 in the
manufacture of a medicament for treating cancer.
21. The use of claim 20, wherein the cancer is selected from the group
consisting of colorectal cancer, breast cancer, ovarian cancer,

pancreatic cancer, head and neck cancer, bladder cancer, Kver cancer, renal cancer, melanomas, gastrointestinal cancer, prostate cancer, small cell and non small cell lung cancer, sarcomas, gliomas, T- and B-cell lymphomas.
22. A pharmaceutical composition comprising the cytotoxin according to
any one of claims 9-17 and a pharmaceutically acceptable carrier,
diluent or excipient.
23. A process of preparing a pharmaceutical for treating an animal with
cancer comprising

(a) identifying T-cell epitopes of bouganin;
(b) modifying one or more amino acid residues in a T-cell epitope to
prepare a modified bouganin having reduced propensity to activate T-
cells;
(c) preparing a cytotoxin having a cancer-binding ligand attached to the
modified bouganin; and
(d) suspending the cytotoxin in a pharmaceutically acceptable carrier,
diluent or excipient.

24. The process of claim 23, wherein the cancer is selected from the group
consisting of colorectal cancer, breast cancer, ovarian cancer,
pancreatic cancer, head and neck cancer, bladder cancer, liver cancer,
renal cancer, melanomas, gastrointestinal cancer, prostate cancer,
small cell and non small cell lung cancer, sarcomas, gliomas, T- and B-
cell lymphomas.
25. A nucleic acid molecule encoding a modified bouganin according to
any one of claims 1-8.
26. A nucleic acid molecule encoding a cytotoxin according to claim 9-17.

27. A T-cell epitope peptide having the sequence:
(a) AKVDRKDLELGVYKL (epitope region R1, SEQ ID NO:2),
(b) LGVYKLEFSIEAIHG (epitope region R2, SEQ ID NO:3); or
(c) NGQEIAKFFLIVIQM (epitope region R3, SEQ ID NO:4).
28. The T-cell epitope peptide of claim 27, having a modified sequence
comprising:
AKX1 DRKX2LX3LGVX4K
wherein at least one of X1, X2, X3, and X4 is modified from the non-modified sequence, such as R, as follows: X1 is T or A or Q; X2isGorA; X3 is Q or G; and
X* is N or D or T or A or R or Q or E or G or H or K or S (SEQ ID IMO:8).
29. The T-cell epitope peptide of claim 27, hiaving a modified sequence
comprising:
LGVYKLEFSIEAIHG
wherein X4 is N or D or T or A or R or Q or E or G or H or K or S (SEQ
IDNO:9).
30. The T-cell epitope peptide of claim 27, having a modified sequence
comprising:
NGQEX5AKFFLIVIQM
wherein Xs is Q or A (SEQ ID NO: 10).
31. A nucleic acid molecule encoding the T-cesII epitope peptide according
to any one of claims 27-30.
32. A modified bouganin protein that is modified at the tyrosine residue at
position 70.

33. The modified bouganin protein according to claim 32, wherein the
tyrosine is replaced with an alanine.
34. The modified bouganin protein according to claim 33 having the
sequence:
YNTVSFNLGEAYEYPTFIQDLRNELAKGTPVCQLPVTLQTIADDKRFV LX^ITTTSKKTVKVAIDVTDVANA/GYQDKWDGKDRAVFLDKVPTVAT SKLFPGVTNRVTLTFDGSYQKLVNAAKVDRKOLELGVYKLEFSIEAIH GKTINGQEIAKFFLIVIQMVSEAARFKYIETEWDRGLYGSFKPNFKVL NLENNWGDISDAIHKSSPQCTTINPALQLISPSNDPWWNKVSQISPD MGILKFKSSK[SEQ ID NO. 129].

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Patent Number 258750
Indian Patent Application Number 5870/DELNP/2006
PG Journal Number 06/2014
Publication Date 07-Feb-2014
Grant Date 05-Feb-2014
Date of Filing 09-Oct-2006
Name of Patentee MERCK PATENT GMBH
Applicant Address FRANKFURTER STRASSE 250, D-64293 DARMSTADT, GERMANY
Inventors:
# Inventor's Name Inventor's Address
1 HELLENDOORN KOEN 80 FAIRWELL ROAD, STOCKTON-ON-TEES TS 19 7 JB, UNITED KINGDOM
2 CIZEAU JEANNICK 602-170 HARGRAVE STREET, WINNIPEG, MANITOBA R3C 3H4, CANADA
3 MACDONALD GLEN CHRISTOPHER 475 RAGLAN ROAD, WINNIPEG, MANITOBA R3G 3E4, CANADA
4 ENTWISTLE JOYCELYN 380 LINDENWOOD DRIVE EAST, WINNIPEG, MANITOBA R3P 2H1, CANADA
5 BOSC DENIS GEORGES 444 RUE ST. JEAN BAPTISTE, WINNIPEG, MANITOBA R2H, 2X7, CANADA
6 GLOVER NICHOLAS RONALD 2389 DEER RUN AVENUE, OAKVILLE, ONTARIO L6J 6K7, CANADA
7 BAKER MATTHEW THE HOLTS, SERGEANTS YARD, HIGH STREET, HORNIGSEA, CAMBRIDGE CB5 9 JG, UNITED KINGDOM
8 CARR FRANCIS J. THE HOLDINGS, BALMEDIE, ABERDEENSHIRE AB23 8XU, UNITED KINGDOM
PCT International Classification Number C07K 19/00
PCT International Application Number PCT/CA2005/000410
PCT International Filing date 2005-03-18
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/630,571 2004-11-26 U.S.A.
2 60/554,580 2004-03-19 U.S.A.