Indian Patents
Title of Invention

HYDROXAMIC ACID COMPOUND
Abstract Antibacterial compounds of formula (I) are provided. As well as stereisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, pharmaceutical composition comprising such compounds, method of treating bacterial infections by the administration of such compounds, and processes for the preparation of the compounds.
Full Text ANTIBACTERIAL AGENTS

This application claims benefit of priority to the following US Provisional Patent Applications, serial no. 60/438,523, filed January 8,2003; serial no. 60/466,974, filed April 30,2003; and serial no.

60/520,211 filed November 13,2003; each of which is incorporated herein by reference in its entirety for any purpose.


FIELD OF THE INVENTION

This invention pertains generally to treating infections caused by gram-negative bacteria. More specifically, the invention described herein pertains to treating gram-negative infections by inhibiting activityof UDP-3-0- (R-3-hydroxydecanoyl)-N-acetylglucosamine deacetylase (LpxC). The present invention provides small molecule inhibitors of LpxC, pharmaceutical formulations containing such inhibitors, methods of treating patients with such pharmaceutical formulations, and to methods of preparing such pharmaceutical formulations and inhibitors. The inhibitors can be used to treat Gram- negative infections of patients alone and in combination with other antibacterials.


BACKGROUND OF THE INVENTION

Over the past several decades, the frequency of antimicrobial resistance and its association with serious infectious diseases have increased at alarming rates. The increasing prevalence of resistance among nosocomial pathogens is particularly disconcerting. Of the over 2 million nosocomial infections occurring each year in the United States, 50 to 60% are caused by antimicrobial-resistant strains of bacteria. This high rate of resistance increases the morbidity, mortality, and costs associated with nosocomial infections. In the United States, nosocomial infections are thought to contribute to or cause more than 77,000 deaths per year and cost approximately $5 to $10 billion annually. Among Gram-positive organisms, the most important resistant pathogens are methicillin-(oxacillin-) resistant
Staphylococcus aureus,B-lactam-resistant andmultidrug-resistant pneumococci, and vancomycin- resistantenterococci. Important causes of Gram-negative resistance include extended-spectrumB- lactamases(ESBLs) in Klebsiella pneumoniae, Escherichia coli, and Proteus mirabilis, high-level third-generation cephalosporin (Amp C)B-lactamase resistance among Enterobacter species and
Citrobacter freundii, andmultidrug-resistance genes observed in Pseudomonas aeruginosa,

Acinetobacter, and Stenotrophomonas maltophilia. (Jones RN 2001 Chest 119 (supplement), 397S-404S : Resistance patterns among nosocomial pathogens: Trends over the past few years.)
The problem of antibacterial resistance is compounded by the existence of bacterial strains resistant to multiple antibacterials. For example, Pseudomonas aeruginosa isolates resistant to fluoroquinolones are virtually all resistant to additional antibacterials (SahmDF et al 2001
Antimicrobial Agents and Chemotherapy 45,267-274 : Evaluation of current activities of fluoroquinolones against gram-negative bacilli using centralized in vitro testing and electronic surveillance.)
Thus there is a need for new antibacterials, particularly antibacterials with novel mechanisms of action. Most of the antibacterial discovery effort in the pharmaceutical industry is aimed at development of drugs effective against gram-positive bacteria. However, there is also a need for new gram-negative antibacterials. Gram-negative bacteria are in general more resistant to a large number of antibacterials and chemotherapeutic agents than are gram-positive bacteria. A survey of recently reported antibacterials of natural origin showed that over 90% lacked activity against Escherichia coli, although they were active against gram-positive bacteria. The outer membrane of gram-negative bacteria contributes to this intrinsic resistance by acting as an efficient permeability barrier, because the narrow porin channels limit the penetration of hydrophilic solutes and the low fluidity of the lipopolysaccharide leaflet slows down the inward diffusion of lipophilic solutes. A second mechanism contributes to the intrinsic resistance of gram-negative bacteria. Recent studies showed that multiple drug efflux pumps, sometimes with unusually broad specificity, act as this second factor to create the general intrinsic resistance of gram-negative bacteria. When their expression levels are elevated as a consequence of physiological regulation or genetic alteration, they can frequently produce impressive levels of resistance to a wide variety of antimicrobial agents. (Nikaido H 1998 Clinical Infectious
Diseases 27 (Suppl 1), S32-41: Antibacterial resistance caused by gram-negativemultidrug efflux pumps.)
Historically, most development of antimicrobial agents has been relatively empirical. Active compounds have generally been found via screening soil, sewage, water, and other natural substances to detect antimicrobial-producing organisms, or by screening various chemical compounds. Once a leading candidate has been found and its chemical structure determined, a series of analogs is made to identify an optimal compound for further clinical development. A more rational approach involves the defining of new targets, such as genes or enzymatic functions, responsible for a crucial cellular

essential activity. Once this has been done, inhibitors or blockers of the function or gene product can be developed.

In order to identify potential targets for novel gram-negative antibacterial agents, studies aimed at identifying all essential and important genes in Pseudomonas aeruginosa have been performed.

Among the essential genes identified was lpxC, that encodes the enzymeuridyldiphospho-3-0- (R- hydroxydecanoyl)-N-acetylglucosamine deacetylase (LpxC). This enzyme is the first committed step in the synthesis of lipid A, the lipid moiety of lipopolysaccharide, that is an essential component of all gram-negative bacteria. It therefore is an attractive target for novel antibacterials. In order to be useful as antibacterial agents, LpxC inhibitors would not only have to inhibit the enzymatic activity of LpxC from a variety of bacteria, but would have to defeat the intrinsic resistance mechanisms of gram- negative bacteria, as described above: they would have to penetrate the outer membrane and be relatively unsusceptible tomultidrug efflux pumps.

Researchers have identified a few compounds with antibacterial activity that target lipid A biosynthesis. WO 97/42179 to Patchett et al. discloses compounds of the formula:
EMI3.1

The compounds possess activity against certain gram-negative organisms, for example Escherichia coli, but are not active against other medically important gram-negative bacteria, for example Pseudomonas aeruginosa. Subsequent studies have found that the primary reason for their inactivity against particular, medically important gram-negative bacteria is their poor ability to inhibit P. aeruginosa LpxC; efflux by the major multidrug efflux pump or inability to penetrate the outer membrane were not the critical factors.

Jackman et al. , in J. Biol. Chem. (vol. 275, no. 15, April 14,2000,pps. 11002-11009), discuss the mechanism of lipid A biosynthesis in the context of gram-negative bacteria and discloses a newclass ofhydroxamate-containing inhibitors of LpxC. Wyckoff et al. , in Trends in Microbiology(vol.

6, no. 4, April1998, pps. 154-159), discuss the role of LpxC in lipid A biosynthesis and its role in

regulation.Wyckoff et al. disclose a few oxazoline hydroxamic acids that inhibit bacterial growth.

However, Wyckoff et al. also discuss the shortcomings of the available deacetylase inhibitors as bactericidal agents against Pseudomonas and that more work is needed to be done in the area.

Thus, an increasing need exists for LpxC inhibitors that have activity as bactericidal agents against gram-negative bacteria. It is, accordingly, an object, of this invention to provide compounds and combinations of such compounds for use in the preparation of antibacterials and other pharmaceuticals capable of inhibiting Gram-negative bacterial infections.

U. S. Patent Publication No. 2001/0053555(U. S. Patent Application Serial No. 08/958,638) published December 20,2001, corresponding to WO 98/18754 published May 7,1998 discloses a combinatorial library of hydroxylamine, hydroxamic acid, hydroxyurea andhydroxylsulfonamide compounds purported to be potentially useful as inhibitors of metalloproteases. U. S. Patent No.

6,281, 245, a continuation in part of U. S.08/958, 638 claims a method of inhibiting adeformylase enzyme by administering one of the hydroxylamine compounds from the combinatorial library asdisclosed in U. S. Patent Publication No. 2001/0053555 and the corresponding WO 98/18754. Related to the above disclosed patent publications is WO 99/57097, published November 11,1999, that discloses a method of solid phase synthesis of the hydroxylamine library of compounds. WO 00/61134 (to British BiotechPharmaceuticals Limited), published October 19,2000, discloses compounds of the formula below:
EMI4.1

The compounds are useful as antimicrobial agents that are believed to have bactericidal activity at least in part to intracellular inhibition of bacterial polypeptidedeformylase.

In an earlier to British Biotech Pharmaceuticals Limited, WO 99/39704, published August 12, 1999, compounds of the formula below are disclosed :

EMI5.1

The compounds are useful as antimicrobial agents useful against gram-negative and gram positive bacteria.

Recently, De NovoPharmaceuticals LTD disclosed in WO 02/50081, published June 27,2002, antibacterial and antiprotozoal agents having the formulae shown below:
EMI5.2
The patent publication discusses that the antibacterial activity is due, at least in part, tointracellular inhibition of bacterial polypeptidedeformylase.


SUMMARY OF THE INVENTION

The present invention provides novel compounds, pharmaceutical formulations including the compounds, methods of inhibitingUDP-3-O-(R-3-hydroxydecanoyl)-N-acetylglucosamine deacetylase (LpxC), and methods of treating gram-negative bacterial infections.

In one embodiment, the present invention provides compounds of formulaI :
EMI5.3

I or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein E is absent or selected from the group consisting of (1) H,(2) substituted or unsubstitutedCl-C6-alkyl,

(3) substituted or unsubstitutedC2-C6-alkenyl, (4) substituted or unsubstitutedC2-C6-alkynyl,(5) substituted or unsubstituted aryl, (6) substituted or unsubstituted heterocyclyl, and (7) substituted or unsubstituted heteroaryl ; L is absent or selected from the group consisting of (1) substituted or unsubstitutedCl-C6-alkyl, (2) -(NH)0-1-(CH2)j-NR3L-(CH2)k-, (3) -(NH)0-1-C(R1L,R2L)-NR3L-C(R1L,R2L)-, (4) -C(R1L,R2L)-O-C(R1L,R2L)-, (5) -(CH2)j-NR3L-C(R1L,2RL)-CONH-(CH2)k-, (6)-CO-C (R1L, RzL)-NHCO-, (7)-CONH-, (8)-NHCO-, wherein
R1L,R2L, andR3L are independently selected from the group consisting of (a) H, (b) substituted or unsubstitutedCI-C6-alkyl,(c)Cl-C6-alkyl substituted with aryl, (d)Cl-C6-alkyl substituted with heterocyclyl, and (e) Cl-C6-alkyl substituted with heteroaryl, orRIL and R3L, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S; j is an integer of 0-4 ; k is an integer of 0-4;D is absent or selected from the group consisting of (1) substituted or unsubstitutedC3-C8-cycloalkyl, (2) substituted or unsubstituted aryl, (3) substituted or unsubstituted heterocyclyl, and (4) substituted or unsubstituted heteroaryl;G is absent or selected from the group consisting of (1)- (CH2) i-O- (CH2) ;-,

(2) -(CH2)i-S-(CH2)i-, (3) -(CH2)i-NRg-(CH2)i-, (4) -C (=O)-, (5) -NHC(=O)-, (6) -C(=O)NH-,(7)- (CH2)iNHCH2C (=O) NH-, (8)--C-C-,(9) -C#C-C#C-, and (10)-C=C- ; wherein
Rg is H or substituted or unsubstitutedCl-C6-alkyl ; i is an interger of 0-4; Y is selected from the group consisting of (1) substituted or unsubstitutedC3-C8-cycloalkyl, (2) substituted or unsubstituted aryl, (3) substituted or unsubstituted heterocyclyl, and (4) substituted or unsubstituted heteroaryl; X is selected from the group consisting of(1)- (C=O)-, (2) -C1-C6-alkyl-(C=O)-, (3)-C2-C6-alkenyl4C=O)-,(4)-C2-C6-alkynyl-(C=O)-, and (5) -CH2-; or when B is absent, X andA, together with the atoms to which they are attached can form a heterocyclic ring, having from 5 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S; B is a absent or
EMI7.1
wherein Rlb andR2b, are independently selected from the group consisting of (a) H, (b) substituted or unsubstitutedCl-C6-alkyl,

(c) substituted or unsubstituted C2-C6-alkenyl, (d) substituted or unsubstitutedC2-C6-alkynyl, (e) substituted or unsubstituted aryl, (f) substituted or unsubstituted heterocyclyl, (g) substituted or unsubstituted heteroaryl, (h)Cl-C6-alkyl substituted with aryl, (i)Cl-C6-alkyl substituted with heterocyclyl, and (j) C1-C6-alkyl substituted with heteroaryl, orRlb andR2b, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 5 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N, O and S; q is an integer of 0-4;R3 is H or substituted or unsubstitutedCl-C6-alkyl, or R3 and A, together with the atoms to which they are attached can form a substituted or unsubstituted 3-10 membered cycloalkyl or a heterocyclic ring system, wherein the heterocyclic ring system may have from 3 to 10 ring atoms, with 1 to 2 rings being in the ring system and contain from 1-4 heteroatoms selected from N,O and S; R4 is H or substituted or unsubstituted C1-C6-alkyl, or R4 and A, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S; n is an integer of 0-6; A is selected from the group consisting of (1) H, (a) -(CH2) rC (R1a, R2a) (CH2) sOR3A, (3) -(CH2)rC(R1a,2Ra) N(R4aRsa)(4)- (CH2) rC(Rla, R2a) N(R4a) COR3a, (5) - (CH2) rC (R1a,R2a)NHCON(R4a,R5a), (6) -(CH2)rC(R1a,R2a)NHC(=NH)N(R4a,R5a), (7) -CH(R1a,R2a), (8) -C#CH,(9) dCH2) rC (R, R) CN,(10)- (CH2) rC(Rla, R2a) CO2R3a, and

(11)- (CH2) rC (R1a,R2a) CON (R4a, R5a), wherein R1a, R2a, R3a, R4a, andRusa are independently selected from the group consisting of (a) H, (b) substituted or unsubstituted C1-C6-alkyl, (c) substituted or unsubstituted aryl, (d) substituted or unsubstituted heterocyclyl, (e) substituted or unsubstituted heteroaryl,(f)Cl-C6-alkyl substituted with aryl,(g)Cl-C6-alkyl substituted with, heterocyclyl, and (h) Cl-C6-alkyl substituted with heteroaryl, orR4a and R5a together withthe N atom to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 5 to8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S; r is an integer of 0-4; s is an integer of 0-4; Q is absent or selected from the group consisting of (1) -C (=O) N (R1, R2), (2) -NHC (=O) N(RI,R2),(3)-N (OH) C (=O) N(Ri, R2), (4) -CH (OH) C (=O) N (RI, R2), (5) -CH[N(R2q,R3q)]C(=O) N (R1,R2),(6)-CHRIqC (=O) N(Ri,R2), (7)-CO2H, (8) -C (=O) NHSO2R4q, (9)-SO2NH2,.

(10) -N(OH)C(=O)R1q, (11) -N(OH)SO2R4q, (12) -NHSO2R4q, (13)-SH, (14) -CH (SH)(CH2)01C (=O) N (R1, R2), (15) -CH (SH)(CH2) 0-1CO2H,(16)-CH (OH)(CH2)o-tC02H, (17) -CH (SH) CH2C02R

(18) -CH (OH)(CH2) SO2NH2, (19) -CH(CH2SH)NHCOR1q, (20) -CH (CH2SH) NHSO2R4q, (21) -CH (CH2SR5q) C02H, (22) -CH (CH2SH)NHS02NH2, (23) -CH (CH20H) CO2H, (24)-CH (CH20H) NHS02NH2, (25) -C(=O)CH2CO2H, (26) -C (=O)(CH2) o-iCONH2, (27) -OSO2NHR5q, (28)-SO2NHNH2,(29)-P (=O) (OH)2,
EMI10.1
wherein R1 is selected-from the group consisting of(1) H, (2)-OH, (3) -OC1-6-alkyl, (4) -N(R2q,R3q), and (5) substituted or unsubstituted C1. 6-alkyl; R2 is selected from the group consisting of (1) H, (2) substituted or unsubstitutedCl-C6-alkyl, (3) substituted or unsubstituted C2-C6-alkenyl, (4) substituted or unsubstitutedC2-C6-alkenyl, (5) substituted or unsubstituted aryl,

(6) substituted or unsubstituted heterocyclyl, (7) substituted or unsubstituted heteroaryl, (8)Ci-C6-alkyl substituted with aryl, (9)Cl-C6-alkyl substituted with heterocyclyl, and (10)Cl-C6-alkyl substituted with heteroaryl, orRl andR2, together with the N atom to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 10 ring atoms, wherein 1-4 ring atoms of the heterocyclic ring system are selected from N,O and S, or R2 andR4, together with the N atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 10 ring atoms, wherein 1-4 ring atoms of the heterocyclic ring system are selected from N,O and S;Rlq, R2q, R3q, R4q, and R5q are selected fromH orCl-C6 alkyl, whereinB is absent, or E, L, G, and B are absent, or E, L, and G are absent, or E, L, and B are absent, or E, L, D, G, and B are absent.

In one aspect, the invention provides a method of inhibiting a deacetylase enzyme in a gram- negative bacteria, thereby affecting bacterial growth, comprising administering to a patient in need of such inhibition a compound of formulaI.

In another aspect, the invention provides a method of inhibiting LpxC, thereby modulating the virulence of a bacterial infection, comprising administering to a patient in need of such inhibition a compound of formula I.

In another aspect, the invention provides a method for treating a subject with a gram-negative bacterial infection comprising administering to the subject in need thereof an antibacterially effective amount of a compound of formula I witha pharmaceutically acceptable carrier. In a preferred embodiment of the method of treatment, the subject is a mammal and in some embodiments, a human.

In another aspect, the invention provides a method of administering an inhibitory amount of a compound of formula I to fermentative or non-fermentative gram-negative bacteria. In a preferred embodiment of the method of administering an inhibitory amount of a compound of formula I to fermentative or non-fermentative gram-negative bacteria, the gram-negative bacteria are selected from the group consisting of Pseudomonas aeruginosa, Stenotrophomonas maltophila, Burkholderia cepacia, Alcaligenes xylosoxidans, Acinetobacter, Enterobacteriaceae, Haemophilus, and Neisseria species.

In another embodiment, the invention provides a method of administering an inhibitory amount of a compound of formula I to gram-negative bacteria, such as Enterobacteriaceae which is selected

from the group consisting of organisms such as Serratia, Proteus, Klebsiella, Enterobacter, Citrobacter,
Salmonella, Providencia, Morganella,Cedecea, and Edwardsiella species and Escherichia coli.

Another embodiment of the invention provides a pharmaceutical composition comprising an effective amount of a compound of Formula I with a pharmaceutically acceptable carrier thereof.

Pharmaceutical formulations according to the present invention are provided which include any of the compounds described above in combination with a pharmaceutically acceptable carrier.

Another embodiment of the invention provides a method ofco-administering the compound of formula I with other therapeutic agents that are selected for their particular usefulness against the condition that is being treated.

For example, the compound of formula I is useful in combination with other anti-bacterial agents. The compound of formula I augments the sensitivity of gram-negative bacteria to existing classes of antibacterials. Combinations of the presently disclosed compounds with other anti-bacterial agents are within the scope of the invention. Such anti-bacterial agents include, but are not limited to,erythromyciri, rifampicin, Nalidixic acid, carbenicillin, bacitracin, cycloserine, fosfomycin, and vancomycin.


DETAILED DESCRIPTION

The present invention provides novel compounds, methods for inhibiting LpxC in gram- negative bacteria, and novel methods for treating bacterial infections. The compounds provided herein can be formulated into pharmaceutical formulations and medicaments that are useful in the methods of the invention. The invention also provides for the use of the compounds in preparing medicaments and pharmaceutical formulations, for use of the compounds in inhibiting LpxC, and for use of the compounds in treating bacterial infections in a subject.

The following abbreviations and definitions are used throughout this application:

"LpxC"is an abbreviation that stands forUDP-3-0- (R-3-hydroxydecanoyl)-N-acetylglucosamine deacetylase.

Generally, reference to a certain element such as hydrogen or H is meant to include all isotopes of that element. For example, if an R group is defined to include hydrogen or H, it also includes deuterium and tritium.

The phrase "alkyl" refers to alkyl groups that do not contain heteroatoms. Thus the phrase includes straight chain alkyl groups such as methyl, ethyl, propyl, butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, undecyl, dodecyl and the like. The phrase also includes branched chain isomers of straight chain alkyl groups, including but not limited to, the following that are provided by way of example:-CH (CH3)2,-CH (CH3) (CH2CH3),-CH (CH2CH3)2,- C (CH3) 3, -C (CH2CH3) 3, -CH2CH (CH3)2,-CH2CH (CH3)(CH2CH3),-CH2CH (CH2CH3) 2,- CH2C (CH3)3,-CH2C (CH2CH3) 3, -CH (CH3) CH (CH3)(CH2CH3),-CH2CH2CH (CH3) 2,-CH2CH2CH (CH3)(CH2CH3),-CH2CH2CH(CH2CH3)2,-CH2CH2C (CH3) 3,-CH2CH2C (CH2CH3) 3, -CH (CH3) CH2CH (CH3) 2, -CH (CH3) CH (CH3) CH (CH3)2,-CH (CH2CH3) CH (CH3) CH (CH3) (CH2CH3), and others. The phrase also includes cyclic alkyl groups such as cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl and such rings substituted with straight and branched chain alkyl groups as defined above. Thus the phrase alkyl groups includes primary alkyl groups, secondary alkyl groups, and tertiary alkyl groups. Preferred alkyl groups include straight and branched chain alkyl groups and cyclic alkyl groups having 1 to 12 carbon atoms.

The phrase"substituted alkyl"refers to an alkyl group as defined above in which one or more bonds to a carbon (s) or hydrogen (s) are replaced by a bond to non-hydrogen and non-carbon atoms such as, but not limited to, a halogen atom such as F,Cl, Br, and I; an oxygen atom in groups such as hydroxyl groups, alkoxy groups, aryloxy groups, and ester groups; a sulfur atom in groups such as thiol groups, alkyl and aryl sulfide groups, sulfone groups, sulfonyl groups, and sulfoxide groups ; a nitrogen atom in groups such as amines, amides, alkylamines, dialkylamines, arylamines,alkylarylamines, diarylamines,N-oxides, imides, and enamines; a silicon atom in groups such as in trialkylsilyl groups, dialkylarylsilyl groups, alkyldiarylsilyl groups, and triarylsilyl groups; and other heteroatoms in various other groups. Substituted alkyl groups also include groups in which one or more bonds to a carbon (s) or hydrogen (s) atom is replaced by a higher-order bond (e. g.,a double-or triple-bond) to a heteroatom such as oxygen in oxo, carbonyl, carboxyl, and ester groups; nitrogen in groups such as imines, oximes, hydrazones, and nitriles. Substituted alkyl groups further include alkyl groups in which one or

more bonds to a carbon (s) or hydrogen (s) atoms is replaced by a bond to an aryl, heterocyclyl group, or cycloalkyl group. Preferred substituted alkyl groups include, among others, alkyl groups in which one or more bonds to a carbon or hydrogen atomis/are replaced by one or more bonds to fluorine atoms.

Another preferred substituted alkyl group is the trifluoromethyl group and other alkyl groups that contain the trifluoromethyl group. Other preferred substituted alkyl groups include those in which one or more bonds to a carbon or hydrogen atom is replaced by a bond to an oxygen atom such that the substituted alkyl group contains a hydroxyl, alkoxy, or aryloxy group. Still other preferred substituted alkyl groups include alkyl groups that have an amine, or a substituted or unsubstituted alkylamine, dialkylamine, arylamine, (alkyl) (aryl) amine, diarylamine,heterocyclylamine, diheterocyclylamine, (alkyl) (heterocyclyl) amine, or (aryl) (heterocyclyl) amine group.

The phrase"alkenyl"refers to straight and branched chain and cyclic groups such as those described with respect to alkyl groups as defined above, except that at least one double bond exists between two carbon atoms. Examples include, but are not limited to vinyl,-CH=C (H) (CH3),-CH=C (CH3) 2, -C (CH3) =C(H) 2,-C (CH3) =C (H) (CH3), -C (CH2CH3) =CH2, cyclohexenyl, cyclopentenyl,cyclohexadienyl, butadienyl, pentadienyl, andhexadienyl among others.

The phrase"substituted alkenyl"has the same meaning with respect to alkenyl groups that substituted alkyl groups had with respect to unsubstituted alkyl groups. A substituted alkenyl group includes alkenyl groups in which a non-carbon or non-hydrogen atom is bonded to a carbon double bonded to another carbon and those in which one of the non-carbon or non-hydrogen atoms is bonded to a carbon not involved in a double bond to another carbon.

The phrase"alkynyl"refers to straight and branched chain groups such as those described with respect to alkyl groups as defined above, except that at least one triple bond exists between two carbon atoms. Examples include, but are not limitedto-C--C(H),-C~C(CH3),-C=C (CH2CH3),-C (H2) C-C (H), -C (H)2C=C (CH3), and-C(H)2C=C(CH2CH3) among others. The phrase"substitutedalkynyl"has the same meaning with respect to alkynyl groups that substituted alkyl groups had with respect to unsubstituted alkyl groups. A substituted alkynyl group includes alkynyl groups in which a non-carbon or non-hydrogen atom is bonded to a carbon triple bonded to another carbon and those in which a non-carbon or non-hydrogen atom is bonded to a carbon not involved in a triple bond to another carbon.

Thephrase"heterocyclyl"refers to both aromatic and nonaromatic ring compounds includingmonocyclic, bicyclic, and polycyclic ring compounds such as, but not limited to,quinuclidinyl, containing 3 or more ring members of which one or more is a heteroatom such as, but not limited to,

N,O, and S. Although thephrase"unsubstituted heterocyclyl"includes condensed heterocyclic rings such as benzimidazolyl, it does not include heterocyclyl groups that have other groups such as alkyl or halo groups bonded to one of the ring members as compounds such as2-methylbenzimidazolyl are substituted heterocyclyl groups. Examples of heterocyclyl groups include, but are not limited to: unsaturated 3 to 8 membered rings containing 1 to 4 nitrogen atoms such as, but not limited to pyrrolyl,pyrrolinyl, imidazolyl, pyrazolyl, pyridyl, dihydropyridyl, pyrimidyl, pyrazinyl, pyridazinyl, triazolyl (e. g.4H-1, 2,4-triazolyl,lu-1, 2,3-triazolyl, 2H-1, 2,3-triazolyl etc. ), tetrazolyl, (e. g. 1H- tetrazolyl, 2H tetrazolyl, etc. ); saturated 3 to 8 membered rings containing 1 to 4 nitrogen atoms such as, but not limited to, pyrrolidinyl, imidazolidinyl, piperidinyl, piperazinyl ; condensed unsaturated heterocyclic groups containing 1 to 4 nitrogen atoms such as, but not limited to, indolyl, isoindolyl, indolinyl,indolizinyl,benzimidazolyl, quinolyl, isoquinolyl, indazolyl, benzotriazolyl; unsaturated 3 to
8 membered rings containing 1 to 2 oxygen atoms and 1 to 3 nitrogen atoms such as, but not limited to, oxazolyl, isoxazolyl, oxadiazolyl (e. g. 1,2, 4-oxadiazolyl, 1,3, 4-oxadiazolyl, 1,2, 5-oxadiazolyl, etc. ) ; saturated 3 to 8 membered rings containing 1 to 2 oxygen atoms and 1 to 3 nitrogen atoms such as, but not limited to, morpholinyl; unsaturated condensed heterocyclic groups containing 1 to 2 oxygen atoms and 1 to 3 nitrogen atoms, for example, benzoxazolyl, benzoxadiazolyl, benzoxazinyl (e. g. 2H-1,4- benzoxazinyl etc. ) ; unsaturated 3 to 8 membered rings containing 1 to 3 sulfur atoms and 1 to3 nitrogen atoms such as, but not limited to, thiazolyl, isothiazolyl,thiadiazolyl (e. g. 1,2,3-thiadiazolyl,
1,2, 4-thiadiazolyl, 1,3, 4-thiadiazolyl, 1,2, 5-thiadiazolyl, etc. ) ; saturated 3 to 8 membered rings containing 1 to 2 sulfur atoms and 1 to 3 nitrogen atoms such as, but not limited to, thiazolodinyl; saturated and unsaturated 3 to 8 membered rings containing 1 to 2 sulfur atoms such as, but not limited to, thienyl,dihydrodithiinyl, dihydrodithionyl, tetrahydrothiophene,tetrahydrothiopyran ; unsaturated condensed heterocyclic rings containing 1 to 2 sulfur atoms and 1 to 3 nitrogen atoms such as, but not limited to,benzothiazolyl,benzothiadiazolyl, benzothiazinyl (e. g.2H-1, 4-benzothiazinyl, etc.), dihydrobenzothiazinyl (e. g. 2H-3,4-dihydrobenzothiazinyl, etc. ), unsaturated 3 to 8 membered rings containing oxygen atoms such as, but not limited to furyl; unsaturated condensed heterocyclic rings containing 1 to 2 oxygen atoms such as benzodioxolyl(e. g. 1,3-benzodioxoyl, etc. ); unsaturated 3 to 8 membered rings containing an oxygen atom and 1 to 2 sulfur atoms such as, but not limited to, dihydrooxathiinyl; saturated 3 to 8 membered rings containing 1 to 2 oxygen atoms and 1 to 2 sulfur atoms such as 1, 4-oxathiane ; unsaturated condensed rings containing 1 to 2 sulfur atoms such as benzothienyl, benzodithiinyl; and unsaturated condensed heterocyclic rings containing an oxygen atom and 1 to 2 oxygen atoms such as benzoxathiinyl. Heterocyclyl group also include those described above in which one or more S atoms in the ring is double-bonded to one or two oxygen atoms

(sulfoxides and sulfones). For example, heterocyclyl groups include tetrahydrothiophene,' tetrahydrothiophene oxide, and tetrahydrothiophene1,1-dioxide. Preferred heterocyclyl groups contain 5 or 6 ring members. More preferred heterocyclyl groups include morpholine, piperazine, piperidine,pyrrolidine, imidazole, pyrazole, 1,2, 3-triazole, 1,2, 4-triazole, tetrazole, thiomorpholine, thiomorpholine in which the S atom of the thiomorpholine is bonded to one or more O atoms, pyrrole, homopiperazine, oxazolidin-2-one,pyrrolidin-2-one, oxazole, quinuclidine, thiazole, isoxazole, furan, and tetrahydrofuran.

The phrase"substitutedheterocyclyl"refers to a heterocyclyl group as defined above in which one of the ring members is bonded to a non-hydrogen atom such as described above with respect to substituted alkyl groups and substituted aryl groups. Examples, include, but are not limited to, 2-methylbenzimidazolyl,5-methylbenzimidazolyl, 5-chlorobenzthiazolyl, 1-methyl piperazinyl, and 2- chloropyridyl among others.

The phrase"aryl"refers to aryl groups that do not contain heteroatoms. Thus the phrase includes, but is not limited to, groups such as phenyl, biphenyl, anthracenyl, naphtlienyl by way of example. Although thephrase"unsubstituted aryl"includes groups containing condensed rings such as naphthalene, it does not include aryl groups that have other groups such as alkyl or halo groups bonded to one of the ring members, as aryl groups such as tolyl are considered herein to be substituted aryl groups as described below. A preferred unsubstituted aryl group is phenyl. Unsubstituted aryl groups may be bonded to one or more carbon atom (s), oxygen atom (s), nitrogen atom (s), and/or sulfur atom (s) in the parent compound, however.

The phrase"substituted aryl group"has the same meaning with respect to unsubstituted aryl groups that substituted alkyl groups had with respect to unsubstituted alkyl groups. However, a substituted aryl group also includes aryl groups in which one of the aromatic carbons is bonded to one of the non-carbon or non-hydrogen atoms described above and also includes aryl groups in which one or more aromatic carbons of the aryl group is bonded to a substituted and/or unsubstituted alkyl, alkenyl, or alkynyl group as defined herein. This includes bonding arrangements in which two carbon atoms of an aryl group are bonded to two atoms of an alkyl, alkenyl, or alkynyl group to define a fused ring system (e. g. dihydronaphthyl or tetrahydronaphthyl). Thus, thephrase"substituted aryl"includes, but is not limited totolyl, and hydroxyphenyl among others. Preferred substituents include straight and branched chain alkylgroups,-CH3,-C2H5,-CH2OH,-OH,-OCH3,-OC2H5,-OCF3,-CN,-N02,-C02H,-CO2CH3,-CONH2,-NH2,-F,-Cl, Br,-CF3,-N (CH3) 2,-NHS02CH3,-NHCOCH3.

The term"heteroaryl", as used herein, refers to a cyclic or bicyclic aromatic radical having from five to ten ring atoms in each ring of which one atom of the cyclic or bicyclic ring is selected from S,O and N; zero, one or two ring atoms are additional heteroatoms independently selected from
S, 0 and N; and the remaining ring atoms are carbon, the radical being joined to the rest of the molecule via any of the ring atoms, such as, for example, pyridyl, pyrazinyl, pyrimidinyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, oxazolyl, isooxazolyl, thiadiazolyl, oxadiazolyl, thiophenyl, furanyl, quinolinyl, isoquinolinyl, and naphthyridinyl, and the like.

Theterm"substituted heteroaryl"as used herein refers to a heteroaryl group as defined herein substituted by independent replacement of one, two or three of the hydrogen atoms thereon withCl,
Br, F,I, OH, CN,Cl-C3-alkyl,Cl-C6-alkoxy,Cl-C6-alkoxy substituted with aryl, haloalkyl, thioalkoxy, amino, alkylamino, dialkylamino, mercapto, nitro, carboxaldehyde, carboxy, alkoxycarbonyl and carboxamide. In addition, any one substituent may be an aryl, heteroaryl, or heterocycloalkyl group.

Preferredsubstituents include straight and branched chain alkylgroups,-CH3,-C2H5,-CH2OH,-OH,-OCH3,-OC2Hs,-OCF3,-CN,-N02,-C02H,-C02CH3,-CONH2,-NH2,-F,-Cl, Br,-CF3,-N (CH3) 2,- NHSO2CH3,-NHCOCH3.

The term"biaryl"refers to a group or substituent to which two aryl groups, which are not condensed to each other, are bound. Exemplary biaryl compounds include, for example, phenylbenzene, diphenyldiazene, 4-methylthio-1-phenylbenzene,phenoxybenzene, (2- phenylethynyl) benzene, diphenyl ketone, (4-phenylbuta-1, 3-diynyl) benzene, phenylbenzylamine, (phenylmethoxy) benzene, and the like. Preferred optionally substituted biaryl groups include: 2- (phenylamino)-N- [4- (2-phenylethynyl) phenyl] acetamide, 1,4-diphenylbenzene,N- [4- (2- phenylethynyl)phenyl]-2- [benzylamino] acetamide, 2-amino-N- [4- (2- phenylethynyl) phenyl] propanamide,2-amino-N- [4- (2-phenylethynyl) phenyl] acetamide, 2-(cyclopropylamino)-N- [4- (2-phenylethynyl) phenyl] acetamide,2- (ethylamino)-N- [4- (2- phenylethynyl) phenyl] acetamide,2- [ (2-methylpropyl) amino]-N- [4- (2- phenylethynyl) phenyl] acetamide, 5-phenyl-2H-benzo [d] 1, 3-dioxolene,2-chloro-l-methoxy4-phenylbenzene,2- [ (imidazolylmethyl) amino]-N- [4- (2-phenylethynyl) phenyl] acetamide,4-phenyl-1- phenoxybenzene,N- (2-aminoethyl) [4- (2-phenylethynyl) phenyl] carboxamide, 2-{[(4- fluorophenyl) methyl]amino}-N- [4- (2-phenylethynyl) phenyl] acetamide,2-{[(4- methylphenyl) methyl]amino}-N- [4- (2-phenylethynyl) phenyl] acetamide, 4-phenyl-1- (trifluoromethyl) benzene,1-butyl-4-phenylbenzene,2- (cyclohexylamino)-N- [4- (2- phenylethynyl) phenyl] acetamide, 2- (ethylmethylamino)-N- [4- (2-phenylethynyl) phenyl] acetamide, 2-

(butylamino)-N- [4- (2-phenylethynyl) phenyl] acetamide,N- [4- (2-phenylethynyl) phenyl]-2- (4- pyridylamino) acetamide,N- [4- (2-phenylethynyl) phenyl]-2- (quinuclidin-3-ylamino) acetamide,

imidino, oxo, oxamidino, methoxamidino, imidino, guanidino, sulfonamido, carboxyl, formyl, alkyl, substituted alkyl, haloloweralkyl, loweralkoxy, haloloweralkoxy, loweralkoxyalkyl, alkylcarbonyl,arylcarbonyl, aralkylcarbonyl, heteroarylcarbonyl, heteroaralkylcarbonyl, alkylthio, aminoalkyl, cyanoalkyl, benzyl, pyridyl, pyrazolyl, pyrrole, thiophene, imidazolyl, and the like.

Representative substituted amidino andheterocycloamidino groups include, for example, those shown below. These amidino andheterocycloamidino groups can be further substituted as will be apparent to those having skill in the organic and medicinal chemistry arts in conjunction with the disclosure herein.
EMI19.1


Representative substituted alkylcarbonylamino, alkyloxycarbonylamino,aminoalkyloxycarbonylamino, and arylcarbonylamino groups include, for example, those shown below. These groups can be further substituted as will be apparent to those having skill in the organic and medicinal chemistry arts in conjunction with the disclosure herein.
EMI19.2


Representative substituted aminocarbonyl groups include, for example, those shown below.

These can be further substituted by heterocyclo groups and heteroaryl groups as will be apparent to those having skill in the organic and medicinal chemistry arts in conjunction with the disclosure herein. Prefered aminocarbonyl groups include: N- (2-cyanoethyl) carboxamide, N- (3- methoxypropyl) carboxamide,N-cyclopropylcarboxamide,N- (2-hydroxy-isopropyl) carboxamide, methyl 2-carbonylamino-3-hydroxypropanoate,N- (2-hydroxypropyl) carboxamide,N- (2-hydroxy- isopropyl) carboxamide,N-[2-hydroxy-1-(hydroxymethyl) ethyl] carboxamide,N- (2-carbonylaminoethyl) acetamide,N- (2- (2-pyridyl) ethyl) carboxamide, N- (2-pyridylmethyl) carboxamide, N- (oxolan-2-ylmethyl) carboxamide,N- (4-hydroxypyrrolidin-2-yl) carboxamide, N- [2- (2-

hydroxyethoxy) ethyl] carboxamide,N- (4-hydroxycyclohexyl) carboxamide,N-[2-(2-oxo-4- imidazolinyl) ethyl] carboxamide, N- (carbonylaminomethyl) acetamide, N- (3-pyrrolidinylpropyl) carboxamide, N-[l-(carbonylaminomethyl) pyrrolidin-3-yl] acetamide,N- (2- morpholin-4-ylethyl) carboxamide, N- [3- (2-oxopyrrolidinyl) propyl] carboxamide, 4-methyl-2-oxopiperazinecarbaldehyde,N-(2-hydroxy-3-pyrrolidinylpropyl) carboxamide,N- (2-hydroxy-3- morpholin-4-ylpropyl) carboxamide,N-{2-[(5-cyano-2-pyridyl) amino] ethyl} carboxamide, 3- (dimethylamino) pyrrolidinecarbaldehyde,N- [ (5-methylpyrazin-2-yl) methyl] carboxamide,2, 2,2-trifluoro-N- (l-formylpyrrolidin-3-yl) acetamide,
EMI20.1

Representative substituted alkoxycarbonyl groups include, for example, those shown below.

These alkoxycarbonyl groups can be further substituted as will be apparent to those having skill in the organic and medicinal chemistry arts in conjunction with the disclosure herein.
EMI20.2


The term"protected"with respect to hydroxyl groups, amine groups, andsulfhydryl groups refers to forms of these functionalities that are protected from undesirable reaction with a protecting group known to those skilled in the art such as those set forth in Protective Groups in Organic Synthesis, Greene, T. W.; Wuts, P. G. M. , John Wiley & Sons, New York, NY, (3rd Edition, 1999) that

can be added or removed using the procedures set forth therein. Examples of protected hydroxyl groups include, but are not limited to, silyl ethers such as those obtained by reaction of a hydroxyl group with a reagent such as, but not limited to, t-butyldimethyl-chlorosilane, trimethylchlorosilane, triisopropylchlorosilane,triethylchlorosilane ; substituted methyl and ethyl ethers such as, but not limited to methoxymethyl ether,methythiomethyl ether, benzyloxymethyl ether, t-butoxymethyl ether,
2-methoxyethoxymethyl ether, tetrahydropyranyl ethers, 1-ethoxyethyl ether, allyl ether, benzyl ether; esters such as, but not limited to,benzoylformate, formate, acetate, trichloroacetate, and trifluoracetate.

Examples of protected amine groups include, but are not limited to, amides such as, formamide, acetamide,trifluoroacetamide, and benzamide ; imides, such as phthalimide, and dithiosuccinimide ; and others. Examples of protectedsulfhydryl groups include, but are not limited to, thioether such as
S-benzyl thioether, and S-4-picolyl thioether ; substituted S-methyl derivatives such as hemithio, dithio and aminothio acetals; and others.

A"pharmaceutically acceptablesalt"includes a salt with an inorganic base, organic base, inorganic acid, organic acid, or basic or acidic amino acid. As salts of inorganic bases, the invention includes, for example, alkali metals such as sodium or potassium ; alkaline earth metals such as calcium and magnesium or aluminum ; and ammonia. As salts of organic bases, the invention includes, for example, trimethylamine, triethylamine, pyridine, picoline, ethanolamine, diethanolamine, and triethanolamine. As salts of inorganic acids, the instant invention includes, for example, hydrochloric acid, hydroboric acid, nitric acid, sulfuric acid, and phosphoric acid. As salts of organic acids, the instant invention includes, for example, formic acid, acetic acid, trifluoroacetic acid, fumaric acid, oxalic acid, tartaric acid, maleic acid, citric acid, succinic acid, malic acid,methanesulfonic acid,benzenesulfonic acid, and p-toluenesulfonic acid. As salts of basic amino acids, the instant invention includes, for example, arginine, lysine and ornithine. Acidic amino acids include, for example, aspartic acid and glutamic acid.

As used herein, theterm"pharmaceutically acceptable ester"refers to esters that hydrolyze in vivo and include those that break down readily in the human body to leave the parent compound or a salt thereof. Suitable ester groups include, for example, those derived from pharmaceutically acceptable aliphatic carboxylic acids, particularlyalkanoic, alkenoic, cycloalkanoic and alkanedioic acids, in which each alkyl or alkenylmoiety advantageously has not more than 6 carbon atoms.

Representative examples of particular esters include, but are not limited to, formates, acetates, propionates, butyrates, acrylates and ethylsuccinates.

Theterm"pharmaceutically acceptable prodrugs"as used herein refers to those prodrugs of the compounds of the present invention that are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response, and the like, commensurate with a reasonablebenefit/risk ratio, and effective for their intended use, as well as the zwitterionic forms, where possible, of the compounds of the invention.

Theterm"prodrug"refers to compounds that are rapidly transformed in vivo to yield the parent compound of the above formula, for example by hydrolysis in blood. A thorough discussion is provided in T. Higuchi and V. Stella, Pro-drugs as Novel Delivery Systems, Vol. 14 of the A. C. S.

Symposium Series, and in Edward B. Roche, ed. , Bioreversible Carriers in Drug Design, American
Pharmaceutical Association and Pergamon Press, 1987, both of which are incorporated herein by reference.

The term"antibacterialagent"refers to agents synthesized or modified in the laboratory that have either bactericidal or bacteriostatic activity. An"active"agent in this context will inhibit the growth of P. aeruginosa and other gram-negative bacteria. The term"inhibiting thegrowth"indicates that the rate of increase in the numbers of a population of a particular bacterium is reduced. Thus, the term includes situations in which the bacterial population increases but at a reduced rate, as well as situations where the growth of the population is stopped, as well as situations where the numbers of the bacteria in the population are reduced or the population even eliminated. If an enzyme activity assay is used to screen for inhibitors, one can make modifications in uptake/efflux, solubility, half-life, etc. to compounds in order to correlate enzyme inhibition with growth inhibition. The activity of antibacterial agents is not necessarily limited to bacteria but may also encompass activity against parasites, virus, and fungi.

The subject invention also includes isotopically-labeled LpxC inhibitors, that are structurally identical to those disclosed above, but for the fact that one or more atoms are replaced by an atom having an atomic mass or mass number different from the atomic mass or mass number usually found in nature. Examples of isotopes that can be incorporated into compounds of the invention include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, sulfur, fluorine and chlorine, such as 2H,3H,13C, 14C, l5N, 18O, 17O, 31p, 32p, 35S, l8F and36C1, respectively. Compounds of the present invention, prodrugs thereof, and pharmaceutically acceptable salts of said compounds and of said prodrugs that contain the aforementioned isotopes and/or other isotopes of other atoms are within the scope of this invention. Certain isotopically labeled compounds of the present invention, for example those into which radioactive isotopes such as 3H and14C are incorporated, are useful in drugand/or

substrate tissue distribution assays. Tritiated, i. e.,3H, and carbon-14, i.e., 14C, isotopes are particularly preferred for their ease of preparation and detectability. Further, substitution with heavier isotopes such as deuterium, i. e.,2H, may afford certain therapeutic advantages resulting from greater metabolic stability, for example increased in vivo half-life or reduced dosage requirements and, hence, may be preferred in some circumstances. Isotopically labeled compounds of this invention and prodrugs thereof can generally be prepared by carrying out known or referenced procedures and by substituting a readily available isotopically labeled reagent for anon-isotopically labeled reagent.

The present invention provides novel compounds, pharmaceutical formulations including the compounds, methods of inhibitingUDP-3-0-(R-3-hydroxydecanoyl)-N-acetylglucosamine deacetylase (LpxC), and methods of treating gram-negative bacterial infections.

In one embodiment, the present invention provides compounds of formulaI :
EMI23.1

I or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein E is absent or selected from the group consisting of (1) H, (2) substituted or unsubstitutedCl-C6-alkyl, (3) substituted or unsubstitutedC2-C6-alkenyl, (4) substituted or unsubstitutedC2-C6-alkynyl, (5) substituted or unsubstituted aryl, (6) substituted or unsubstituted heterocyclyl, and (7) substituted or unsubstituted heteroaryl ; L is absent or selected from the group consisting of (1) substituted or unsubstitutedCl-C6-alkyl, (2) -(NH)0-1-(CH2)j-NR3L-(CH2)k-, (3) -(NH)0-1-C(R1L,R2L)-NR3L-C(R1L,R2L)-, (4) -C(R1L,R2L)-O-C(R1L,R2L)-,(5) (CH2)j-NR3L-C(R1L,R2L)-CONH-(CH2)k-, (6)-CO-C (RlL, R2L) NHCO-,

(7) -CONH-, (8) -NHCO-, whereinRlL, R2L, andR3L are independently selected from the group consisting of (a) H,(b) substituted or unsubstitutedCl-C6-alkyl,(c)Cl-C6-alkyl substituted with aryl, (d)Cl-C6-alkyl substituted with heterocyclyl, and(e) Cl-C6-alkyl substituted with heteroaryl,or ruz and R3L, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S, j is an integer of 0-4; k is an integer of0-4 ;D is absent or selected from the group consisting of (1) substituted or unsubstitutedC3-C8-cycloalkyl, (2) substituted or unsubstituted aryl, (3) substituted or unsubstituted heterocyclyl, and (4) substitutedor. unsubstituted heteroaryl;G is absent or selected from the group consisting of (1)- (CH2) i-O-(CH2)i-, (2) -(CH2)i-S-(CH2)i-, (3) -(CH2)i-NRg-(CH2)i-, (4) -C (=O)-, (5) -NHC (=O)-, (6) -C (=O)NH-, (7)- (CH2) iNHCH2C (=O) NH-, (8) -C#C-, (9) -C#C-C#C-, and (10)-C=C-; wherein
Rg is H or substituted or unsubstitutedCI-C6-alkyl ; i is an interger of 0-4;

Y is selected from the group consisting of (1) substituted or unsubstitutedC3-Cg-cycloalkyl, (2) substituted or unsubstituted aryl, (3) substituted or unsubstituted heterocyclyl, and (4) substituted or unsubstituted heteroaryl; X is selected from the group consisting of (1)- (C=O)-, (2) -C1-C6-alkyl-(C=O)-, (3)-C2-C6-alkenyl- (C=O)-,(4)-C2-C6-alkynyl- (C=O)-, and (5) -CH2-; or when B is absent, X andA, together with the atoms to which they are attached can form a heterocyclic ring, having from 5 to8 ring atoms, wherein 1-2 ring atoms of the heterocyclic. ring system are selected from N,O and S; B is a absent or
EMI25.1
whereinRlb andR2b, are independently selected from the group consisting of(a) H, (b) substituted or unsubstitutedCl-C6-alkyl, (c) substituted or unsubstitutedC2-C6-alkenyl, (d) substituted or unsubstitutedC2-C6-alkynyl, (e) substituted or unsubstituted aryl,(f) substituted or unsubstituted heterocyclyl, (g) substituted or unsubstituted heteroaryl, (h) Cl-C6-alkyl substituted with aryl, (i) Cl-C6-alkyl substituted with heterocyclyl, and (j) C1-C6-alkyl substituted with heteroaryl, orRlb and together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S; q is an integer of 0-4;

R3 is H or substituted or unsubstituted C1-C6-alkyl, or R3 and A, together with the atoms to which they are attached can form a substituted or unsubstituted3-10 membered cycloalkyl or a heterocyclic ring system, wherein the heterocyclic ring system may have from 3 to 10 ring atoms, with 1 to 2 rings being in the ring system and contain from 1-4 heteroatoms selected from N,O and S; R4 is H or substituted or unsubstitutedCl-C6-alkyl, or R4 and A, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S; n is an integer of 0-2; A is selected from the group consisting of (1) H, (2) -dCH2) rC (R1a,R2a)(CH2)sOR3a, (3) (CH2) rC(RIaR2a) N(R4aWa), (4)- (CH2) rC (R1a, R2a) N (R4a) COR3a, (5) -(CH2)rC(R1a,R2a)NHCON(R4a,R5a),(6)- (CH2),. C (Rla, R2a) NHC (=NH) N(R4a,R5a), (7) -CH(R1a,R2a),

or R4a and R5a together with the N atom to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N, O and S; r is an integer of 0-4; s is an integer of 0-4; Q is absent or selected from the group consisting of (1) -C(=O) N (R1,R2),(2)-NHC (=O) N(RI,R2), (3) -N (OH) C (=O) N (Rl,R2), (4) -CH (OH) C (=O) N(Ri,R2), (5) -CH [N(R2q, R3q)]C(=O) N (R1, R2), (6) -CHR1qC (=O) N(Ri, R2), (7) -CO2H, (8) -C(=O)NHSO2R4q, (9)-S02NH2,(10)-N (OH) C(=O)R, (11) -N(OH)SO2R4q, (12) -NHSO2R4q, (13)-SH, (14) -CH (SH)(CH2) 0-1C (=O) N (RI,R2), (15) -CH (SH)(CH2) 0-1CO2H,(16)-CH (OH)(CH2) 0-1CO2H, (17) -CH (SH)CH2CO2Rlq, (18) -CH (OH)(CH2) SO2NH2, (19) -CH(CH2SH)NHCOR1q,(20)-CH(CH2SH) NHSO2R4q, (21) -CH(CH2SR5q)CO2H, (22) -CH (CH2SH) NHSO2NH2, (23) -CH (CH2OH) C02H,(24)-CH (CH20H)NHS02NH2, (25) -C (=O)CH2CO2H, (26) -C (=O)(CH2) 0-1CONH2, (27)-OSO2NHRsq,

EMI28.1
Rl is selected from the group consisting of (1)-H, (2) -OH, (3)-OCl 6-alkyl,(4)-N (R2q, R39), and (5) substituted or unsubstitutedCl 6-alkyl ; R2 is selected from the group consisting of (1) H, (2) substituted or unsubstitutedCl-C6-alkyl, (3) substituted or unsubstituted C2-C6-alkenyl, (4) substituted or unsubstitutedC2-C6-alkenyl, (5) substituted or unsubstituted aryl, (6) substituted or unsubstituted heterocyclyl, (7) substituted or unsubstituted heteroaryl, (8) Cl-C6-alkyl substituted with aryl, (9)Cl-C6-alkyl substituted with heterocyclyl, and (10)Cl-C6-alkyl substituted with heteroaryl, or R1 and R2, together with the N atom to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 10 ring atoms, wherein 1-4 ring atoms of the heterocyclic ring system are selected from N,0 and S,
R1q, R2q, R3q, R4q, and R5q are selected from H or Cl-C6 alkyl, wherein B is absent, or E, L, G, and B are absent, or E, L, and G are absent, or E, L, and B are absent, or E, L, D, G, and B are absent.

In another embodiment, the present invention provides compounds of formula I:

EMI29.1
or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein E is absent or selected from the group consisting of (1)H, (2) substituted or unsubstitutedCl-C6-alkyl, (3) substituted or unsubstituted aryl, (4) substituted or unsubstituted heterocyclyl, and (5) substituted or unsubstituted heteroaryl ; L is absent or selected from the group consisting of (1) -(CH2)J NR3L (CH2)k-, (2) -C(R1L,R2L)j-NR3L-C(R1L,R2L)k-, (3) -C(R1L,R2L)j-O-C(R1L,R2L)k-, (4) -(CH2)j-NR3L-C(R1L,R2L)k-CONH-(CH2)k-, (5) -CO-C(R1L,R2L)-NHCO-, (6) -CONH-, and (7)-NHCO-, whereinRlL,R2L, R3L are independently selected from the group consisting of (a) H, (b) substituted or unsubstitutedCl-C6-alkyl,(c)Cl-C6-alkyl substituted with aryl, (d) Cl-C6-alkyl substituted with heterocyclyl, (e)Cl-C6-alkyl substituted with heteroaryl, orRIL and R3L, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 5 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S; j is an integer of 0-4; k is an integer of0-4 ; D is absent or selected from the group consisting of

(1) substituted or unsubstitutedC3-C8-cycloalkyl, (2) substituted or unsubstituted aryl, (3) substituted or unsubstituted heterocyclyl, (4) substituted or unsubstituted heteroaryl, and G is absent or selected from the group consisting of (1) -C(=O)-, (2) -NHC(=O)-,(4)- (CH2)iNHCH2C(=O)NH-,(5) -C#C-, and (6) wherein i is aninterger of 0-4 ; Y is selected from the group consisting of (1) substituted or unsubstitutedC3-C8-cycloalkyl, (2) substituted or unsubstituted aryl,(3) substituted or unsubstituted heterocyclyl, and (4) substituted or unsubstituted heteroaryl; X is selected from the group consisting of (1) -(C=O)-, (2) -C1-C6-alkyl-(C=Oy, (3)-C2-C6-alkenyl- (C=O)-, (4) -C2-C6-alkynyl-(C=O)-, and (5) -CH2-; or when B is absent, X and A, together with the atoms to which they are attached can form a heterocyclic ring, having from 5 to8 ring atoms, wherein1-2 ring atoms of the heterocyclic ring system are selected from N,O and S; B is absent or
EMI30.1
whereinRlb and R2b are independently selected from the group consisting of (a) H (b) substituted or unsubstituted Cl-C6-alkyl,

(c) substituted or unsubstitutedC2-C6-alkenyl, (d) substituted or unsubstitutedC2-C6-alkenyl, (e) substituted or unsubstituted aryl, (f) substituted or unsubstituted heterocyclyl, (g) substituted or unsubstituted heteroaryl, (h)Cl-C6-alkyl substituted with aryl, (i)Cl-C6-alkyl substituted with heterocyclyl, and (j)Cl-C6-alkyl substituted with heteroaryl, or Rlb andR2b, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 5 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S; q is an integer of 0-2; R3 is H or substituted or unsubstituted Cl-C6-alkyl, or R3 and A, together with the atoms to which they are attached can form a substituted or unsubstituted 3-10 membered cycloalkyl or a heterocyclic ring system, wherein the heterocyclic ring system may have from 3 to 10 ring atoms, with 1 to 2 rings being in the ring system and contain from 1-4 heteroatoms selected from N,O and S; R4 is H or substituted or unsubstituted Cl-C6-alkyl, or R4 andA, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 5 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S; A is selected from the group consisting of (1) H, (2) -(CH2)rC(R1a,R2a)(CH2)sOR3a, (3) -(CH2)rC(R1a,R2a)N(R4a,5Ra), (4)-(CH2)@ C(R1a,R2a)N(R4a)COR3a, (5) - (CH2) C (Rla,R2a) NHCON (R4a,Ra),(6)-(CH2)@ rC(Rla, R2a)NHC(=NH) N(R4aRSa) (7) -CH(R1a,R2a), (8) -C#CH,(9)-(CH2)rC (Rla, R2a) CN, and(10)- (CH2) rC (R1a,R2a)CO2R3A,

wherein Rla,Rota, R3a, R4a, and R5a, are independently selected from the group consisting of (a) H, (b) substituted or unsubstituted C1-C6-alkyl,(c)

orRland R2, together with the N atom to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 10 ring atoms, wherein 1-4 ring atoms of the heterocyclic ring system are selected from N,O and S,Rlq, R2q, andR3q are selected from H orCI-C6 alkyl, wherein B is absent, or E, L, G, and B are absent, or E, L, and G are absent, or E, L, and B are absent, or E, L,D, G, and B are absent.

In another embodiment, the present invention provides compounds of formulaII :
EMI33.1
or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein D-G-Y taken together, is selected from the group consisting of
EMI33.2


EMI34.1

Wherein
R is selected from the group consistingof-CH3,-C2Hs,-CH20H,-0H,-OCH3,-OC2Hs,- OCF3,-CN,-N02,-C02H,-C02CH3,-CONH2,-NH2,-F,-Cl,-Br,-CF3,-N (CH3) 2,-NHS02CH3,and-NHCOCH3 ;
X is selected from the group consisting of(1)- (C=O)-, (2) -C1-C6-alkyl-(C=O)-, and (3) -C2-C6-alkenyl-(C=O)-.

In another embodiment, the present invention provides compounds of formulam:

EMI35.1
or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein D-G-Y taken together, is selected from the group consisting of
EMI35.2


EMI36.1

WhereinR is selected from the group consistingof-CH3,-C2Hs,-CH20H,-OH,-OCH3,-OC2H5,-OCF3,-CN,-NO2,-CO2H,-CO2CH3,-CONH2,-NH2,-F,-Cl,-Br,-CF3,-N (CH3) 2,-NHS02CH3,and-NHCOCH3 ; X is selected from the groups consisting of(1)- {C=O)-, (2) -C1-C6-alkyl-(C=O)-, and (3) -C2-C6-alkenyl-(C=O)-.

In another embodiment, the present invention provides compounds of formula IV:
EMI36.2
or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, whereinD-G-Y taken together, is selected from the group consisting of

EMI37.1


EMI38.1

Wherein
R is selected from the group consisting of-CH3, -C2H5, -CH2OH, -OH, -OCH3, -OC2H5, - OCF3, -CN, -NO2, -CO2H, -CO2CH3, -CONH2, -NH2, -F, -Cl, -Br, -CF3, -N(CH3)2, -NHSO2CH3,and-NHCOCH3 ; X is selected from the groups consisting of (1) -(C=O)-,(2)-Cl-C6-alkyl- (C=O)-, and (3)-C2-C6-alkenyl- (C=O)-.

In another embodiment, the present invention provides compounds of formula V:
EMI38.2
. V or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, whereinD-G-Y taken together, is selected from the group consisting of
EMI38.3


EMI39.1


Wherein
R is selected from the group consistingof-CH3,-C2Hs,-CH20H,-OH,-OCH3,-OC2Hs,-OCF3,-CN,-NO2,-C02H,-C02CH3,-CONH2,-NHz,-F,-Cl,-Br,-CF3,-N (CH3) 2,-NHSO2CH3,and-NHCOCH3 ; X is selected from the groups consisting of (1) -(C=O)-,(2)-Cl-C6-alkyl-(C=O)-, and (3)-C2-C6-alkenyl- (C=O)-.

In another embodiment, the present invention provides compounds of formula VI:
EMI40.1

VI or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein E is absent or selected from the group consisting of (1) H, (2) substituted or unsubstituted C1-C6-alkyl, (3) substituted or unsubstituted aryl, (4) substituted or unsubstituted heterocyclyl, and (5) substituted or unsubstituted heteroaryl, orE and R3L, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 10 ring atoms, wherein 1-4 ring atoms of the heterocyclic ring system are selected from N,O and S, R1L, R3L are independently selected from the group consisting of (1) H, (2) substituted or unsubstituted C1-C6-alkyl, (3) Cl-C6-alkyl substituted with aryl, (4)Cl-C6-alkyl substituted with heterocyclyl, and

(5)Cl-C6-alkyl substituted with heteroaryl, orRI L and R3L, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S.

In another embodiment, the present invention provides compounds of formula VII :
EMI41.1
Vil or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein
E is absent or selected from the group consisting of (1)H,.

(2) substituted or unsubstitutedCl-C6-alkyl, (3) substituted or unsubstituted aryl, (4) substituted or unsubstituted heterocyclyl, and (5) substituted or unsubstituted heteroaryl, or E andR3L, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 10 ring atoms, wherein 1-4 ring atoms of the heterocyclic ring system are selected from N,O and S;RlL, R3L are independently selected from the group consisting of (1) H, (2) substituted or unsubstituted C1-C6-alkyl, (3)Cl-C6-alkyl substituted with aryl, (4) C1-C6-alkyl substituted with heterocyclyl, and (5) C1-C6-alkyl substituted with heteroaryl, orR, I together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S.

In another embodiment, the present invention provides compounds of formulaVIII :

EMI42.1
or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein E is absent or selected from the group consisting of (1) H, (2) substituted or unsubstitutedCl-C6-alkyl, (3) substituted or unsubstituted aryl, (4) substituted or unsubstituted heterocyclyl, and (5) substituted or unsubstituted heteroaryl,. or E andR3L, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 10 ring atoms, wherein 1-4 ring atoms of the heterocyclic ring system are selected from N,O and S;RlL, R3L are independently selected from the group consisting of (1) H, (2) substituted or unsubstitutedCl-C6-alkyl, (3)Cl-C6-alkyl substituted with aryl, (4) Cl-C6-alkyl substituted with heterocyclyl, and (5) Cl-C6-alkyl substituted with heteroaryl, orRIL and R3L, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S.

In another embodiment, the present invention provides compounds of formula IX :

EMI43.1
or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein E is absent or selected from the group consisting of (1) H, (2) substituted or unsubstitutedCl-C6-alkyl, (3) substituted or unsubstituted aryl,(4) substituted or unsubstituted heterocyclyl, and (5) substituted or unsubstituted heteroaryl, or E and R3L, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 10 ring atoms, wherein 1-4 ring atoms of the heterocyclic ring system are selected from N,O andS ; RIL, R3L are independently selected from the group consisting of (1) H, (2) substituted or unsubstituted


EMI44.1
or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein E is absent or selected from the group consisting of(1) H, (2) substituted or unsubstituted C1-C6-alkyl, (3) substituted or unsubstituted aryl, (4) substituted or unsubstituted heterocyclyl, and (5) substituted or unsubstituted heteroaryl, or E andR3L, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 10 ring atoms, wherein 1-4 ring atoms of the heterocyclic ring system are selected from N,O and S;Roll, R3L are independently selected from the group consisting of (1) H, (2) substituted or unsubstituted Ci-C6-alkyl, (3)Cl-C6-alkyl substituted with aryl,ss (4)Cl-C6-alkylsubstitutedwithheterocyclyl, and (5)Cl-C6-alkyl substituted with heteroaryl, orR1L and R3L, together with the atoms to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S.

In another embodiment, the present invention provides compounds of formula XI:
EMI44.2


or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein Y-X taken together, is selected from the group consisting of
EMI45.1
In another embodiment, the present invention provides compounds of formulaXII :
EMI45.2
XII or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, whereinRlb and R2b are independently selected from the group consisting of (1) H, (2) substituted or unsubstitutedCl-C6-alkyl, (3) substituted or unsubstitutedC2-C6-alkenyl, (4) substituted or unsubstitutedC2-C6-alkenyl, (5) substituted or unsubstituted aryl,

(6) substituted or unsubstituted heterocyclyl, (7) substituted or unsubstituted heteroaryl, (8) C1-C6alkyl substituted with aryl, (9)Cl-C6-alkyl substituted with heterocyclyl, and (10)Cl-C6-alkyl substituted with heteroaryl ; q is an integer of 0-2 ; In another embodiment, the present invention provides compounds of formulaXIII-
EMI46.1
xm or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, whereinR4 is selected from the group consisting of (1) H, (2) substituted or unsubstitutedCl-C6-alkyl, (3)Cl-C6-alkyl substituted with aryl, (4)Cl-C6-alkyl substituted with heterocyclyl, and(5)Cl-C6-alkyl substituted with heteroaryl; A is Hor-CH (CH3) OH- ; R1 is H or substituted or unsubstitutedCl 6-alkyl ; R2 is selected from the group consisting of (1) H, (2) substituted or unsubstitutedCl-C6-alkyl, (3) substituted or unsubstituted aryl, (4) substituted or unsubstituted heterocyclyl, (5) substituted or unsubstituted heteroaryl, (6) Cl-C6-alkyl substituted with aryl, (7) C1-C6-alkyl substituted with heterocyclyl, (8)Cl-C6-alkyl substituted with heteroaryl,

or R1 and R2 together with the N atom to which they are attached can form a substituted or unsubstituted heterocyclic ring, having from 3 to 10 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N,O and S.

In another embodiment, the present invention provides compounds of formulaXIV :
EMI47.1
or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein D-G-Y taken together is selected from the group consisting of
EMI47.2
R-'ND/
9 R/\ I \/R N/\ I R,/\ \ % R R R R N R-C w R X R= R R R
Nv R = t== g > > - R-- v or
EMI47.3


EMI48.1

Wherein
R is selected from the group consisting of-CH3, -C2H5, -CH2OH, -OH, -OCH3, -OC2H5, -OCF3,-CN,-NO2,-CO2H,-CO2CH3,-CONH2,-NH2,-F,-Cl,-Br,-CF3,-N (CH3) 2,-NHS02CH3,and-NHCOCH3 ; R4 is selected from the group consisting of (1)H, (2) substituted or unsubstituted C1-C6-alkyl, (3)CI-C6-alkyl substituted with aryl, (4)Cl-C6-alkyl substituted with heterocyclyl, and (5)CI-C6-alkyl substituted with heteroaryl.

In another embodiment, the present invention provides compounds of formula XV:

EMI49.1
or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein D-G-Y taken together, is selected from the group consisting of
EMI49.2


EMI50.1

Wherein
R is selected from the group consistingof-CH3,-C2Hs,-CH2OH,-0H,-OCH3,-OC2Hs,-
OCF3, -CN, -NO2, -CO2H, -CO2CH3, -CONH2, -NH2, -F, -Cl, -Br, -CF3, -N (CH3) 2,-NHSO2CH3, and -NHCOCH3; In another embodiment, the present invention provides compounds of formula XVI :
EMI50.2
XVI or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein D-G-Y taken together, is selected from the group consisting of
EMI50.3


EMI51.1


EMI52.1

Wherein
R is selected from the group consistingof-CH3,-c2Hs-CH2OH,-OH,-OCH3,-OC2Hs,-OCF3,-CN,-NO2,-CO2H,-CO2CH3,-CONH2,-NH2,-F,-Cl,-Br,-CF3,-N (CH3)2,- NHSO2CH3,and-NHCOCH3 ; R4 is selected from the group consisting of (1) H, (2) substituted or unsubstituted C1-C6-alkyl, (3) C1-C6-alkyl substituted with aryl, -alkyl substituted with heterocyclyl, and (5)Cl-C6-alkyl substituted with heteroaryl ; In another embodiment, the present invention provides compounds of formula XVII :
EMI52.2

XVII or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein D-G-Y taken together, is selected from the group consisting of
EMI52.3


EMI53.1


Wherein
R is selected from the group consistingof-CH3,-C2HS,-CH2OH,-OH,-OCH3,-OC2H5,- OCF3,-CN,-N02,-C02H,-C02CH3,-CONH2,-NH2,-F,-Cl,-Br,-CF3,-N (CH3) 2,NHSO2CH3,and-NHCOCH3 ;
In one aspect, the invention provides a method of inhibiting a deacetylase enzyme in a gram- negative bacteria, thereby affecting bacterial growth, comprising administering to a patient in need of such inhibition a compound of formula I.

In another aspect, the invention provides a method of inhibiting LpxC, thereby modulating the virulence of a bacterial infection, comprising administering to a patient in need of such inhibition a compound of formulaI.

In some embodiments of the method of inhibiting LpxC using a compound of formula I, the
ICso value of the compound is less than or equal to 10 uM with respect to LpxC. In other such embodiments, theICso value is less than or equal to1, uM, is less than or equal to 0.1 FM, is less than or equal to 0.050uM, is less than or equal to 0.030jim, is less than or equal to 0. 025uM, or is less than or equal to 0. 010pM.

In one aspect of the invention, methods for treating a subject comprising administering to the subject an antibacterially effective amount of a compound of formula I, together with a pharmaceutically acceptable carrier is provided. In a preferred embodiment of the method of treatment, the subject is a mammal and some embodiments, a human.

In another aspect, the invention provides a method of administering an inhibitory amount of a compound of formula I to fermentative or non-fermentative gram-negative bacteria. In a preferred embodiment of the method of administering an inhibitory amount of a compound of formula I to fermentative or non-fermentative gram-negative bacteria, the gram-negative bacteria are selected from the group consisting of Pseudomonas aeruginosa, Stenotrophomonas maltophila, Burkholderia cepacia,
Alcaligenes xylosoxidans, Acinetobacter, Enterobacteriaceae, Haemophilus, Neisseria species.

In another embodiment, the invention provides a method of administering an inhibitory amount ofa compound of formula I to gram-negative bacteria, such as Enterobacteriaceae that is selected from the group consisting of organisms such as Serratia, Proteus, Klebsiella, Enterobacter, Citrobacter,
Salmonella, Providencia, Morganella, Cedecea, and Edwardsiella species and Escherichia coli.

Another embodiment of the invention provides a pharmaceutical composition comprising an effective amount of a compound of Formula I with a pharmaceutically acceptable carrier thereof.

Pharmaceutical formulations according to the present invention are provided which include any of the compounds described above in combination with a pharmaceutically acceptable carrier.

Another embodiment of the invention provides a method of co-administering the compound of formula I with other therapeutic agents that are selected for their particular usefulness against the condition that is being treated.

For example, the compound of formula I is useful in combination with other anti-bacterial agents. The compound of formula I augments the sensitivity of gram-negative bacteria to existing classes of antibacterials. Combinations of the presently disclosed compounds with other anti-bacterial agents are within the scope of the invention. Such anti-bacterial agents include, but are not limited to, erythromycin, rifampicin, Nalidixic acid, carbenicillin, bacitracin,cycloserine, fosfomycin, andvancomycin.

A further aspect of the invention is the use of LpxC inhibitors for the treatment of an infection, particularly a bacterial infection. A bacterial infection treated with the compounds of the invention can be a primary infection or a co-infection caused by a species of bacteria and one or more additional infectious agents selected from the group consisting of bacteria, virus, parasite and fungus.

The term"treating", as used herein, refers to reversing, alleviating, inhibiting the progress of, or preventing the disorder or condition to which such term applies, or one or more symptoms of such disorder or condition. The term"treatment", as used herein, refers to the act of treating, as"treating"is defined immediately above.

The compounds of the invention can be used for treating conditions caused by the bacterial production of endotoxin and, in particular, by gram-negative bacteria and bacteria that use LpxC in the biosynthesis of lipopolysaccharide (LPS) or endotoxin.

The compounds of the invention also are useful in the conditions that are caused or exacerbated by the bacterial production of lipid A and LPS or endotoxin, such as sepsis, septic shock, systemic inflammation, localized inflammation,chronic obstructive pulmonary disease (COPD) and acute

exacerbations of chronic bronchitis (AECB). For these conditions, treatment includes the administration of a compound of the invention, or a combination of compounds of the invention, optionally with a second agent wherein the second agent is a second antibacterial agent or a second non-antibacterial agent.

For sepsis, septic shock, systemic inflammation, localized inflammation, chronic obstructive pulmonary disease (COPD) and acute exacerbations of chronic bronchitis(AECB), preferred second non-antibacterial agents include antiendotoxins including endotoxin receptor-binding antibodies, endotoxin-binding antibodies,antiCD14-binding protein antibodiesantilipopolysaccharide-binding protein antibodies and tyrosine kinase inhibitors.

In treatment of serious or chronic respiratory tract infections, the compounds of the present invention may also be used with second non-antibacterial agents administered via inhalation.

Preferred non-antibacterial agents used in this treatment include anti-inflammatory steroids, non- steroidal anti-inflammatory agents, bronchiodilators, mucolytics, anti-asthma therapeutics and lung fluid surfactants. In particular, thenon-antibacterial agent may be selected from a group consisting of albuterol, salbuterol,budesonide, beclomethasone, dexamethasone, nedocromil, beclomethasone, fluticasone, flunisolide, triamcinolone, ibuprofin,rofecoxib, naproxen, celecoxib, nedocromil, ipratropium,metaproterenol, pirbuterol,salmeterol, bronchiodilators, mucolytics, calfactant, beractant, poractant alfa, surfaxin and pulmozyme (also calleddornase alfa).

The compounds of the invention can be used, alone or in combination with a second antibacterial agent for the treatment of a serious or chronic respiratory tract infection including serious lung and nosocomial infections such as those caused by Enterobacter aerogenes, Enterobacter cloacae,
Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Proteus mirabilis, Serratia marcescens,
Stenotrophomonasmaltophilia, Pseudomonas aeruginosa, Burkholderia cepacia, Acinetobactercalcoaceticus, Alcaligenes xylosoxidans, Flavobacteriummeningosepticum, Providencia stuartii and
Citrobacter freund, community lung infections such as those caused by Haemophilus Influenzae,
Legionella species, Moraxella catarrhalis, Branhamella catarrhalis, Enterobacter species, Acinetobacter species, Klebsiella species, and Proteus species, and infections caused by other bacterial species such as Neisseria species, Shigella species, Salmonella species, Helicobacterpylori, Vibrionaceae and

Bordetella species as well as the infections is caused by aBrucella species, Francisellatularensisand/or YersiniaPestis.

When used for treating Gram-negative bacteria, the compounds of the present invention can be used to sensitize gram-negative bacteria to the effects of a second agent.

When the compounds of the present invention are used in combination with a second antibacterial agent, non-limiting examples of antibacterial agents may be selected from the following groups: (1) Macrolides or ketolides such as erythromycin, azithromycin, clarithromycin and telithromycin; (2) Beta-lactams including penicillin, cephalosporin, and carbapenems such as carbapenem,imipenem, and meropenem; (3) Monobactams such as penicillin G, penicillin V, methicillin, oxacillin, cloxacillin,dicloxacillin,nafcillin, ampicillin, amoxicillin, carbenicillin, ticarcillin, mezlocillin, piperacillin, azlocillin, temocillin, cepalothin, cephapirin, cephradine, cephaloridine, cefazolin,cefamandole,cefuroxime, cephalexin, cefprozil, cefaclor, loracarbef, cefoxitin,cefmetazole, cefotaxime,ceftizoxime, ceftriaxone, cefoperazone, ceftazidime, cefixime, cefpodoxime,ceftibuten, cefdinir,cefpirome, cefepime, and astreonam; (4) Quinolones such as nalidixic acid, oxolinic acid,norfloxacin, pefloxacin, enoxacin, ofloxacin, levofloxacin, ciprofloxacin, temafloxacin, lomefloxacin, fleroxacin, grepafloxacin, sparfloxacin,trovafloxacin, clinafloxacin, gatifloxacin, moxifloxacin, sitafloxacin, ganefloxacin, gemifloxacin and pazufloxacin; (5) Antibacterial sulfonamides and antibacterial sulphanilamides, including para-aminobenzoic acid, sulfadiazine, sulfisoxazole, sulfamethoxazole andsulfathalidine ; (6)Aminoglycosides such as streptomycin, neomycin,kanamycin, paromycin, gentamicin, tobramycin, amikacin,netilmicin,spectinomycin, sisomicin, dibekalin and isepamicin; (7) Tetracyclines such as tetracycline, chlortetracycline, demeclocycline, minocycline,oxytetracycline,methacycline, doxycycline;

(8)Rifamycins such as rifampicin (also called rifampin), rifapentine, rifabutin,bezoxazinorifamycin andrifaximin ; (9)Lincosamides such as lincomycin and clindamycin; (10) Glycopeptides such as vancomycin and teicoplanin; (11) Streptogramins such as quinupristin and daflopristin; (12)Oxazolidinones such as linezolid; (13) Polymyxin, colistin andcolymycin ; (14)Trimethoprim and bacitracin.

The second antibacterial agent may be administered in combination with the compounds of the present inventions wherein the second antibacterial agent is administered prior to, simultaneously, or after the compound or compounds of the present invention. When simultaneous administration of a compound of the invention with a second agent is desired and the route of administration is the same, then a compound of the invention may be formulated with a second agent into the same dosage form.

An example of a dosage form containinga compound of the invention and a second agent is a tablet or a capsule.

When used for treating a serious or chronic respiratory tract infections, the compounds of the invention may be used alone or in combination with a second antibacterial agent administered via inhalation. In the case of inhalation, a preferred second antibacterial agent is selected from a group consistingof tobramycin, gentamicin, aztreonam, ciprofloxacin, polymyxin, colistin, colymycin, azithromycin andclarithromycin.

Pharmaceutical Compositions
Pharmaceutical compositions of the present invention comprise atherapeutically effective amount of a compound of the present invention formulated together with one or more pharmaceutically acceptable carriers. As used herein, the term"pharmaceutically acceptable carrier"

means a non-toxic, inert solid, semi-solid or liquid filler, diluent, encapsulating material or formulation auxiliary of any type. Some examples of materials that can serve as pharmaceutically acceptable carriers are sugars such as lactose, glucose and sucrose; starches such as corn starch and potato starch ; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate ; powdered tragacanth; malt; gelatin; talc; excipients such as cocoa butter and suppository waxes; oils such as peanut oil, cottonseed oil; safflower oil; sesame oil; olive oil; corn oil and soybean oil; glycols; such a propylene glycol; esters such as ethyl oleate and ethyl laurate; agar; buffering agents such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water ; isotonic saline; Ringer's solution; ethyl alcohol, and phosphate buffer solutions, as well as other non- toxic compatible lubricants such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, releasing agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the composition, according to the judgment of the formulator. The pharmaceutical compositions of this invention can be administered to humans and other animals orally, rectally, parenterally,intracisternally,intravaginally, intraperitoneally, topically (as by powders, ointments, or drops), bucally, or as an oral or nasal spray, or a liquid aerosol or dry powder formulation for inhalation.

Liquid dosage forms for oral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active compounds, the liquid dosage forms may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.

Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation may also be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3- butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, U. S. P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can

be employed including synthetic mono-ordiglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables.

The injectable formulations can be sterilized, for example, by filtration through a bacterial- retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions that can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.

In order to prolong the effect of a drug, it is often desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution that, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorptionof a parenterally administered drug form may be accomplished by dissolving or suspending the drug in an oil vehicle. Injectable depot forms are made by formingmicroencapsule matrices of the drug in biodegradable polymers such aspolylactide- polyglycolide. Depending upon the ratio of drug to polymer and the nature of the particular polymer employed, the rate of drug release can be controlled. Examples of other biodegradable polymers include poly (orthoesters) and poly (anhydrides). Depot injectable formulations may also be prepared by entrapping the drug in liposomes or microemulsions that are compatible with body tissues.

Compositions for rectal or vaginal administration are preferably suppositories that can be prepared by mixing the compounds of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.

Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active compound is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate ordicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicicacid ; b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia,

polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may also comprise buffering agents.

Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.

The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient (s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes.

Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.

The active compounds can also be in micro-encapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art. In such solid dosage forms the active compound may be admixed with at least one inert diluent such as sucrose, lactose or starch. Such dosage forms may also comprise, as is normal practice, additional substances other than inert diluents, e. g., tableting lubricants and othertableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may also comprise buffering agents. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient (s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes.

Dosage forms for topical ortransdermal administration of a compound of this invention include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches. The active component is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as may be required. Ophthalmic formulations, ear drops, and the like are also contemplated as being within the scope of this invention.

The ointments, pastes, creams and gels may contain, in addition to an active compound of this invention, excipients such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof.

Compositions of the invention may also be formulated for delivery as a liquid aerosol or inhalable dry powder. Liquid aerosol formulations may be nebulized predominantly into particle sizes that can be delivered to the terminal and respiratory bronchioles where bacteria reside in patients with bronchial infections, such as chronic bronchitis and pneumonia. Pathogenic bacteria are commonly present throughout airways down to bronchi, bronchioli and lung parenchema, particularly in terminal and respiratory bronchioles. During exacerbation of infection, bacteria can also be present in alveoli.

Liquid aerosol and inhalable dry powder formulations are preferably delivered throughout the endobronchial tree to the terminal bronchioles and eventually to the parenchymal tissue.

Aerosolized formulations of the invention may be delivered using an aerosol forming device, such as a jet, vibrating porous plate or ultrasonic nebulizer, preferably selected to allow the formation of a aerosol particles having with a mass medium average diameter predominantly between 1 to5 pm.

Further, the formulation preferably has balanced osmolarity ionic strength and chloride concentration, and the smallest aerosolizable volume able to deliver effective dose of the compounds of the invention to the site of the infection. Additionally, the aerosolized formulation preferably does not impair negatively the functionality of the airways and does not cause undesirable side effects.

Aerosolization devices suitable for administration of aerosol formulations of the invention include, for example, jet, vibrating porous plate, ultrasonic nebulizers and energized dry powder inhalers, that are able to nebulize the formulation of the invention into aerosol particle size predominantly in the size range from1-5 um. Predominantly in this application means that at least 70% but preferably more than 90% of all generated aerosol particles are 1 to 5 pm range. A jet nebulizer works by air pressure to break a liquid solution into aerosol droplets. Vibrating porous plate nebulizers work by using a sonic vacuum produced by a rapidly vibrating porous plate to extrude a solvent droplet through a porous plate. An ultrasonic nebulizer works by a piezoelectric crystal that shears a liquid into small aerosol droplets. A variety of suitable devices are available, including, for example, AeroNeb and AeroDose vibrating porous plate nebulizers (AeroGen,Inc., Sunnyvale, California), Sidestream7 nebulizers (Medic-Aid Ltd. , West Sussex, England), Pari LC7 and Pari LC Star7 jet nebulizers (Pari Respiratory Equipment,Inc., Richmond, Virginia), and Aerosonic (DeVilbiss

Medizinische Produkte (Deutschland) GmbH, Heiden, Germany) andUltraAire7 (OmronHealthcare,Inc., Vernon Hills, Illinois) ultrasonic nebulizers.

Compounds of the invention may also be formulated for use as topical powders and sprays that can contain, in addition to the compounds of this invention, excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates and polyamide powder, or mixtures of these substances.

Sprays can additionally contain customary propellants such as chlorofluorohydrocarbons.

Transdermal patches have the added advantage of providing controlled delivery of a compound to the body. Such dosage forms can be made by dissolving or dispensing the compound in the proper medium. Absorption enhancers can also be used to increase the flux of the compound across the skin.

The rate can be controlled by either providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.

According to the methods of treatment of the present invention, bacterial infections are treated or prevented in a patient such as a human or lower mammal by administering to the patient a therapeutically effective amount ofa compound of the invention, in such amounts and for such time as is necessary to achieve the desired result.By a"therapeutically effective amount"of a compound of the invention is meant a sufficient amount of the compound to treat bacterial infections, at a reasonablebenefit/risk ratio applicable to any medical treatment. It will be understood, however, that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular patient will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed ; and like factors well known in the medical arts.

The total daily dose of the compounds of this invention administered to a human or other mammal in single or in divided doses can be in amounts, for example, from 0.01 to 50 mg/kg body weight or more usually from 0.1 to 25 mg/kg body weight. Single dose compositions may contain such amounts or submultiples thereof to make up the daily dose. In general, treatment regimens according to the present invention comprise administration to a patient in need of such treatment from about 10 mg to about 2000 mg of the compound (s) of this invention per day in single or multiple doses.

Methods of formulation are well known in the art and are disclosed, for example, inRemington : The Science and Practice of Pharmacy, Mack Publishing Company, Easton, Pa.,19th
Edition(1995). Pharmaceutical compositions for use in the present invention can be in the form of sterile, non-pyrogenic liquid solutions or suspensions, coated capsules, suppositories, lyophilized powders, transdermal patches or other forms known in the art.

A"kit"as used in the instant application includes a container for containing the pharmaceutical compositions and may also include divided containers such as a divided bottle or a divided foil packet.

The container can be in any conventional shape or form as known in the art that is made of a pharmaceutically acceptable material, for example a paper or cardboard box, a glass or plastic bottle or jar, a resealable bag (for example, to hold a"refill"of tablets for placement into a different container), or a blister pack with individual doses for pressing out of the pack according to a therapeutic schedule.

The container employed can depend on the exact dosage form involved, for example a conventional cardboard box would not generally be used to hold a liquid suspension. It is feasible that more than one container can be used together in a single package to market a single dosage form. For example, tablets may be contained in a bottle that is in turn contained within a box.

An example of such a kit is a so-called blister pack. Blister packs are well known in the packaging industry and are being widely used for the packaging of pharmaceutical unit dosage forms (tablets, capsules, and the like). Blister packs generally consist of a sheet of relatively stiff material covered with a foil of a preferably transparent plastic material. During the packaging process, recesses are formed in the plastic foil. The recesses have the size and shape of individual tablets or capsules to be packed or may have the size and shape to accommodate multiple tabletsand/or capsules to be packed. Next, the tablets or capsules are placed in the recesses accordingly and the sheet of relatively stiff material is sealed against the plastic foil at the face of the foil that is opposite from the direction in which the recesses were formed. As a result, the tablets or capsules are individually sealed or collectively sealed, as desired, in the recesses between the plastic foil and the sheet. Preferably the strength of the sheet is such that the tablets or capsules can be removed from the blister pack by manually applying pressure on the recesses whereby an opening is formed in the sheet at the place of the recess. The tablet or capsule can then be removed via said opening.

It maybe desirable to provide a written memory aid, where the written memory aid is of the type containing information and/or instructions for the physician, pharmacist or other health care provider, or subject, e. g. , in the form of numbers next to the tablets or capsules whereby the numbers correspond with the days of the regimen that the tablets or capsules so specified should be ingested or

a card that contains the same type of information. Another example of such a memory aid is a calendar printed on the card e. g. , as follows"First Week, Monday, Tuesday,"... etc..."Second Week, Monday,Tuesday,..."etc. Other variations of memory aids will be readily apparent. A"dailydose"can be a single tablet or capsule or several tablets or capsules to be taken on a given day. When the kit contains separate compositions, a daily dose of one or more compositions of the kit can consist of one tablet or capsule while a daily dose of another one or more compositions of the kit can consist of several tablets or capsules.

Another specific embodiment of a kit is a dispenser designed to dispense the daily doses one at a time in the order of their intended use. Preferably, the dispenser is equipped with a memory-aid, so as to further facilitate compliance with the regimen. An example of such a memory-aid is a mechanical counter, that indicates the number of daily doses that has been dispensed. Another example of such a memory-aid is a battery-powered micro-chip memory coupled with a liquid crystal readout, or audible reminder signal that, for example, reads out the date that the last daily dose has been takenand/or reminds one when the next dose is to be taken.

The kits of the present invention may also include, in addition to LpxC inhibitors, one or more additional pharmaceutically active compounds. Preferably, the additional compound is another LpxC inhibitor or another compound useful to bacterial infections. The additional compounds may be administered in the same dosage form as the LpxC inhibitor or in different dosage forms. Likewise, the additional compounds can be administered at the same time as the LpxC inhibitor or at different times.

Compositions of the present compounds may also be used in combination with other known antibacterial agents of similar spectrum to (1) synergistically enhance treatment of severe Gram- negative infections covered by the spectrum of this compound or (2) add coverage in severe infections in which multiple organisms are suspected in which another agent of a different spectrum may be required in addition to this compound. Potential agents include members of the aminoglycosides, penicillins, cephalosporins, fluoroquinolones, macrolides, glycopeptides, lipopeptides andoxazolidinones. The treatment can involve administering a composition having both active agents or administration of the inventive compounds followed by or preceded by administration of an additional active antibacterial agent.

Characterization and Purification Methods
Referring to the examples that follow, compounds of the present invention were characterized by high performance liquid chromatography (HPLC) using a Waters Millenium chromatography

system with a 2690 Separation Module(Milford, Massachusetts). The analytical columns were AlltimaC-18 reversed phase, 4.6 x 250 mm from Alltech (Deerfield, Illinois). A gradient elution was used, typically starting with 5% acetonitrile/95% water and progressingto 100% acetonitrile over a period of 40 minutes. All solvents contained 0.1% trifluoroacetic acid (TFA). Compounds were detected by ultraviolet light (UV) absorption at either 220 or 254nm. HPLC solvents were from Burdick and Jackson (Muskegan, Michigan), or Fisher Scientific (Pittsburg, Pennsylvania). In some instances, purity was assessed by thin layer chromatography (TLC) using glass or plastic backed silica gel plates, suchas, for example, Baker-Flex Silica Gel 1 B2-F flexible sheets. TLC results were readily detected visually under ultraviolet light, or by employing well known iodine vapor and other various staining techniques.

Mass spectrometric analysis was performed on one of two LCMS instruments: a Waters System (Alliance HT HPLC and a Micromass ZQ mass spectrometer; Column: EclipseXDB-C18, 2.1 x 50 mm ; solvent system: 5-95% (or 35-95%, or 65-95% or 95-95%) acetonitrile in water with 0.05% TFA; flow rate 0.8 mL/min; molecular weight range 500-1500; cone Voltage 20 V; column temperature40 C) or a Hewlett Packard System (Series 1100 HPLC ; Column: EclipseXDB-C18, 2.1 x 50 mm; solvent system: 1-95% acetonitrile in water with 0.05% TFA ; flow rate 0.4mL/min ; molecular weight range 150-850; cone Voltage 50 V; column temperature30 C). All masses are reported as those of the protonated parent ions.

GCMS analysis was performed on a Hewlet Packard instrument (HP6890 Series gas chromatograph with a Mass Selective Detector 5973; injector volume : 1liL ; initial column temperature:50 C ; final column temperature: 250C ; ramp time: 20 minutes ; gas flow rate: 1mL/min ; column: 5% phenyl methyl siloxane, Model#HP190915-443, dimensions: 30.0 m x 25 m x 0.25 m).

Nuclear magnetic resonance (NMR) analysis was performed with a Varian 300 Mhz NMR(Palo Alto, California). The spectral reference was either TMS or the known chemical shift of the solvent. Some compound samples were run at elevated temperatures (e. g.75 C) to promote increased sample solubility.

The purity of some of the invention compounds was assessed by elemental analysis (Desert Analytics, Tuscon, Arizona) Tuscon, Arizona)
Melting points were determined on a Laboratory Devices Mel-Temp apparatus (Holliston, Massachusetts).

Preparative separations were carried out using a Flash 40 chromatography system and KP-Sil,
60A(Biotage, Charlottesville, Virginia), or by flash column chromatography using silica gel (230-400 mesh) packing material, or by HPLC using a C-18 reversed phase column. Typical solvents employed for the Flash 40 Biotage system and flash column chromatography were dichloromethane, methanol, ethyl acetate, hexane, acetone, aqueous hydroxyamine and triethyl amine. Typical solvents employed for the reverse phase HPLC were varying concentrations of acetonitrile and water with 0.1% trifluoroacetic acid.

Compounds of the present invention can be readily synthesized using the methods described herein, or other methods, that are well known in the art. For example, the synthesis of hxdroxamic acids or similar scaffolds having a wide variety ofsubstituents are comprehensively reviewed in Kline
T, Andersen NH, HarwoodEA, Bowman J, Malanda A, Endsley S, Erwin AL, Doyle M, Fong S,
Harris AL, Mendelsohn B, Mdluli K, Raetz CR, Stover CK, Witte PR, Yabannavar A, ZhuS.,"Potent, novel in vitro inhibitors of the Pseudomonas aeruginosa deacetylase LpxC,"JMed Chem 2002 Jul 4; 45 (14): 3112-29; Patchett, A. A. , Nargund, R., Chen, M. -H., Nishi, H. R. , U. S. Patent 5,925, 659,
1999; Pirrung, M. C. , Chau, J. H. ,"A Convenient Procedure for the Preparation of Amino AcidHydroxamates fromEsters,"J Org. Chem. 1995, 60,8084-8085 ; Nhu, K. , Patel, D. V. ,"A New and
Efficient Solid Phase Synthesisof Hydroxamic Acids,"J. Org Chem. 1997,62, 7088-7089; Patel, D.,
Nhu, K. ,"Methods for Solid-phase Synthesis of Hydroxylamine Compounds and Derivatives, and
Combinatorial Libraries Thereof,"PCT WO98/18754, 1998, Mellor, S. L.,McGuire, C. , Chan, W. C.,"N-Fmoc-aminoxy-2-chlortrityl Polystyrene Resin: A Facile Solid-phase Metliodology for the
Synthesisof Hydroxamic Acids,"Tetrahedron Lett., 1997,38, 3311-3314; Khan, S.I., Grinstaff, M.

W.,"A Facile and Convenient Solid-phase Procedure for Synthesizing Nucleoside HydroxamicAcids,"Terahedron. Lett., 1998,39,8031-8034 ; Zhang, Y. , Li, D.,Houtman, J. C. , Witiak, D. T.,
Seltzer,J.,. Bertics, P. J. , Lauhon, C. T.,"Design,Combinatorial Chemical Synthesis, and in vitro
Characterization of Novel Urea Based GelatinaseInhibitors,"Bioorg. Med. Chem. Lett., 1999,9,2823-2826 ; Ito, Y. , Inubushi, Y. , Zenbayashi, M.,Tomita, S. , Saegusa, T.,"Synthetic Reactions by
Complex Catalysts.XXXI, A Novel and Versatile Methodof Heterocycle Synthesis,"J Am Chem.

Soc., 1973, 95,4447-4448 ; Ito, Y. , Ito, I., Hirao, T. , Saegus, T. ,"Synthetic Reactions by Complex
Catalysts XXXV,"Syn. Comnaun. 1974,4, 97-103; Witte, H. , Seliger, W.,"Cyclische Imidsaurester aus Nitrilen und Aminoalkoholen,"Liebigs Ann. Chem, 1974,996-1009 ; Pattenden, G. , Thom. S. M., "Naturally Occurring Linear Fused Thiazoline-Thiazole Containing Metabolites : Total Synthesis of (-) Didehydromirabazole A, a Cytotoxic Alkaloid from Blue-Green Algae,"J. Chem. Soc. Perkin Trans 1,




1993,1629-1636 ; Boyce, R. J., Mulqueen, G. C., Pattenden, G. , "Total Synthesisof Thiangazole, ANovel Naturally Occurring HIV-1 Inhibitor from Polyangium sp.."Tetrahedron, 1995, 51,7321-7330 ;
Galeotti, N. , Plagnes, E. , Jouin, P.,"Synthesis of Peptidyl Aldehydes fromThiazolines,"lsetraAledron.

Lett. 1997,38, 2459-2462; Charette, A. B. , Chua, P. ,"Mild Method for the Synthesis of Thiazolines from Secondary and TertiaryAmides,"J.Org. Chem., 1998,63, 908-909; Bergeron, R. J. , Wiegand,
J. , McManis, J. S. , McCosar, B. H. , Weimar, W. R.,Brittenham, G. M., Smith, R. E.,"Effects of C-4
Stereochemistry and C-4'Hydroxylation on the Iron Clearing Efficiency and Toxicity ofDesferrithiocin Analogues,"J. Med. Chem. 1999,42, 2432-2440; Raman, P., Razavik H., Kelly, J. W., "Titanium (IV)-mediated Tandem Deprotection-cyclodehydration of Protected Cysteine N-Amides:



The foregoing may be better understood by reference to the following examples, that are presented for illustration and not to limit the scope of the inventive concepts.

EXAMPLES
The following are abbreviations used in the examples:AcOH : Acetic acid aq: Aqueous
ATP: Adenosine triphosphate
Boc:tert-butoxycarbonyl
Boc-Thr (OBn)-OH3- (R)-Benzyloxy-2- (S)-tert-butoxycarbonylamino-butyric acid.

DAP or Dap:Diaminopropionate
DCM:4- (Dicyanomethylene)-2-methyl-6- (4-dimethylaminostyryl)-
4H-pyran
DEAD: Diethyl azodicarboxylate
DIEA:DiisopropylethylamineDME : 1,2-dimethoxyethane
DMF :N, N-Dimethylformamide
DMSO: Dimethyl sulfoxide
DPPA :Diphenyl phosphoryl azide
Et3N: Triethylamine
EDC: N- (3-Dimethylaminopropyl)-N'-ethylcarbodiimide
EDCI:1- (3-dimethylaminopropyl) 3-ethylcarbodiimide
EtOAc: Ethyl acetateEtOH : Ethanol
Fmoc: 9-fluorenylmethoxycarbonylGly-OH : glycine

HATU: 0- (7-azabenzotriaazol-1-yl)-N, N,N'N'=tetramethyluronium hexafluorophophate
HBTU: 2-(lH-benzotriazol-l-yl)-1, 1, 3,3-tetramethyluronium hexafluorophosphate Hex: hexane HOBt : butyl alcohol HOBT :1-Hydroxybenzotriazole HPLC: High Pressure Liquid Chromatography ICso value: The concentration of an inhibitor that causes a 50 % reduction in a measured activity.iPrOH : Isopropanol LC/MS: Liquid Chromatography/Mass Spectrometry LRMS: Low Resolution Mass Spectrometry MeOH : Methanol NaOMe: sodium methoxidenm : Nanometer NMP N-Methylpyrrolidone PPh3: triphenyl phosphineRP-HPLC: Reversed-phase high-pressure liquid chromatographyRT : Room temperature sat: Saturated TEA: Triethylamine TFA:Trifluoroacetic acid THF : Tetrahydrofuran Thr: Threonine TLC: Thin Layer Chromatography

Trt-Br: Tert-butyl bromide
Nomenclature for the Example compounds was provided using ACD Name version 5.07 software (November 14,2001) available from Advanced Chemistry Development, Inc. Some of the compounds and starting materials were named using standard IUPAC nomenclature.


*Synthesis of N-Aroyl Threonine Analogues and Formation of Hydroxamate Example 1: Synthesisof 3-bromo-4-fluoro-N-{(lS, 2R)-2-hydroxy-1-[(hydroxyamino) carbonyl] propyl} benzamide (3).
EMI71.1


Reagent MW Eq.g/ml mmolBenzoic acid (1) 219.02 1.0 2.152 g 9.83L-Thr-OMe-HCl 169.61 1.2 1. 968 g 11.6 EDCI 191.71 1.2 2.218 g11. 6 HOBt 135.131.1 1.410 g10. 4 DIEA 129.25 4.0 6.8 mL 39.0 DMF 60 mL Preparation of (2S,3R)-2- (3-bromo4-fluoro-benzoylamino)-3-hydroxy-butyric acid methyl ester (2)
Diisopropylethylamine (6.8 mL, 39.0 mmol) was added to a stirred solution of 3-bromo-4-fluorobenzoic acid 1 (2.152gi 9.83 mmol), L-threonine methyl ester hydrochloride (1.968 g, 11.6mmol), EDCI (2.218 g, 11.6 mmol) and HOBt (1.410 g, 10.4 mmol) in anhydrous DMF (60 mL) at 0 C underN2. The solution was stirred at 0 C for 1 h and at room temperature for20 h. The solution was diluted with EtOAc (300 mL) and washed with 1.0 M HCl (2 x 80mL), saturatedNaHCO3 (2 x 80mL), H20 (4 x 80mL), dried overMgS04, filtered and concentrated in vacuo to give a colorless syrup which solidified on standing to afford 3.280 g (100%) of (2S,3R)-2- (3-bromo-4-fluoro-

benzoylamino)-3-hydroxy-butyric acid methyl ester 2 as a white solid, mp 73-74 C. MS(ES+) m/z 333.9(Cl2Hl3BrFN04+H requires 334.00).

Preparation of 3-bromo-4-fluoro-N-{(1S, 2R)-2-hydroxy-1-[(hydroxyamino) carbonyl] propyl}benzamide (3)
EMI72.1

To a solution of hydroxylamine hydrochloride (66 mg, 0.95 mmol) in anhydrous MeOH (2.0 mL) at 0 C under N2 atmosphere was added sodium methoxide (25 wt% in MeOH, 360 mg, 1.67 mmol). A precipitate formed immediately and the cloudy white solution was stirred for 10 minutes at 0 C. A solution of methyl (2S, 3R)-2- [ (3-bromo-4-fluorophenyl) carbonylamino]-3-hydroxybutanoate (2) (284 mg, 0.850 mmol) in MeOH (2.0 mL) was added and the reaction stirred 2 h at 0 C and then warmed gradually to room temperature overnight (17 h total). Aqueous 1.0 MHCI (10 mL) was added and the solution extracted with 4: 1 chloroform/isopropyl alcohol (4 x 20 mL). The organic layers were combined, dried overNa2S04 and concentrated to give a pink foam. The crude solid was triturated with diethyl ether (2 x 8 mL) and dried in vacuo to give3-bromo4-fluoro-N-{(lS, 2R)-2-hydroxy-1- [(hydroxyamino) carbonyl] propyl} benzamide 3 as a white foam: mp 152-153 C. Rf (10: 1 CH2Cl2/MeOH on silica gel) = 0.53.

Preparation of Hydroxamates Example 2: Synthesisof 4-benzoyl-N-{(lS, 2R)-2-hydroxy-1-[(hydroxyamino) carbonyl] benzamide
EMI72.2


Procedure:
To a solution of hydroxylamine hydrochloride (121 mg, 1.74 mmol) in anhydrous MeOH (2.0mL) at0 C under N2 atmosphere was added sodiummethoxide (25 wt% in MeOH, 680 mg, 3.14 mmol). A precipitate was immediately observed and the cloudy white solution was stirred for 10 minutes at 0 C. A solution of methyl (2S, 3R)-3-hydroxy-2-{[4- (phenylcarbonyl) phenyl]carbonylamino} butanoate (1) (534 mg, 1.56 mmol) in MeOH (3.0 mL) was added and the reaction stirred 3 h at0 C, then warmed gradually to ambient temperature overnight (18 h total). Aqueous 0.5 M HCl (20 mL) was added and the solution extracted with 5: 1chloroform/isopropyl alcohol (4 x 40 mL). The organic layers were combined, dried overNa2SO4 and concentrated to give an orange foam. Purification by silica gel chromatography (increasing eluant polarity from 30: 1CH2Cl2/MeOH to 15:1CH2ClMeOH) afforded 228 mg (43%) of 4-benzoyl-N- {(1S,2R)-2-hydroxy-1-[(hydroxyamino) carbonyl]propyl}benzamide.

Example 3: Synthesis of (2R,3R)-3-hydroxy-1-{[4-(trifluoromethoxy)phenyl]carbonyl} pyrrolidine-2-carbohydroxamic acid
Preparation of((2R, 3R)-3-hydroxy-1-{[4-(trifluoromethoxy) phenyl] carbonyl} pyrrolidin-2-yl)-N- (phenylmethoxy) carboxamide (2)
EMI73.1

O OH H O /O O NH
N benzylhydroxylamine HCI ..-OH F3Cs HATU, HOBt, DIEA, DMF N... OH
O C to r. t. F3Csow
1 2 Procedure:
To a solution of (2R,3R)-3-hydroxy-l- { [4- (trifluoromethoxy) phenyl] carbonyl}pyrrolidine-2- carboxylic acid (1) (405 mg, 1.27 mmol), benzylhydroxylamine hydrochloride (243mg, 1.52 mmol), HATU (556 mg, 1.46 mmol), and HOBt (178mg, 1.32 mmol) in DMF (10 mL) at 0 C was addeddiisopropylethylamine(710 N, L, 4 : 07 mmol) with stirring. The cooling bath was removed after one hour and the reaction mixture stirred at ambient temperature for 18 h and then diluted with EtOAc (200 mL). The organic layer was washed with 1.0 M HCl (2 x 60 mL), sat.NaHC03 (2 x 60 mL) andH20 (5 x 60mL), dried overMgS04 and concentrated to give 493 mg (92%) of((2R, 3R)-3-hydroxy-1-

{[4-(trifluoromethoxy) phenyl]carbonyl} pyrrolidin-2-yl)-N-(phenylmethoxy) carboxamide (2), a colorless oil that slowly crystallized upon standing. Rf(25 :1CH2Cl2/MeOH) = 0.35.

Prepartion of (2R, 3R)-3-hydroxy-1-{[4-(trifluoromethoxy)phenyl] carbonyl}pyrrolidine-2- carbohydroxamic acid (2)
EMI74.1
1 2 Procedure:
To a solution of ( (2R, 3R)-3-hydroxy-1-1 [4- (trifluoromethoxy) phenyl] carbonyllpyrrolidin-2- yl)-N- (phenylmethoxy) carboxamide (1) (143 mg, 0. 337 mmol) in EtOH (10 mL) was added 20% Pd (OH) 2/C (50 mg). The solution was purged with hydrogen gas (approx. 0.5 L from a 1 L balloon) and then stirred under an atmosphere of H2 (balloon pressure). TLC analysis showed no starting material after one hour. The solution was diluted with EtOAc (10mL) and filtered through celite, washing with 20: 1 EtOAc/EtOH(50mL). The solution was concentrated and dried in vacuo to afford 90 mg (80%) of (2R,3R)-3-hydroxy-1-{[4-(trifluoromethoxy) phenyllcarbonyl} pyrrolidine-2- carbohydroxamic acid (2) as a sticky white foam: mp 64-65 C. Rf (10:1CH2Cl2/MeOH) = 0.29.

Synthesis of N-Benzyl Threonine Analogues by Reductive Amination Example 4: Synthesis of (2S, 3R)-3-hydroxy-2-{[4-phenylphenyl)methyl]amino}butanehydroxamic acid (3).
EMI74.2
Reagent MW Eq.g/ml mmol 4-biphenylcarboxaldehyde 182.22 1.0 1. 104 g 6.06

L-Thr-OMe-HCl 169.61 1.0 1.030 g 6.07 NaBH(OAc) 3 211.94 1.4 1.800 g 8.49 Et3N 101.19 2.0 1. 70 mL 12.1 THF 25mL
Triethylamine (1.70 mL, 12.1 mmol) was added to a stirred suspensionof L-threonine methyl ester hydrochloride (1.030 g, 6.07 mmol) and 4-biphenylcarboxaldehyde (1.104 g, 6.06 mmol) in THF (25 mL). After 20 min, NaBH (OAc)3 was added and the suspension stirred for 20 h. The reaction was monitored by TLC (50: 1DCM/MeOH,Rf=0. 4). The reaction mixture was quenched with saturatedNaHCO3 (50 mL), extracted with EtOAc (2 x 120 mL), dried overMgS04, filtered and concentrated to give a yellow oil. Purification by silica gel chromatography(150 : 1 DCM/MeOH) afforded 1.220 g (67% yield, 98% pure) of (2S,3R)-2-[(biphenyl-4-ylmethyl)-amino]-3-hydroxy-butyric acid methyl ester 2 as a pale yellow oil.

HPLC (260 nm, 34 min run) 14.2 min; LRMS (ES+) m/z 299.9 (C18H21NO3 +H requires 300.10).

Compound 3 was then formed by the additionof NH2OH in MeOH/NaOMe at0 C, warming to ambient temparture of the period of several hours. LCMS MH+ 301.15.

General Methods for Making Phenyl-benzoic acids and Phenyl-benzoate esters (see Example 5 below)
EMI75.1


Suzuki Procedures Using Pd(dppi) CI2-DCM Catalyst and aTHF/H20 Mixture
EMI76.1
Reagent MW EQg/ml mmolBromoAreneWl ~300 1 100mg-0. 33Boronic Acid #2 - 1.2 - #0. 40 Na2C03 105.99 3104 m #0. 99 Pd (dppf) Cl2 816.63 0.1-0. 227-54mg-0. 033-0.066 THF (3) (sparged with argon for 5 min. ) 0.75 ml water(l) (sparged with argon for 5 min.) 0.25 ml Standard Procedure
1 eq aryl halide (1) was added to 1.2 eq. (2) and Pd (dppf) Cl2 in THF, followed by addition of water and stirred 8 hours at RT. Upon completion (usually over night), the reactions are diluted with ethyl acetate (5-10 ml) and water (1ml). The organic layer is separated and washed with NaHCO3 (2x3 ml), water(lx3 ml), brine(lx3 ml), dried withNa2S04, filtered and concentrated in an 8 ml glass vial. The residue is dissolved in DMSO and injected on a preparatory HPLC reverse phase column to afford > 80 % yield.

Suzuki Procedures Using Pd(dppf) Cl2-DCM Catalyst and DMF Solvent
EMI76.2


Reagent MW EQg/ml mmolBromoArene #1 #500 1 20mg-0. 04BoronicAcid#2-200 2-14 mg-0. 08
Pd (dppf) Cl2 816.63 0.25 10mg-0. 01-0.02
TEA 101.19 5 28pL-0. 2
DMF (dry & sparged with argon for 5 min. ) 0.5 ml
Standard Procedure
The haloarene 1 and boronic acid 2 were weighed out and placed in the reaction flask. The
DMF was sparged with argon for 5-10 minutes, followed by TEA addition, and the reaction was lightly bubbled with argon. The solid Pd(dppf) Cl2 catalyst was added in one portion. The vial was flushed with argon, capped tight and stirred or shaken at-80 C. Upon reaching completion (over night), the reaction was filtered and injected on a preparatory HPLC reverse phase column (80% yield).

Synthesis of Methyl DAP Analogues
Example 5:3- (R)-Amino-2- (S)- [ (4'-ethyl-biphenyl-4-carbonyl)-amino]-butyl-hydroxamic acid (8)
EMI77.1


Preparation of N-triphenylmethyl allo-threonine methyl ester(2).

'hic HCI
EMI78.1

Reagent MW EQg/ml mmolH-allo-Thr-OMe-HCI (1) 169.7 1.2 2.0 g 12.0
Trt-Br 323.24 1.0 3.23 g 10.0
DIEA 129.25 3.0 5. 2 ml 30.0
CHCl3 (dry) 100 ml
For similar procedures see: Righi, P.; Scardovi, N.; Marotta, E.; ten Holte, P.; Zwanenburg, B.

Organic Letters 2002,4 (4), 497-500.

A solution of trityl bromide (3.2g, 10. 0mmol) inCHC13(40ml) was added dropwise to a stirred solutionof allo-threonine methyl ester HCl salt (1) (2. 0g,12. 0mmol) and DIEA (5.2ml, 30.0mmol) inCHC13(60ml) at rt under N2. The reaction could be followed by TLC eluting withEtOAc/Hex (40: 60) (Rf=0. 3). After stirring 12 h, the reaction was concentrated to a brown oil. The crude product was diluted with EtOAc (170ml) and washed with 0.2 N citric acid(2x50ml), water(2x50ml), brine (50ml), dried (Na2SO4), filtered and concentrated under reduced pressure to yield 3.73g (85% yield, . 95% pure) of a yellow solid.

HPLC (220nm, 41min. run) 30. 90 min.; HPLC (220nm, 17min. run) 14.86 min.; LCMS:
LC(214nm) 3.06 min. , MS (ES+) m/z 376.2(C24H25N03+H requires 376.18).

Preparationof 3-Azido-2-(S)-(trityl-amino)-butyric acid methyl ester (3).
EMI78.2


2 3 Reagent MW Eq.g/ml mmol

Trt-allo-Thr-OMe (2) 375.46 1.0 4.08 g 10.88
PPh3 262.29 1.0 2. 85 g 10.88
DEAD(neat) 174.161. 6 2.93 ml 17.82
DPPA 275.7 2.7 6. 40 ml 29.7
THF (dry) 50 ml
For similar procedures see: Matsuda, A.; Yasuoka, J.; Sasaki, T.; Ueda, T. J. Med. Chem. 1991, 34,999-1002.

A solution of pure DEAD (2.9ml, 17.8mmol) in THF(5ml) was added slowly dropwise to a stirred solutionof trt-allo-threonine methyl ester (2) (4.1g, 10.9mmol) and PPh3 (2.9g, 10.9mmol) in THF(40ml) at0'C under'N2. After 3 min. , a solution of DPPA (6.4ml, 29.7mmol) in THF (5ml) was added to the orange-yellow reaction solution at0 C. After 1h, the reaction was allowed to warm to rt. After 40h, the reaction had reached completion by TLC(Hexane/DCM/EtOAc (64: 20: 16) (Rf=0.6)). and LCMS. The yellow solution was concentrated to give 18g of crude material that was purified by column chromatography eluting withHexane/EtOAc (88: 12) giving 3. 5g of 70% pure product after evaporation. The product was purified again (to remove trityl alcohol and a crotyl side- product formed during the reaction by elimination) by column chromatography eluting withHexane/DCM/EtOAc (76: 20: 4) giving 1.65g (38% yield) of a pale yellow oil after concentration and drying in vacuo. Note that the trityl protecting group would hydrolyze when exposed to TFA while running the sample on HPLC.

Alternately, the reaction could be carried out in dry DCM. A reaction using 5.44g (14.5 mmol) of trt-allo-threonine methyl ester (2) in DCM (100ml) with PPh3 (3.8g, 14.5mmol), pure DEAD (3.4ml, 21.8mmol) in DCM(5ml) and DPPA (6.3ml, 24.0mmol) in DCM(10ml) were combined following the procedure above. After 3 days, the reaction did not progress further by TLC and LCMS.

After the same work up, 2.97g of the product was obtained in51% yield.

HPLC(220nm, 41min. run) 40.5 min.; HPLC(220nm, 17min. run) 16.32 min. ; LCMS: LC(214nm) 3.7 min. , MS (ES+) m/z 401.2(C24H25N302 +H requires 401.15).

Preparation of 2- (S)-Amino-3- (R)-azido-butyric acid methyl esterHCI Salt (4).
EMI80.1


Reagent MW EQg/ml mmolTrt-Azido-Thr-OMe (3) 400.471. 0 4.79 g 11.98
TFA57 ml
CHCl3 (dry) 3 ml
A solution of Trt-Azido-Thr-OMe (3) (4.8g, 12.0mmol) was dissolved in a 95% TFA/DCM solution(60ml) at rt with stirring. After 2.5 h, the reaction was complete by LCMS. The bright yellow solution was diluted with 0.5 Naq.HCI (300ml). The aqueous layer was extracted with DCM(2x30ml) and then lyophilized to dryness. The white solid was dissolved in AcCN/water (50: 50) (100ml) and again lyophilized to dryness to produce a consistent powder and remove as much of the
TFA as possible. Theazido-Thr'product (4), 2.26g (97% yield, 95% pure) of a white solid, was obtained as theHCI salt.

HPLC(220nm, 41min. run) 7.91 min.; HPLC (220nm, 17min. run) 3.36 min ; LCMS:
LC (214nm) 0.48 min. , MS (ES+) m/z 159.3 (C5H10N4O2 +H requires 159.08).

Preparationof 3- (R)-Azido-2- (S)- [ (4'-ethyl-biphenyl-4-carbonyl)-amino]-butyric acid methyl ester(6).
EMI80.2
Reagent MW EQg/ml mmolAzido-Thr-OMe-HCI (4) 194.62 1.0195 mg 1.0 Biphenyl Acid (5) 226.27 1.0 226 mg 1.0 HOBT153 1.0158 mg 1.0

EDC-HC1 191.17 1.3 249 mg 1.3
DIEA 129.25 2.5 0.44 ml 2.5
DCM (dry) 10 mlA EDCHC1 (249mg, 1. 3mmol) was added to a stirred colorless solution of azido-Thr- OMe-HCI (4) (195mg,

RT. The reaction was exposed toaspirator vacuum to remove the nitrogen and then opened to the hydrogen gas at balloon pressure(~1 atm). The reaction stirred for 3h at which time the hydrogen was exchanged for nitrogen. The reaction was filtered through a pad of celite to remove the palladium.

The celite pad was washed with MeOH (30ml). The combined fractions of MeOH were evaporated under reduced pressure and dried in vacuo to give 225mg(99po yield) of pure produce (7) as a white solid.

HPLC(220nm, 17min. run) 10.79 min.; LCMS: LC(214nm)2. 21 min., MS (ES+)m/z 341.2(C2oH24N202 +H requires 341.18).

Preparation of3"Amino-2-(S)-[(4'-ethyl-biphenyl-4-carbonyl)-amino]-butyl-hydroxamic acid(8)
EMI82.1

Reagent MW EQg/ml mmol.

Amino-Thr-OMe (7) 340.42 1.0 225 mg 0.66
H2NOH-HCI 69.49 10.0 460 mg 6.6
NaOMe 54.02-12. 0-430 mg 7.92
MeOH (dry) 7 ml
DCM (dry) 5 ml
To a stirred suspension of biphenyl-amino-Thr methyl ester (7) (225mg, 0.6mmol) and hydroxylamine HC1 salt (460mg, 6.6mmol) in MeOH(7ml) and DCM(5ml) was added fresh solid NaOMe powder (430mg, 7.92mmol) in one portion. After stirring for 2 min. at rt under nitrogen, the pH of the reaction on wet pH paper was approximately 7-8. The suspension had change from larger particles of white solid to a finely-divided milky consistency. The pH of the reaction was checked after adding small portions of NaOMe(50-lOOmg) and allowing 2 min. for the reaction to equilibrate.

The pH of the reaction reached a stable 11-12 after the final portion of NaOMe was added (250mg total). The reaction was initiated at pH 11 and proceeded quickly. After 30 min. , the reaction reached 85% completion as determined by LCMS, and the reaction was placed in a-10 C bath. The cold mixture filtered over fine filter paper on a Biichner funnel. The white residue was washed with MeOH

(15ml). The organic fractions were collected and concentrated under reduced pressure to give crude product (750mg). The crude product (only one150 mg portion) was dissolved in DMSO(lml), AcCN (100p1) and water(100pal), passed through a Teflon syringe filter, and the clear filtrate was injected on a preparative HPLC. The purification used a20x50 mm Ultro 120C18 column running a 22 ml/min 2% gradient (AcCN/water, 0.1% TFA) for 16 min. The purified fractions were lyophilized to dryness.

The product as the TFA salt was dissolved in AcCN/water (50: 50)(5ml), 1N aq. HCl (1 equivalent) and lyophilized again to give 11.5 mg of white powder as an HCl salt(23% yield).

HPLC(220nm, 41min. run) 19.31 min.; HPLC(220nm, 17min. run) 9.39 min ; LCMS: LC (214nm) 1.98 min. , MS (ES+)m/z 342.2(Cl9H23N303 +H requires 342.17).

Synthesis of 4'Benzamide Biphenyl Threonine Hydroxamic Acid Example 6: Biphenyl-4,4'-dicarboxylic acid41- [ (3-Boc-amino-propyl)-amidel 4- [ ( (2R)-hydroxy-(lS)-hydroxycarbamoyl-propyl)-amide] (6), and Example 7: Biphenyl-4,4'-dicarboxylic acid 4'-[(3-amino-propyl)-amide] 4-[((2R)-hydroxy-(1S)- hydroxycarbamoyl-propyl)-amide] (7)

EMI84.1
Synthesis of (2S,3R)-2-amino-3- (phenylmethoxy)-N- (phenylmethoxy) butanamide (1)
EMI84.2
Procedure:
To asuspension of benzylhydroxylamine hydrochloride (8.310 g, 52.06mmol), Boc-Thr (OBn)OH (14.01 g, 45.28mmol), EDCI (10.01 g, 52.21 mmol), and HOBt (6.90 g, 51.06 mmol) in CH2Cl2 (300 mL) at 0 C was added diisopropylethylamine (28.3 mL, 162 mmol) with stirring. The cooling bath was removed after one hour and the reaction mixture stirred at ambient temperature for 20 h and was then diluted withCH2C12 (300 mL). The organic layer was washed with 1.0 M HCl (2 x 200 mL),

sat.NaHCO3 (2 x 200 mL) and brine (200 mL), dried overMgSO4 and concentrated to give 14.5 g of a white solid. The crude solid was treated with a solution of trifluoroacetic acid (90 mL) inCH2CI2 (90 mL) and stirred for 2.5 h. The reaction mixture was concentrated by rotary evaporation and then diluted with CH2Cl2 (600 mL). The organic layer was washed with sat.NaHCO3 (2 x 200 mL), dried overMgS04 and concentrated to give a dark orange oil. Purification by silica gel chromatography (50: 1CH2Cl2/MeOH) afforded (2S, 3R)-2-amino-3-(phenylmethoxy)-N-(phenylmethoxy) butanamide (A) (8.9 g, ) as a pale yellow oil. Rf (50: 1CH2Cl2/MeOH on silica gel) = 0.2.

Preparation of (1S,2R)-4'-(2-benzyloxy-1-benzylovcarbamoyl-propylcarbamoyl)-biphenyl4- carboxylic acid (3).

ReagentMW Eq.g/mL mmol Amine(1) 314.38 1.0 0.944 g 3.00 Dicarboxylic acid (2) 242.23 1.9 1. 360 g 5.61 BOP 442.3 1.5 2.007 g 4.54 DIEA 129.25 3.3 1.7 mL 9.76 DMF 200mL
To a suspension of 4, 4'-biphenyldicarboxylic acid 2 (1.360g, 5.61 mmol) in DMF (180 mL) was added BOP (2.007 g, 4.54 mmol) and DIEA (1.7mL, 9.8mmol). A solution of(lS, 2R) -2-amino- 3,N-bis-benzyloxy-butyramide 1 (944 mg, 3.00 mmol) in DMF (20 mL) was added and the reaction stirred for 18h. The solution was diluted with EtOAc (250 mL) and washed with 1.0 M HC1 (500mL). The aqueous layer was extracted with EtOAc (250 mL) and the organic layers combined. The organic layer was washed with 1.0 M HCl (250mL), dried overMgS04, and concentrated to give a crude yellow solid. Purification by silica gel chromatography (60: 1 CH2Cl2/MeOH) gave 210 mg(lS, 2R)-4'-(2-benzyloxy-l-benzyloxycarbamoyl-propylcarbamoyl)-biphenyl4-carboxylic acid 3.

(13% yield) as a yellow solid. Rf= 0.80 (10: 1CH2Cl21MeOH) ; LRMS (ES+)walz 539.1(C32H30N206 + H requires539. 22).

Preparationof biphenyl-4, 4'-dicarboxylic acid4'- [(3-(Boc)-amino-propyl)-amide]-4-[(2R)- benzyloxy-(1S)-benzyloxycarbamoyl-propyl)-amide] (5).

ReagentMW Eq.g/mL mmolBiphenylcarboxylic acid (3) 538.59 1.0 0.200 g 0.371 Amine (4) 174.24 1.1 0.071 g 0.407 EDCI 191.71 1.1 0.078 g 0.407 HOBt 135.13 1.0 0.052 g 0.385 DIEA 129.25 2.7 180 L 1.0 DMF 2 mL
To a solution of biphenylcarboxylic acid 3 (200 mg, 0.371mmol), EDCI (78 mg,0. 407 mmol), and HOBt (52 mg, 0.385 mmol) in DMF(-2 mL) was added t-ButylN- (3-aminopropyl) carbamate 4 (71 mg, 0.407 mmol) and DIEA(180 pal, 1.0 mmol). The reaction mixture was stirred 24 h, diluted with EtOAc (150mL), washed with 1.0 M HCl (2 x 60 mL), saturatedNaHCO3 (2 x 60 mL),Ha0 (3 x 60 mL), dried overMgS04 and concentrated to give a crude white solid. Purification by silica gel chromatography (25: 1CH2Cl2/MeOH) afforded 194 mg (75% yield) of biphenyl-4, 4'-dicarboxylic acid 4'- [(3-(Boc)-amino-propyl)-amide]-4-[(2R)-benzyloxy-(1S)-benzyloxycarbamoyl-propyl)-amide] 5 as a white solid. Rf = 0. 15(50 : 1CH2Cl2/MeOH) ; LRMS (ES+) mlz 695.2 (C40H46N4O7 + H requires 695.35).

Preparationof Biphenyl-4, 4'-dicarboxylic acid 4'-[(3-Boc-amino-propyl]-amide] 4-[((2R)- hydroxy-(1S)-hydroxycarbamoyl-propyl)-amide] (6).

Reagent MW Eq. g/mL mmol Biphenyl diamide (5) 694. 82 1.00 0.190 g 0.273 Pd (OH)2 (20%/C) 106.42 0.15 0.020 g 0.040 H2(g) balloon THF 5. 0 mL MeOH 3. 0 mL

A solution of dibenzyl-piotected threonine hydroxamic acid 5 (190 mg, 0.273 mmol) in THF (5 mL) and MeOH (3 mL) was charged with Pd (OH)2(20%/C, 20 mg, 0.04 mmol) and stirred under a hydrogen atmosphere (balloon pressure) forl6 h. The crude mixture was filtered through a plug of celite eluting with 2: 1MeOH/THF (15 mL) and concentrated to give an orange syrup. Purification by silica gel chromatography (5: 1: 1THF/MeOH/CH2Cl2 afforded 110 mg (78% yield) of biphenyl-4,4'-dicarboxylic acid4'-[(3-Boc-amino-propyl)-amide] 4-[((2R)-hydroxy-(lS)-hydroxycarbamoyl-propyl)- amide] as a white foam, mp75-77 C. Rf = 0.20 (10: 1CH2Cl2/MeOH) ; LRMS (ES+) m/z 515. 4(C26H34N407 + H requires 515.26).

Preparation of Biphenyl-4,4'-dicarboxylic acid4'-[(3-amino-propyl)-amide] 4-[((2R)-hydroxy-(lS)-hydroxycarbamoyl-propyl)-amide] (7).

Reagent MW Eq.g/mL mmol Boc-protected amine (6) 514.57 1.00 0.080 g 0.155 TFA 3.0 mL CH2C12 3.0mL
A flask containing Boc-protected amine 6 (80 mg, 0.155 mmol) was treated with 50%TFA/CH2Cl2 (6.0 mL) and stirred for 2.5 h. The reaction mixture was concentrated by rotary . evaporation to give a brown syrup. Purification byRP-HPLC(C18 column,CH3CN gradient 5-70%,0. 1% TFA, UV analysis 300 rim, 36 min) and lyophilization of the collected fractions afforded 14 mg (21% yield) of biphenyl4, 4'-dicarboxylicacid4'-[(3-amino-propyl)-amide] 4-[((2R)-hydroxy-(lS)-hydroxycarbamoyl-propyl)-amide] as a white solid. LRMS (ES+) m/z 415.3(C2lH26N405 + H requires 415.20) ;RP-HPLC (300 nm, 36 min run) 18.2 min.

Example 8: Synthesis ofN- (2- (N-hydroxycarbamoy !) (2S)-2- { [4- (4- ethylphenyl) phenyl] carbonylamino} ethyl) acetamide (4)

EMI88.1

H
Ac20, pyridine Ac) H2N-O-Trt Resin,
O H HOXtN NFmoc U, D EA, NMP
THF
0 H
1 2
T'-
H NH
N Ac 1. Piperidine, DMF (NH
H 2. HATU, DIEA, NMP H (3' N"C. N
I-N Fcmoc 0 N 4-Ethyl-biphenyl-0 H
O H 4-carboxylic acid
3. TFA, water/
4 Preparationof 3-Acetylamino-2- (9H-fluoren-9-ylmethoxycarbonylamino)-propionic acid (2).
EMI88.2


HAN N
H2NX Ac20, pyridine Ac BO H THF. HO) lN'Fm C
0 H) f H
O H O H
2
Reagent MW EQg/ml mmol
Fmoc-DAP-H(1) 326.4 1.0 980 mg 3. 0 Acetic anhydride 102.09 1.5 425 uL 4.5
Pyridine 79.1 2.0 483 uL 6.0
THF20ml
Acetic anhydride in THF(5ml) was added to a cloudy mixture of Fmoc-DAP-H (1)(980mg,
3. 0mmol) and pyridine(483uL, 6. 0mmol) in THF(15ml) with stirring at rt. After 4 hours, the clear pale yellow solution had reacted completely by LCMS. The reaction was evaporated under reduced pressure. The residue was dissolved in EtOAc(150ml) and washed with 0. 1M NaHSO4 (50ml), water(50ml), sat. brine(50ml), dried withNa2S04, filtered and concentrated under reduced pressure to give

1.1 g of crude product as a white solid. The crude product was purified by prep. HPLC to give 0.99 g (90% yield) of acyl-DAP (2).

Preparation of(2-Acetylamino-l-hydroxycarbamoyl-ethyl)-carbamic acid 9H-fluoren-9-ylmethyl ester trityl resin (3).
EMI89.1


H H Ac N H2N-O-Trt Resin, NHsAc
HATU, DIEA, NMP HO OI, H. Fmoc 4,. O. N OI. H. Fmoc
2 3
2 3 Reagent MW EQg/ml mmolHzN-0-Trt Resin 1.0 120 mg 0.113Fmoc-DAP (Ac) -H (1) 368.4 5.0 980 mg 0.564 HATU380 5. 00. 146 g 0.564 DIEA 129.25 10.0 196 ul 1.13 NMP 1. 7 ml
A solutionof Fmoc-DAP (Ac) -H (1) (980mg, 0.56mmol), HATU (0.146g,0. 56mmol) in NMP(1. 7ml) was made. After 2 min. of shaking, the activated acid was added to the deprotectedH2N-O-Trt Resin (120 mg, 0.113mmol) at rt with shaking. [Deprotection of the Fmoc group from the resin was accomplished using 20% piperizine in DMF(4ml) for 2 hours twice. The resin was drained and washed with DMF (2x5ml) and DCM(2x5ml).] After shaking for 20 hours, the reaction was drained and washed with DMF(2x5ml) and DCM(2x5ml). The resin was dried and used as is in the next reaction.

Preparation ofN-(2-5-hydroxycarbamoyl) (2S)-2-{[4-(4-ethylphenyl) phenyl] carbonylamino} ethyl) acetamide (4) Preparation of(2-Acetylamino-l-hydroxycarbamoyl-ethyl)-carbamic acid9H-fluoren-9-ylmethyl ester trityl resin (3).

EMI90.1


Oqz
H NH
CNAc 1. Piperidine, DMF gNHo /Ac > H, l
H Fmoc 2. HATU, DIEA, NMP H N) uNJw O N 4-Ethyl-biphenyl-0 H
H H 4-carboxylic acid I w
3 3. TFA, water
4
4
Reagent MW EQg/ml mmol
Fmoc-DAP (Ac)-Trt Resin (3) 1.0 120 mg 0.113
4'-Etbiphenyl 4-carboxy acid 226.3 5.091 mg 0.4 HATU 380 5.0 152 mg 0.4
DIEA 129.25 10.0 140 ul 0. 8
NMP 1. 0 ml
The resin was treated with 20% piperizine in DMF (4ml) for 2 hours twice. The resin was drained and washed with DMF (2x5ml) and DCM(2x5ml). The resin was driedira vacuo. A solutionof 4'-Ethyl-biphenyl-4-carboxylic acid(9lmg, 0.4mmol), HATU (152g, 0.4mmol) in NMP(l.Oml) was made. After 2 min. of shaking, the activated acid was added to the deprotected H-DAP (Ac)-Trt resin(120 mg, 0.113mmol) at rt with shaking. After shaking for 18 hours, the reaction was drained and washed with DMF(2x5ml) and DCM(2x5ml). The resin was driedin. vacuo. The product was cleaved from the resin through treatment with a solution of TFA(500uL), DCM(500uL) and water (50uL) for 25 min. The resin was filtered and washed with fresh DCM (2ml). The combined TFA and
DCM fractions are evaporated under reduced pressure. The residue was diluted withCH3CN/water(1 :1) (10ml) and lyophilized. The crude product was purified by prep. HPLC. The crude product was dissolved in DMSO(lml), passed through a Teflon syringe filter, and the clear filtrate was injected on a preparative HPLC. The purification used a20x50 mm Ultro 120 C18 column running a 22ml/min
2% gradient (AcCN/water, 0.1% TFA) for 16 min. The purified fractions were lyophilized to dryness.

The solid residue was lyophilized again from CH3CN/water (1: 1)(5ml) give 8. 6 mg of pure product (4)(-21% yield).

Example 9: Synthesis of 4'-Ethyl-biphenyl-4-carboxylic acid(1-hydroxycarbamoyl-2-methanesulfonylamino-ethyl)-amide (3)

Preparation of4'-Ethyl-biphenyl-4-carboxylic acid(2-amino-1-hydroxycarbamoyl-ethyl)-amide. trityl resin (2).
EMI91.1


Alloc NH2
NH 1. Dimethyl barbituric (
H ( 0 acid, Pd (PPh3) 4, ^"o, N (N VOIN, PPh a
2
1 Reagent MWEQg/ml mmol Biphenyl-DAP (Alloc)-Trt Resin (1) 1.0 500 mg0. 35 Dimethyl barbituric acid 156.14 10.0 600 mg 3.5 Pd (PPh3) 4 1135.6 1.0 438 mg 0.35 PPh3 262.3 2.0 202 mg 0.7 DCM 11.0 ml
Pd(PPh3) 4 (438mg, 0. 35 mmol) was added to a vial containing biphenyl-DAP (Alloc) -Trt Resin (1)(500mg, 0.35mmol), Dimethyl barbituric acid (600mg, 3. 5mmol) and PPh3 (438mg, 0.35mmol) in DCM(l lml) at rt under argon. The mixture was sparged with argon and shaken for 16 hours. The bright yellow mixture was drained and washed with DMF (8x10ml) and DCM(8xl0ml). The resin was driedin vacuo to give the deprotected DAP resin 2.

Preparation of4'-Ethyl-biphenyl-4-carboxylic acid(1-hydroxycarbamoyl-2-methanesulfonylamino-ethyl)-amide (3).
EMI91.2
o
0 o ; s,
NH2 NH
H O
H w N) + 1. MsCI, Lutidine, DCM H (iro, N, ,,,) 0. HO'C.

0 H I. 2. TFA, water O H 2. /. 3 / Reagent MW EQg/ml mmol

Biphenyl-DAP-Trt Resin (2) 1.0 160 mg 0.11 Methanesulfonyl chloride 114.55 10.0 85 uL 1.1 Lutidine107. 16 15.0 190 uL 1.6 DCM 1. 5 mlMethanesulfonyl chloride(85uL, l. lmmol) was added to a mixture of deprotected DAP resin (2) (160mg, 0. 11mmol) and lutidine(190uL, 1. 6mmol) in DCM(1.5ml). After shaking for 16 hours, the mixture was drained and washed with DMF (lOx2ml) and DCM(5x2ml). The product was cleaved from the resin through treatment withTFA/water (4: 1)(1. 5ml). After shaking for 45 min. , the TFA solution was collected from the resin by filtration, and the resin was washed with TFA(lml) and TFA/water(1 :1)(10ml). The combined TFA fractions were concentrated under reduced pressure to a reddish-brown solid. The product, identified by LCMS, was purified by prep. HPLC using a20x50 mm Ultro 120C18 column running a 22 ml/min 4% gradient(AcCN/water,. 0.1% TFA) for 16 min.

The purified fractions were lyophilized to dryness. The solid residue was lyophilized again from CH3CN/water (1: 1)(5ml) give 4 mg of pure product as a white solid (3)(#9% yield).

Example 10: Synthesis of4'-Ethyl-biphenyl-4-carboxylic acid[2- (3, 3-dimethyl-ureido)-l-hydroxycarbamoyl-ethyl]-amide (3) (Continued from compound 2 of Example 9 above)
EMI92.1
91-2-
NH2 NH
H 0 1. Dimethylcarbamyl H 0 o'N chloride, lutidine, DCM C.

H 2. TFA, water p H -,-ou Reagent MW EQg/ml mmol Biphenyl-DAP-Trt Resin (2) 1. 0 125 mg 0.096 Dimethylcarbamyl chloride 107.5 10.0103 mg 0.96 Lutidine 107.16 20.0 225 uL1 : 92 DCM 1.5 ml

Dimethylcarbamyl chloride(103mg, 0.96mmol) was added to a mixture of deprotected DAP resin (2) (125mg, 0.096mmol) and lutidine (225uL, 1.92mmol) in DCM(1.5ml). After shaking at rt for 5 hours, the mixture was drained and washed with DCM(5x2ml), DMF(5x2ml) and DCM(5x2ml). The product was cleaved from the resin through treatment with TFA/water (4: 1)(1.5ml).

After shaking for 45 min. , the TFA solution was collected from the resin by filtration, and the resin was washed with TFA/water (1: 1) (2ml). The combined TFA fractions were concentrated under reduced pressure to a reddish-brown solid. The product, identified by LCMS, was purified by prep.

HPLC using a20x50 mm Ultro 120 C18 column running a 22 ml/min 4% gradient (AcCN/water, 0. 1 % TFA) for 16 min. The purified fractions were lyophilized to dryness. The solid residue was lyophilized again from CH3CN/. water (1: 1)(5ml) give5 mg of pure product as a white solid (3)(~13% yield).

Example 11: Synthesis of4'-Ethyl-biphenyl-4-carboxylic acid[2-(2-amino-ethylamino)-1-hydroxycarbamoyl-ethyl]-amide (2).
EMI93.1


Reagent MW EQg/ml mmol Biphenyl-DAP-hydroxamate(1) 327.4 1.0 20 mg 0.096Boc-amino-acetaldehyde 159.19 4.0 6.4 mg 0.4 NaBH3CN 62.84 10.0 3.1 mg 0.05 Acetic acid 60.05 20.0 6 uL 1.00 DCM 1.5 mol
NaBH3CN (3.1mg,0.05mmol) followed by acetic acid(6uL,l.Ommol) were sequentially added to a stirred suspension ofbiphenyl-DAP-hydroxamate (1)(20mg, 0. 096mmol) and Boc-amino- acetaldehyde (6.4mg, 0.4mmol) in MeOH (1.5ml) in a 4 ml vial. The reaction was followed by LCMS. After stirring 12 hours, the cloudy reaction was only 50% complete. The reaction was concentrated under reduced pressure to a thick slurry that was dissolved in DMSO. The product was

purified by prep. HPLC using a20x50 mm Ultro 120 C18 column running a 22 ml/min 3% gradient (AcCN/water, 0.1% TFA) for 16 min. The purified fractions were lyophilized to dryness. The dried powder was dissolved in CH3CN/water(1 :1) (lml) and 1M HC1 (700uL). After heating at 50 C for 75 min. , the reaction mixture was again lyophilized to dryness to produce 7.1 mg of product (2) as a2xHCl salt white powder(-17% yield).

Example-12 : Synthesis ofN- (l- (N-hydroxycarbamoyl) (lS, 2R)-2-hydroxypropyl) [4- (2- phenylethynyl) phenyl] carboxamide
EMI94.1
Preparation of 4-Phenylethynyl-benzoic acid (3)
EMI94.2
ReagentMW EQg/ml mmol Iodo-benzoate 1 262 1.0 20.0 g 76.34 Ethynyl-benzene 2 102 1. 1 8.56 g 83.96PdCl2 (PPh3)2 702 0.012 0.65 g 0.92 Cul 190 0.0240. 35g 1.83

TEA 101 1.516 ml 114.5 d=0.726 THF (dry & sparged with argon for 5 min. ) 110 ml
The 4-iodo-benzoic acid methyl ester 1 (20. 0g, 76.34mmol), ethynyl-benzene 2 (8.56g, 83.96mmol),PdCl2 (PPh3) 2 (0.65g, 0.92mmol), and Cul (0.35g, 1.83mmol) were mixed with THF(110ml) in a round bottom under argon. The dry THF was sparged with dry, oxygen-free argon for at least 5 min. immediately before use. The reaction was cooled to10 C and TEA(16ml) was added.

The cooling bath was removed and the reaction was stirred at RT under argon. After 2.5h, the reaction was diluted with EtOAc (400 ml) and the solids were filtered off through a pad of celite. The organic filtrate was washed with 1M HCl (60ml), sat. aq.NaHCO3(60ml), water(60ml), brine(60ml), dried withNa2S04, filtered and concentrated under reduced pressure. The crude solid methyl ester was dissolved in MeOH(400ml), 6MNaOH(30ml) and water (50ml). The reaction was stirred at70 C until a clear solution was formed (aboutlh). The reaction could be followed by LCMS. The reaction was cooled and diluted with water(500ml) and hexane(100ml). The pH was adjusted to pH 6-7. The white solid that formed was collected and washed with water(3x60ml) and hexane (3x60ml). The solid 3 was driedira vacuo yielding 17.3g (approximately quantitative yield in 99% purity).

Preperation of 3-Hydroxy-2-(4-phenylethynyl-benzoylamino)-butyric acid methyl ester (4)
EMI95.1
Reagent MW EQ g/ml mmol 4-Phenylethynyl-benzoic acid (3) 222 1. 0 1. 55 g 7.0 Threonine methyl esterHCl 169.65 1.4 1. 66 g 9.8 HBTU 380 1.0 2. 66 g 7.0 DIEA 125.28 2.5 3. 05 ml 17.5 DMF 21 ml




A solution of threonine (1.66g, 9. 8mmol) and DIEA (1. 53ml, 8.8mmol) in DMF (10ml) was added to a stirred solution of 4-phenylethynyl-benzoic acid 3 (1. 55g, 7.0mmol) and DIEA (1. 53ml, 8. 8mmol) in DMF (11ml) at rt. After 12 h, the reaction was diluted with EtOAc (300ml) and washed with0. 5M HC1(2x60ml), sat. aq.NaHCO3(60ml), 50% diluted brine(60ml), sat. brine (60ml), dried withNa2S04, filtered and concentrated under reduced pressure. Upon drying in vacuo, 2.34g of white solid was obtained (approximately quantitative yield in 99% purity).

Preperation of N (2-Hydroxy-1-hydroxycarbamoyl-propyl)-4-phenylethynyl-benzamide (5)
EMI96.1

Reagent MW EQ g/ml mmol
Tolanoic-Thr-OMe (4) 340.42 1.0 2.34 g 7.0 H2NOH-HCl 69.49 10.0 4.81 g 70. 0
NaOMe 54.02 > 11.0 > 4.16 g > 77.0
MeOH (dry) 50 ml
DCM (dry) 30 ml
A solution of tolanoic-Thr methyl ester (4) (2.34g, 7. 0mmol) in MeOH (20ml) and DCM (30ml) was added to a cooled (-10 C bath) suspension of hydroxylamine HCl salt (4.81g, 70. 0mmol) and NaOMe (4.16g, 77. 0mmol) in MeOH (30ml). Follow reaction by LCMS. After stirring for 2 hours, the reaction seems to stall at 50% completion. Add an additional 1 equivalent of NaOMe (0.416g). After 3 hours, the reaction was 75% complete. Add an additional 0.5 equivalent of NaOMe (0. 21g). After 4 hours, the reaction was 90% complete. Add an additional 0.15 equivalent of NaOMe (0.064g) for a total of 12.65 equivalentsof NaOMe. The pH of the reaction was between 11-
12 and had reacted about 95% completion. The reaction was diluted with EtOAc(500ml) and washed with sat. aq. NaHCO3(2x60ml), 50% diluted brine(60ml), sat. brine(60ml), dried with Na2SO4, filtered and concentrated under reduced pressure. The residue was dissolved in minimal DMA. The

product was purified by prep. HPLC using a reverse phase Ultro 120 C18 column running a 2% gradient (AcCN/water, 0. 1% TFA). The purified fractions were lyophilized to dryness. The product as the TFA salt was dissolved in AcCN/water (50: 50)(80mol), 1N aq. HC1 (13 equivalent) and lyophilized again to give 1.3 g of white powder in 55% yield and > 97% purity.

Example 13: Synthesis of3- (R)-Amino-2- (S)- (3-phenylethynyl-benzoylamino)-butyl-hydroxamic acid (10) Preparationof 3- (R)-Azido-2- (S)- (3-phenylethynyl-benzoylamino)-butyric acid methyl ester (9).
EMI97.1


The synthesis of compound 4 is described above. The tolanyl compound (9) was made by the same procedures as for compound (6). The product (9) was obtained in 92% yield (952mg).

HPLC(220nm, 41min.run) 32. 64 min.; HPLC(220nm, 17min. run) 15.08 min LCMS: LC(214nm) 3.16 min. , MS (ES+) m/z 363.1(C2oHl8N403 +H requires 363.14).

Preparation of 3-eR)-Amino-2-(S)-(3-phenylethynyl-benzoylamino)-butyl-hydroxamic acid (10)
EMI97.2
Reagent MW Eq. g/ml mmol Ammo-Thr-OMe (9) 362.38 1. 0 726 mg 2.0 PPh3 262. 29 1.0 526 mg 2.0



H2NOH-HCI 69.49 10.0 1.4 g 20.0
NaOMe 54.02 #12.0 1.3 g 24.0
THF (dry) 20 ml
MeOH (dry) 20 ml
Triphenylphosphine (526mg, 2. 0mmol) was added to a stirred solution of tolanyl-azido-Thr methyl ester (9) (726mg, 2. 0mmol) at rt. After 3 days the reaction reached completion as judged by TLC (EtOAc/Hex (2: 1) ) and LCMS. The reaction was concentrated under reduced pressure to give an ivory colored solid. The crude amino-phosphine was dissolved in MeOH(20ml) to give a pale yellow solution. To the solution of amino-phosphine was added sequentially hydroxylamine HCl salt (1.4g, 20.0mmol) followed by fresh solid NaOMe powder (1.3g, 24.0mmol) to make a milky pH 10 suspension. After 36 h, the reaction was complete by LCMS. The reaction was evaporated under reduced pressure to give a yellow solid that was dried in vacuo. The crude product (2.75g) was triturated with ether(3x50ml) to remove impurities (P (O)Ph3) and then was dissolved in abs.EtOH(120ml) with sonication for 15 min.. A fine white powder was suction filtered off, and the clear yellowethanolic portion was concentrated to a small volume. The crude product was dissolved in DMSO(8ml) and purified by preparative HPLC (Ultro 120 C1875x300mm column) running a gradient(AcCN/water, 0.1% TFA) from 5 to 70% for 55 min. The purified fractions were pooled together and lyophilized to dryness. The product as the TFA salt was dissolved inAcCN/water (50: 50) (100ml), IN aq. HC1(1 equivalent) and lyophilized again to give 325 mg of light yellow powder as the HC1 salt (43% yield).

HPLC(220nm, 41min. run) 18.31 min.; HPLC(220nm, 17min. run) 9.11min ; LCMS: LC (214nm) 1.91 min. , MS (ES+) m/z 338.1(CloHIoN303 +H requires 338.14).

Synthesis of 4'-(N-Acylamino)-Tolan Dap Analogs Example 14: Synthesis of 4-({4-[(aminoacetyl) amino] phenyl}ethynyl)-N-[(1S)-1-(aminomethyl)-2-(hydroxyamino)-2-oxoethyl] benzamide
EMI99.1

EMI99.2

EMI99.3

EMI99.4
Preparationof 2-N-Boc-amino-N- (4-iodo-phenyl)-acetamide (2).
EMI99.5


ReagentMW Eq.g/ml mmol Boc-Gly-OH 175.19 1.00 1.752 g 10.04-Iodoaniline(1) 219.03 1.04 2.290 g 10.4

EDCI 191.71 1.04 1. 994 g 10.4 HOBt 135.13 1.00 1.351 g 10.0 DCM18 rnL DMF1 mL
A solution of Boc-Gly-OH (1.752 g, 10.0 mmol) in DCM (18 mL) and DMF (1 mL) was treated with EDCI (1.994 g, 10.4 mmol) and HOBt (1.351 g, 10.0 mmol). After stirring 15 min, 4- iodoaniline 1 (2.290 g, 10.4 mmol) was added and the reaction monitored by TLC (25: 1 DCM/MeOH(Rf= 0.6)). After 24 h the solution was diluted with EtOAc (250mL), washed with 1.0 M HCl (3 x 100 mL), sat.NaHCO3 (3 x 100mL), brine (3 x 100mL), dried overMgS04, filtered and concentrated in vacuo to afford 2.900 g (77% yield) of a white solid.

Preparation of(2S)-3-N-Boc-amino- (4-ethynyl-benzoylamino)-propionic acid methyl ester (4).
EMI100.1


Reagent MW Eq. g/mL mmol 4-Ethynylbenzoic acid (3) 146.14 1.0 0.910 g 6.22 H-Dap (Boc)-OMe-HCl 254.71 1.2 1.903 g 7. 47 EDCI 191.71 1.2 1.432 g 7.47 HOBt 135.13 1. 1 0.910 g 6.73 DIEA 129.25 3.2 3.5 mL 20.0 DMF 50 mL
Triethylamine (3.5 mL, 20.0 mmol) was added to a stirred solution of 4-ethynylbenzoic acid 3 (910 mg, 6.22 mmol), H-Dap (Boc)-OMe hydrochloride (1.903 g, 7.47 mmol), EDCI (1.432 g, 7.47 mmol), and HOBt (910 mg, 6.73 mmol) in DMF (50.0 mL). After stirring 20 h, the reaction mixture was diluted with EtOAc (400 mL), washed with 1.0 M HCl (2 x 100 mL), saturatedNaHCO3 (2 x 100 mL),Ha0 (4 x 100 mL), dried overMgS04, filtered and concentrated in vacuo to give 2.140 g (99% yield) of a tan solid, mp =110-111 C. LRMS (ES+)m/z 346.9(Cl8H22N20s + H requires 347.10).

EMI101.1


To a suspension of methyl(2S)-3- [ (tert-butoxy) carbonylamino]-2- [ (4- ethynylphenyl) carbonylamino] propanoate (4) (200mg, 0. 577 mmol) and2- [ (tert- butoxy)carbonylamino]-N- (4-iodophenyl) acetamide (2) (476 mg, 1.26 mmol) was added Et3N (350, uL, 2.5 mmol). The solution was purged with a stream of N2 for several minutes andPdCl2 (PPh3) 2 (20 mg, 0.028 mmol) and CuI (10.6 mg, 0.055 mmol) were added. The reaction mixture was stirred at ambient temperature for 22 h and then concentrated by rotary evaporation. The crude black residue was chromatographed twice by silica gel chromatography (30: 1CHzClz/MeOH) to give 285 mg (83%) of methyl(2S)-3- [ (tert-butoxy) carbonylamino]-2- ( {4- [2- (4- f 2- [ (tert- butoxy) carbonylamino] acetylamino} phenyl) ethynyl] phenyl} carbonylamino) propanoate (5) as a yellow foam.
EMI101.2


To a solution of hydroxylamine hydrochloride (98 mg, 1.41 mmol) in MeOH (1.3 mL) at 0 C was added 25 wt% NaOMe (460 mg, 2.13 mmol). The solution was stirred at0 C for 15 min and then charged with a solution of methyl(2S)-3-[(tert-butoxy) carbonylamino]-2-({4-[2-(4-{2-[(tert- butoxy) carbonylamino] acetylamino} phenyl) ethynyl] phenyl} carbonylamino) propanoate (4) (279 mg, 0.469 mmol) in THF (1.5 mL) and MeOH (0.6 mL). The reaction was stirred at0 C for 30 min and at room temperature for 2.5 h. The reaction mixture was diluted with 4: 1CHCl3/iPrOH (50 ml) and

washed with 0.1 M HCl (30 mL). The layers were separated and the aqueous layer extracted once more with4 : 1 CHCls/iPrOH (30 ml). The organic layers were combined, dried overNa2SO4, filtered and concentrated. The crude residue was suspended in 10 : 1CH2Cl2/MeOH (4 mL), filtered, and washed with50 : 1 CHzCIz/MeOH (2mL) and Et20 (10 mL) to afford 180 mg(64%) of N- (4- {2- [4- (N-{l-(N-hydroxycarbamoyl) (l S)-2-[(tert-butoxy) carbonylamino] ethyl} carbamoyl) phenyl] ethynyl} phenyl)-2-[(tert-butoxy) carbonylamino] acetamide (6) as a white powder.

To an oven-dried flask containingN- (4- {2- [4- (N- {1- (N-hydroxycarbamoyl) (1S)-2- [ (tert- butoxy) carbonylamino] ethyl} carbamoyl) phenyl] ethynyl}phenyl)-2- [ (tert- butoxy) carbonylamino] acetamide (6) (130 mg, 0.218 mmol) was added 1 :1TFA/CH2C12 (2.5 mL).

The resulting pink solution was stirred for 2 h and concentrated to give a pink gum. The crude residue was rinsed withCH2Cl2 (4mL), concentrated by rotary evaporation and dissolved in THF (2 mL) and
MeOH (0.4mL). A solutionof 4 M HCl in dioxane (200p. L) was added and the resulting precipitate filtered and washed with Et20(10 mL) to afford 90 mg of 4-({4- [ (aminoacetyl) amino] phenyl} ethynyl)-N- [ (lS)-1- (aminomethyl)-2- (hydroxyamino)-2- oxoethyl] benzamide as a pale tan powder.

Reactionof Iodoaniline with Bromoacetyl Bromide
EMI102.1

0
1. Br\J4Br 09 0 benzene, EtsN (1 eq) J
H2N /i \N /i
2. morpholine (excess) H-0-
3 . O O ~-. O o-^,) 0 ON-NH2
H i NH ,
Ho OH
3
Bromoacetyl bromide (1751L, 2.00 mmol) was added dropwise over 5 minutes to a solution of 4-iodoaniline (438 mg, 2.00 mmol) and Et3N(280, ut, 2.00 mmol) in benzene (5mL). The reaction was stirred 1 hour, treated with morpholine (1.0 mL, 11.5 mmol) and stirred overnight. The reaction mixture was diluted with EtOAc (200 mL), washed with aqueous 0.1 M KOH (50 mL),H20 (50 mL), dried overMgS04 and concentrated to give a yellow oil. Purification by silica gel chromatography

(100: 1CH2C12/MeOH) afforded 630 mg (91%)of N- (4-iodophenyl)-2-morpholin-4-ylacetamide as a waxy tan solid. This product was converted to analogues in a similar manner as Examplel Zt.

Example A: Preparation of4- [4- (6-Chloro-pyridin-3-yl)-buta-1, 3-diynyl]-benzoic acid methyl ester.
EMI103.1


Reagent MW EQg/ml mmol H-DAP(Boc)-OMe(1) 254 1.05 5.93 g 23.34-Iodo-benzoic acid 248 1.0 5.49 g 22.2 HOAT 136.1 1.02 3.08 g 22.6 EDC 191.71 1.02 4.33g 22.6 DIEA 129.25 2.5 9.7 ml 55.1 DMF85 ml
DIEA (9.7ml, 55.1mmol) was added to a stirred solution of4-iodo-benzoic acid (5.49g, 22.2mmol), HOAT (3.08g, 22.6mmol), EDC (4.33g, 22. 6mmol) in DMF (85ml). After 2 min. , the HDAP (Boc) -OMe (1) was added in one portion. After 12 hours, the reaction was found complete by LCMS. The reaction was diluted with EtOAc/hexane (1: 1) (500ml). The organic phase was washed with IN HCl(2x80ml), IN NaOH(2x80ml), water(2x80ml), sat. brine (80ml), dried with Na2SO4,

filtered and concentrated under reduced pressure to give crude product. The residue was filtered through a filter plug of silica eluting with EtOAc/hexane (1: 1). The fractions with product were evaporated to give 9.3 g of product(3-tert-Butoxycarbonylamino-2- (4-iodo-benzoylamino)-propionic acid methyl ester) in 93% yield. This product was converted to analogues in a similar manner as the aforementioned Examples.

Example 15 : N- (l- (N-hydroxycarbamoyl) (lS, 2R)-2-hydroxypropyl) (4-12- [4- (morpholin-4- ylmethyl) phenyl] ethynyl} phenyl) carboxamide (5)
EMI104.1
Preparation of (2S, 3R)-2-l4-(4-formyl-phenylethynyl)-benzoylaminol-3-hydroxy-butyrie acid methyl ester (3).
EMI104.2
Reagent MW Eq. g/ml mmol Ethynylbenzene (1) 261.27 1.0 0.745 g 2.85 4-Iodobenzaldehyde (2) 232. 00 1.4 0.902 g 3.89 PdCl2 (PPh3) 2 701.89 0.03 0.070 g 0.10 Cul 190.44 0.06 0.034 g 0. 18 Et3N 101.19 2.3 0. 90 mL 6. 5 THF 50mL

A solution of alkyne 1 (745 mg, 2.85mmol), 4-iodobenzaldehyde 2 (902 mg, 3.89 mmol), and Et3N (9001L, 6.5 mmol) in THF (50mL) was purged with a stream of N2 for two minutes and then treated withPdCl2 (PPh3) 2 (70 mg, 0.10 mmol) and CuI (34 mg, 0.18 mmol). The reaction mixture was stirred 40 h, concentrated by rotary evaporation and purified by silica gel chromatography (40: 1 DCM/MeOH) to give 0.833 g (80% yield) of (2S,3R)-2- [4- (4-formyl-phenylethynyl)-benzoylamind]-3-hydroxy-butyric acid methyl ester 3 as a pale yellow powder, mp = 143-144 C.Rf = 0.3 (25: 1DCM/MeOH) ; LRMS (ES+) m/z 366.1(C2lHlgNOs + H requires 366.13) ; HPLC (300nm, 47 min) 15.3 min.

Preparation of (2S,3R)-3-Hydroxy-2- [4- (4-morpholin-4-ylmethyl-phenylethynyl)-benzoylamino]-butyric acid methyl ester(4).
EMI105.1


Reagent MW Eq.g/ml mmolTolanylaldehyde (3) 365.38 1.0 0.822g 2.25
Morpholine 87.12 1.3 0.260 mL 2.97
NaBH(OAc) 3 211.94 1.4 0.670 g 3.16
THF 15 ml
Sodium triacetoxyborohydride (0.670 g, 3.16 mmol) was added to a solution of benzaldehyde 3 (0.822 g, 2.25 mmol) and morpholine (260 L, 2.97 mmol) in THF(15 mL) under N2 atmosphere and the reaction monitored by TLC (25: 1DCM/MeOH, Rf=0. 2). After stirring 4 h, the reaction mixture was quenched with saturatedNaHCO3 (150 mL), extracted with EtOAc (3 x 100 mL), dried over
MgS04, filtered and concentrated to give a yellow syrup. Purification by silica gel chromatography (35: 1DCM/MeOH) afforded 0.844 g (86% yield) of 4 as a sticky white foam.

Preparation of (2S, 3R)-N-(2-Hydroxy-1-hydroxycarbamoyl-propyl)-4-(4-morpholin-4-ylmethyl- phenylethynyl)-benzamide (5).
EMI106.1


ReagentMW Eq.g/ml mmol Methyl ester (4) 436.501. 0 0.829 g 1.90NHxOH-HCl 69.49 3.0 0.400 g 5.76 NaOMe (25 wt%) 54.02 4.5 1.860 g 8.60 MeOH 8 mL THF 3 mL
Sodiummethoxide (25 wt% in MeOH, 1.860 g, 8.60 mmol) was added to a stirred solution of hydroxylamine hydrochloride (400mg, 5. 76 mmol) in anhydrous MeOH(5 mL) at0 C under N2 atmosphere. After stirring 20 min, a solution of methyl ester 4 (829 mg, 1.90 mmol) in 1: 1MeOH/THF (6 mL) was added and the reaction mixture stirred at 0 C for 1 h and at room temperature for 4 h. The reaction was quenched with 1.0 M HCl (6 mL), concentrated by rotary evaporation to remove organic solvents, and diluted with DMSO (4mL). Analytical RP-HPLC (Cls column, CH3CN gradient 5-35%, 0.1% TFA, W analysis 300mn, 16 min) indicateda purity of 85% for the crude product mixture. Purification by preparative RP-HPLC and lyophilization of the collected fractions gave 701 mg (81%) of 5 asa fluffy white solid. LRMS (ES+) m/z 438.1(C24H27N3Os + H requires 438.20) ; RP-HPLC (300nm, 16 min run) 8.7 min.

Resin Procedures for Synthesizing Tolanyl hydroxamates Example 16: Synthesisof 4-[(4-{[(benzylamino) acetyl] amino} phenyl)ethynyl]-N-{(lS, 2R) -2hydroxy-1-[(hydroxyamino) carbonyl]propyl}benzamide
EMI107.1
-NHFmoc 1. Piperdine OtBu 1. Piperdine
2. HATU N
OtBu p NHFmoc 2. HBTU O zozo
J'OH OH
FmocHN"llff
OtBu
OtBu ~ H O
OtBu ~
H2N 6, N 11
N II, N O
N 0 H H I PdCI2 (PPh3) 2, Cul, Et
CH3CN, 22. h
NHz
OtBu
H 0 zon 'O "\N w I NHz
Lutidinia 0 H - \
Bromo Acylchloride Nt/NMP
N) tl/
H
OtBu . HzN ,"N
4@) H (O 80% TFA/H20 \
YNJk H
0 H
0
N
H
0 H
N
J
N \OH
H 0 H 0
H O
H
1. Coupling to Fmoc hydroxylamine resin
The resin was pre-swelled by adding DCM and shaking for 30min. The resin was drained, 20% piperdine was added in DMF, the resin was shaken 1.25 hours, and finally drained and washed in 2xDMF and 2xDCM. After draining completely, 20% piperdine in DMF was added to attain cleavage

in 1.25 hours. The resin was washed 4xDMF, 4xDCM and drained completely. In a separate flask, the amino acid (Fmoc-Thr tBu-OH, or Fmoc-DAP Boc-OH, 4 eq) was mixed, HATU (4 eq), DMF (60 ml) and Hunig's(8 eq) base were added and stirred for 2-3 min. The mixture was added to the resin and shaken 20-24 hours. Subsequently, the resin was drained and run with a standard wash(lxDCM, 4xDMF and 4xDCM). The Fmoc was removed from the amino acid by adding 20% piperdine in DMF and shaken 1.25 hours, drained, and given the standard wash(lxDCM, 4xDMF and 4xDCM).

2. Coupling of 4-iodobenzoic acid to Amino Acid resin
A mixture of 4-iodobenzoic acid (4 eq), HBTU (4 eq), DMF (60 ml) was shaken for several minutes.Hunig's base (8 eq) was subsequently added and the mixture was shaken further for 2-3 min.

The pre-activated mixture was then added to the prepared Thr or DAP resin (Fmoc removed, 7.5g, 5.775 mmol). The reaction is shaken 12-16 hours followed by the standard wash(IxDCM, 4xDMF and 4xDCM).

3. Alkyne coupling on Resin
To the 4-iodobenzoic resin (4 g, 3.08 mmol) was added4-aminophenylacetylene (3 eq), Pd (PPh3) 2Cl2 (0.04 eq), Cul (0.08 eq) and THF (purged with Argon). After mixing for 1 min. , TEA (4.5 eq) was added and the reaction was shaken 12 hours at RT under argon.

4. Aniline coupling with bromoacetyl chloride on Resin
To aniline resin (4g, 3.08 mmol) was added DCM (30 ml) lutidine (10 eq) and shaken for 1 min. Bromoacetyl chloride (8 eq) in DCM (5 ml) was added slowly. After the addition, the slurry was shaken for 1.5 to 1. 75 hours. Subsequent draining and a wash with 2xDCM, 4xDMF and 4xDCM was then performed.

5. Displacement with amines on Resin
To the bromoacetyl resin (125 mg), was added NMP (1.5 ml) followed by amine (0.2 g or ml, ie excess) and the slurry was shaken for 12-16 hours at RT. To neutralize the salt, TEA was added.

The imidazole was heatedat 38 C for 24 h (in the case of anilines, they were heated at 38 C for 48 h). The reaction mixture was drained and washed 4xDMF and 4xDCM.

6. Cleavage from resin and deprotection of Thr tBu and DAP Boc
The resin (125 mg) was soaked inTFA/water (80: 20 v/v) (1.5 ml) at RT for 45 min. Upon cleavage the solution was collected and the resin was washed with moreTFA/water mixture (0.75 ml).

To theTFA/product solution was added acetonitrile/water solution(1 : 1v/v,10 ml) and pure water (2.5

ml). The mixture was frozen in liquid nitrogenfor-15 min and lyophilized. The dry residue was dissolved in theacetonitrile/water solution (1: 1 v/v, 10ml) again followed by addition of 1M aq. HCl (1.2 eq per basic nitrogen), frozen, and lyophilized to a powder.

Synthesisof 3'-Nitro-Tolan Threonine Hydroxamic Acid Example17 :(1S, 2R)- N- (2-hydroxy-1-hydroxycarbamoyl-propyl)-4- (3-nitro-phenylethynyl)- benzamide
EMI109.1
i. 20% piperidine/DMF o ii-DIC, HOBt, DIEA O
DCM, DMF, 36 h FmocHN NO""/\ O-', I w H N. O zizi
Oh %
2 H 3
EMI109.2

Preparation of(lS,2R)-N-(2-tert-butoxy-1-hydroxycarbamoyl-propyl)-4-ethynyl-benzamide on hydroxylamine 2-chlorotrityl resin (3).

Reagent MW Eq. g/mL mmol
Fmoc-threonine/resin (1) 0. 70mmol/g 1.0 0.522 g 0.365
4-Ethynylbenzoic acid (2) 146.14 3.0 0.160 g 1.10
DIC 126.20 4.9 0.28 mL 1.79
HOBt 135.13 3.0 0.148 g 1.10
DIEA 129.25 6.3 0.40mL 2. 30
DCM 1.0mL DMF 3.0 mL

The resin 1 (0.522 g, 0.365 mmol, 0.70 mmol/g) was swelled in DCM (5 mL) for 2 h and drained. The resin was treated with 20% piperidine in DMF (6 mL) for 1 hour, washed with DMF (4 x
6 mL) and DCM (4 x 6 mL) and drained completely. In a separate flask,4-ethynylbenzoic acid 2 (0.160 g, 1.10mmol), DIC (0.280 mL, 1.79 mmol), HOBt (0.148 g, 1.10 mmol) and DIEA (0.4 mL,
2.30 mmol) were dissolved in DCM(1 mL) and DMF (4 mL), stirred 15 min and added to the resin.

After shaking for 36 h, the mixture was drained, washed with DMF (4 x 6 mL) and DCM (4 x 6 mL) and dried in vacuo to give 0.495 g ofa yellow resin.

Preparation of(1S,2R)-N-(2-hydroxy-1-hydroxycarbamoyl-propyl)-4-(3-nitro-phenylethynyl)- benzamide (5).

Reagent MW Eq.g/mL mmol
Alkyne on resin (3) 0.70 mmol/g 1.0 100 mg 0.070l-Iodo-3-nitrobenzene (4) 249.01 5.0 87.1 mg 0.350PdCl2 (PPh3) 2 701.89 0.2 10.0 mg 0.014
Cul 190.44 0.5 7.0 mg 0.036 Et3N 101.19 15150, uL 1.10
DMF 1.5 mL
Resin 3 (100 mg, 0.070 mmol) was swelled in DCM (2mL) for 1 h and drained. A solution of
1-iodo-3-nitrobenzene 4 (87.1 mg, 0.350 mmol) and Et3N (150p, L, 1.10 mmol) in DMF (1.5 mL) was purged with a stream of N2 bubbles for two minutes and added to the resin. After mixing for 5 min,PdCl2 (PPh3)2(10. 0 mg, 0.014 mmol) and CuI (7.0 mg, 0.036 mmol) were added and the mixture shaken for 26 h. The resin was drained, washed with DMF (3 x 2mL), DCM (3 x 2 mL) and cleaved with 10% TFA/DCM (1.5 mL) for 20 min. The solution was collected and the resin was rinsed with additional 10% TFA/DCM (1.0 mL). The cleavage fractions were combined, treated with neat TFA (2.0 mL), stirred for 1 h at rt and concentrated by rotary evaporation to give a crude brown residue.

Purification byRP-HPLC(Cl8 column,CH3CN gradient 5-65%, 0.1% TFA, UV analysis 300nm, 28 min) and lyophilization of the collected fractions afforded 6.0 mg (22% yield) of(1S,2R)- N- (2-hydroxy-l-hydroxycarbamoyl-propyl)-4- (3-nitro-phenylethynyl)-benzamide as a white foam. LRMS (ES+)m/z 384.2(Cl9Hl7N306 + H requires 384.15) ; RP-HPLC (300 nm, 28 min run) 15.2 min.

Synthesis of4'-Trifluoromethoxy-Tolan Dap Hydroxamic AcidExample 18 : (1S)-N-(2-amino-1-hydroxycarbamoyl-ethyl)-4-(4-trifluoromethoxy- phenylethynyl) -benzamide (5)
EMI111.1

NHBoc i. 20% piperidine/DMF NHBoc ,) NrtDOC..

H ii. DIC, HOBT, DIEA H
N,, DCM, DMF, 36 h NJN'OQ FmocHN O I i H 0 \==/OH" ou
2
EMI111.2
Preparation of (lS)-N-(2-(Boc)-amino-l-hydroxycarbamoyl-ethyl)-4-ethynyl-benz-amide on hydroxylamine2-chlorotrityl resin (3).

Reagent MW Eq.g/mL mmol Fmoc-Dap/resin(1) 0.70 mmol/g 1.0 1.330 g 0.9314-Ethynylbenzoic acid (2) 146.14 3.0 0.408 g 2.793 DIC 126.20 4.8 0.70 mL 4.470 HOBt 135.13 3.0 0.377 g 2.793 DIEA 129.25 6.2 1. 0 mL 5.7 DCM 10. 0 mL DMF 2. 0 mL
The resin 1 (1.330 g, 0.931 mmol, 0.70 mmol/g) was swelled in DCM (15 mL) for 2h and drained. The resin was treated with 20% piperidine in DMF (20 mL) for 1 hour, washed with DMF (3 x 15 mL) and DCM (3 x 15 mL) and drained completely. In a separate flask, 4-ethynylbenzoic acid 2 (0.408 g, 2.793 mmol), DIC (0.70 mL, 4.470mmol), HOBt (0.377 g, 2.793 mmol) and DIEA (1.0 mL,

5.7 mmol) were dissolved in DCM (10 mL) and DMF (2 mL), stirred 15 min and added to the resin.

After shaking for 36 h, the mixture was drained, washed with DMF (3 x 15 mL) and DCM (3 x 15mL) and dried in vacuo to give 1.290 g of a yellow resin.

Preparation of(lS)-N-(2-amino-1-hydroxycarbamoyl-ethyl)-4-(4-trifluoromethoxy- phenylethynyl)-benzamide (5).

Reagent MW Eq.g/mL mmol
Alkyne on resin (3) 0.70 mmol/g 1.0 120 mg 0.084
4-CF30-iodobenzene (4) 287.99 4.0 96.8 mg 0.336- PdCl2 (PPh3) 2 701. 89. 0. 3 18.0 mg 0.025
Cul 190.44 0.5 8.0 mg 0.042
Et3N 101. 19 13150LL 1.10
DMF 2.0 mL
Resin 3 (120 mg, 0.084 mmol) was swelled in DCM (2 mL) for 1 h and drained. A solution of
4-(trifluoromethoxy)iodobenzene 4 (96.8 mg, 0.336 mmol) and Et3N (150 L, 1.10 mmol) in DMF (2.0 mL) was purged with a stream of N2 bubbles for two minutes and added to the resin. After mixing for 5 min,PdCl2 (PPh3) 2 (18.0 mg, 0.025 mmol) and CuI (8.0 mg, 0.042 mmol) were added and the mixture shaken for 24 h.. The resin was drained, washed with DMF (3 x 2 mL), DCM(3 x 2 mL) and cleaved with 10% TFA/DCM (2.0 mL) for 20 min. The solution was collected and the resin was rinsed with additional 10% TFA/DCM (1.0 mL). The cleavage fractions were combined, treated with neat TFA (3.0mL), stirred for 1 h at rt and concentrated by rotary evaporation to give a crude brown residue. Purification byRP-HPLC(Ci8 column, CH3CN gradient 5-55%, 0.1% TFA, UV analysis 300 nm, 28 min) and lyophilization of the collected fractions afforded 9.0 mg (25% yield) of(1S)-N- (2-amino-l-hydroxycarbamoyl-ethyl)-4- (4-trifluoromethoxy-phenylethynyl)-benzamide as a white solid.

LRMS (ES+)m/z 408.0(ClgHl6F3N304 + H requires 408. 11); RP-HPLC (300nm, 28 min run) 18.0 min.

Example 19: Synthesis ofN- (l- (N-hydroxycarbamoyl) (lS, 2R)-2-hydroxypropyl) [4- (4- phenylbuta-1, 3-diynyl) phenyl] carboxamide

EMI113.1
ReagentMW EQg/ml mmolDibromovinylbenzoic acid (2) 320 1.0 5.76 g18. 0 Ethynyl-benzene 102 1.4 2.57 g 25.2 Pd2dba3 915 0.01164 mg 0.18(1% cat. ) TMPP 352 0.04 253 mg 0.72 (4%) TEA 101 3.0 7. 5 ml 54.0 DMF 60 ml degassed with argon The4- (2, 2-Dibromo-vinyl)-benzoic acid methyl ester (2) was made by the method of Wang Shen and Le Wang in J. Org. Chem. 1999, 64, 8873-8879.

A solution of 4-(2,2-dibromo-vinyl)-benzoic acid methyl ester (2) (5.76g, 18.0mmol), ethynylbenzene (2.57g, 25.2mmol), Pd2dba3 (164mg, 0. 18mmol), tris (4-methoxyphenyl) phosphine(TMPP) (253mg, 0. 72mmol) were dissolved in argon sparged(5 min. ) DMF (60ml). The reaction was sparged

with argon for 1 min. TEA (7.5ml, 54.0mmol) was added to the stirred reaction mixture that was then heated under argon at85 C for 3.5 hours. The reaction was found complete by LCMS. The reaction was cooled to rt and diluted with EtOAc/hexane (1: 1)(300ml). The organic phase was washed with
1MHC1(2x50m1), 1M NaOH(3x50ml), water(2x50ml), sat. brine(50ml), dried withNa2S04, filtered and concentrated under reduced pressure to obtain 5.25g of crude product as an oil. The oil was treated with approximately 20 ml of a solution of 20%EtOAc/hexane that was heated to dissolve the residue. The walls of the flask were washed with the 20% EtOAc/hexane solution (5ml) that upon cooling gave 1.45g-of pure product (31% yield) as a white solid. Thebalence of the crude reaction product was purified by flash chromatography using EtOAc (8%) /hexane as eluant. The pure fractions were evaporated and dried in vacuo to give addition product typically 25-30% addition yield.

4- (4-Phenyl-buta-1, 3-diynyl) -benzoic acid methyl ester (4) was made according to the method of
Wang Shen and Sheela A. Thomas in Org. Lett. 2000,2 (18), 2857-2860.

Preparationof 4- (4-Phenyl-buta-1, 3-diynyl)-benzoic acid (5)
A 3Maq. solution ofNaOH(20ml) was added to a stirred solution of methyl ester 4 (1.45g,
5.6mmol) in MeOH (100ml) at rt. The reaction solution was heated to reflux for 45 min. until the reaction turned clear. All of the starting material was gone by TLC and HPLC. The reaction was cooled to rt and some MeOH(-50ml) was removed by evaporation under reduced pressure. Water (100ml) was added to the mixture. Conc.HC1 was added dropwise to the stirred solution until acidic by pH paper (pH2). The white precipitate that formed was collected by suction filtration. The solid was washed with water(3x20ml) and hexane(2x20ml) to give after drying 1.35 g of product acid 5 in
99% yield.

Subsequent conversion of compound 5 to compound 7 was performed according to the method described in Example 12 for the synthesis ofN (2-Hydroxy-l-hydroxycarbamoyl-propyl)-4- phenylethynyl-benzamide (compound 5). LCMS MH+ 363.13.

Example B: Synthesis ofN- [ (lS)-l- (aminomethyl)-2- (hydroxyamino)-2-oxoethyI]-4- [4- (4- aminophenyl)buta-1, 3-diynyl] benzamide

Preparation of2- {4- [4- (4-Amino-phenyl)-buta-1, 3-diynyl]-benzoylamino}-3-tert- butoxycarbonylamino-propionic acid methyl ester (2).
EMI115.1


Reagent MW EQg/ml mmol H-DAP (Boc) -OMe 2541. 05 5.12 g 20.11,3-diynyl benzoic acid (1) 261. 3. 1.0 5.0 g 19.1 HOBT 135.1 1.05 2.72 g 20.1 EDC 191.71 1.05 3. 85 g 20.1 DIEA 129.25 3.0 10. 5 ml 60.3 DMF80 ml
DIEA(10.5ml, 60.3mmol) was added to a stirred solution of 4- [4- (4-Amino-phenyl)-buta-1, 3- diynyl] -benzoic acid (1)(5. 0g,19.1mmol), HOBT (2.72g, 20.1mmol), EDC (3.85g, 20.1mmol) in DMF (80ml). After 2 min., the H-DAP(Boc)-OMe was added in one portion. After 12 hours at rt, the reaction was found complete by LCMS. The reaction was diluted withEtOAc/hexane (4: 1)(500ml).

The organic phase was washed with 1NNaOH(2x80ml), water(2x80ml), sat. brine(80ml), dried withNa2S04, filtered and concentrated under reduced pressure to give crude product. The residue was filtered through a filter plug of silica eluting withEtOAc/hexane (4: 1). The fractions with product were evaporated to give 8.02 g of product in 91% yield.

Subsequent conversion of compound 2 to the final hydroxamic acid (for example, Example 892) was performed according to the method described in Example 12 for the synthesisof N-(2-Hydroxy-l- hydroxycarbamoyl-propyl)-4-phenylethynyl-benzamide (compound 5).

Synthesis of 4- (Buta-1, 3-diynyl) -benzoic Acid (4) for making 1,3-diynyl analogues (such as Example 20 below)
EMI116.1
Preparationof 4- (4-trimethylsilanyl-buta-1, 3-diynyl)-benzoic acid methyl ester (3).
EMI116.2


ReagentMW Eq.g/ml mmolMethyl 4-iodobenzoate (2) 262.04 1.0 4.5long 17.2Trimethylsilylbutadiyne(1) 122.24 2.5 5. 240 g 42.8PdCl2 (PPh3)2 701.89 0.04 0.483 g 0.690 Cul 190.44 0.08 0.262 g 1.37 Et3N 101.19 3.0 7. 2 mL 52.0CH3CN 50mL
A solution of methyl 4-iodobenzoate 2 (4.510 g, 17.2mmol),PdCl2 (PPh3)2 (483 mg, 0.690mmol), and CuI (262 mg, 1.37 mmol) inCH3CN (50 mL) was cooled to0 C under N2 atmosphere in the absence of light. Triethylamine (7.2mL, 52.0 mmol) was added, followed by trimethylsilyl-1,3butadiyne 1 (5.240 g, 42.8 mmol) and the reaction stirred 3 h at 0 C and 30 h at ambient temperature.

Removal of solvent by rotary evaporation afforded a crude black residue that was purified by silica gel chromatography (95: 5 hexanes/EtOAc) to give 3.450 g (79% yield)of 4- (4-trimethylsilanyl-buta-1, 3-diynyl)-benzoic acid methyl ester 3 as a brown solid, mp =67-68 C, Preparation of 4-(buta-1, 3-diynyl) -benzoic acid (4).
EMI117.1


Reagent MW Eq.g/ml mmol Methyl ester (3) 252.34 1.0 3.420 g 13.5 KOH 56.11 4.9 3.700 g 65.9H2010 mL THF 26 mL
Potassium hydroxide (3.700 g, 65.9 mmol) was dissolved inHa0 (10 mL) and added to a solutionof 4- (4-trimethylsilanyl-buta-1, 3-diynyl)-benzoic acid methyl ester 3 (3.420 g, 13.5 mmol) in THF (26 mL) in the absence of light. After stirring 16 h, the reaction was quenched with 1.0 M HC1 (120 mL) and the resulting precipitate was filtered, washed with 1: 1hexanes/benzene (150 mL) and dried in vacuo to afford 2.100 g (91% yield, 98% pure) of 4-(buta-1,3 diynyl)-benzoic acid 4 as a brown solid, mp > 230 C. Although diyne 4 was found to be unstable at room temperature it could be stored for several weeks at 0 C with only small amounts of decomposition observed by TLC. Rf = 0.2 (4: 1Hexanes/EtOAc) ; HPLC (300nm, 28 min run) 16.0 min; LRMS (ES+) m/z 171.0(CsIH602 + H requires 171.04).

Synthesis of a3'-Nitrophenyl-Diacetylenic-Dap Hydroxamic Acid Example 20:N- (l- (N-hydroxycarbamoyl) (lS)-2-aminoethyl) {4- [4- (3-nitrophenyl) buta-1, 3- diynyl] phenyl} carboxamide (6)

EMI118.1
i. 20% piperidine/DMF/H FmocHN H, ii. Fmoc-Dap (Boc)-OH FmocHN N'O
1 HATU, DIEA, DMF 2t o
1 2 i. 20% piperidine/DMF 0 NHBoc
H ii. EDCI, HOBt, DIEA
DCM, DMF, 36 h N N10
H 0
O/
3 H
NH2
NU2 oh H
0 2
02N 6
PdCI2 (PPh3) 2, Cul \/6
Et3N, DMF, rt, 36 h i
TFA, DCM
NO2 Preparation of Fmoc-Dap (Boc)-NHOH on hydroxylamine 2-chlorotrityl resin(2).
EMI118.2


NHBoc i. 20% piperidine/DMF H FmocHN'
O ii. Fmoc-Dap (Boc)-OH FmocHN N'O
HATU, DIEA, DMF 2 oReagent MW Eq. g/mL mmol
Hydroxylamine resin(1) 0. 77among 1.0 3.288 g 2.53
Fmoc-Dap (Boc) -OH 426.47 3.0 3.175 g 7.44
HATU 380.25 3.0 2.829g 7.44
DIEA 129.25 10.0 4.3 mL 24.7
DMF35 mL
A suspension of N-Fmoc-hydroxylamine 2-chlorotrityl resin (3.288 g, 2.53 mmol, 0.77mmoUg, Novabiochem) in DCM (40 mL) was shaken for 2 h and drained. The resin was treated with

20% piperidinein DMF (40mL) for 1 hour, washed with DMF (2. x 40mL), treated a second time with 20% piperidine in DMF (40 mL), washed with DMF (3 x 40 mL) and DCM(3x 40 mL) and drained completely. In a separate flask, Fmoc-Dap(Boc)-OH (3.175 g, 7.44mmol), HATU (2.829 g, 7.44 mmol) and DIEA (4.3mL, 24.7 mmol) were dissolved in DMF (35 mL), stirred three minutes and added to the resin. After shaking for 48 h, the mixture was drained, washed with DMF (4 x 40 mL) and DCM (4 x 40 mL) and dried in vacuo to give 3.530 g of a yellow resin.

Preparation of(S)-N- (2-N-Fmoc-amino-l-hydroxycarbamoyl-ethyl)-4-buta-1, 3-diynyl- benzamide on hydroxylamine 2-chlorotrityl resin (4).
EMI119.1
i. 20% piperidine/DMF NHBoc
NHBoc ii. EDCI, HOBt, DIEA O H
DCM, DMF, 36 h N'
N FmocHN. N' \H O
3 H zizi
Reagent MW Eq. g/mL mmol
Fmoc-Dap (Boc)/resin (2) 0.71 mmol/g 1.0 3.530 g 2.53
Butadiynyl benzoic acid (3) 170.16 2.5 1.076 g 6.32
EDCI 191.71 3.0 1.457 g 7.60
HOBt 135.13 3.0 1. 048g 7.75
DIEA 129.25 5.0 2.2 mL 12. 6
DCM 25 mL
DMF5 mL
The resin 2 (3.530 g, 2.53 mmol, 0.71 mmol/g) was swelled in DCM (40 mL) for 2 h and drained. The resin was treated with 20% piperidine in DMF (40 mL) for 1 hour, washed with DMF (4 x40 mL) and DCM (4 x 40 mL) and drained completely. In a separate flask,4-buta-1, 3-diynyl- benzoic acid 3 (1.076 g, 6.32 mmol), EDCI (1.457 g, 7.60mmol), HOBt (1.048 g, 7.75 mmol) and
DIEA (2.2 mL, 12.6 mmol) were dissolved in DCM (25 mL) and DMF (5mL), stirred 45 min and added to the resin. After shaking for 48 h, the mixture was drained, washed with DMF (4 x 40 mL) and DCM (4 x 40 mL) and dried in vacuo to give 3. 35g of a pale brown resin.

Preparation of (S)-N- (2-amino-1-hydroxycarbamoyl-ethyl)-4- [4- (3-nitro-phenyl)-buta-1, 3- diynyl]-benzamide (6).
EMI120.1


BOC NEZ
ON 1
H > i. I 5 NNHOH
NN\O I i H O
Av O PdCI2 (PPh3) 2, Cul // Et3N, DMF, rt, 36 h ii. TFA, DCM
NOz
Reagent MW Eq.g/mL mmol
Diacetylene on resin (4) 0. 77 mmol/g 1.0 176 mg 0.135
1-Iodo-3-nitrobenzene (5)249. 01 3.5 118 mg 0.474PdCI2 (PPh3)2701 : 89 0.07 6.0 mg 0.009
Cul 190.44 0.38 10.0 mg 0.052
Et3N 101.19 10.6200 LL 1.43
DMF 3.0 niL
Resin 4 (176mg, 0.135 mmol) was swelled in DCM (3 mL) for 1h and drained. A solution of1-iodo-3-nitrobenzene 5 (118 mg, 0.474 mmol) and Et3N (200 L, 1.43 mmol) in DMF (3.0 mL) was purged with a stream of N2 bubbles for two minutes and added to the resin. After mixing for 5 min,PdCl2 (PPh3)2 (6.0 mg, 0.009mmol)'and CuI (10.0 mg, 0.052 mmol) were added and the mixture shaken for 36 h. The resin was drained, washed with DMF(4 # 3 mL), DCM (4 x 3 mL) and cleaved with 10% TFA/DCM (2 mL) for 20 min. The solution was collected and the resin was rinsed with additional 10% TFA/DCM (2 mL). The cleavage fractions were combined, treated with neat TFA (4.0 mL), stirred for 1 h at rt and concentrated by rotary evaporation to give a crude brown residue.

Purification byRP-HPLC(C1$ column, CH3CN gradient5-65%, 0.1% TFA, UV analysis 300nm, 30 min) and lyophilization of the collected fractions afforded 12.0 mg (22%) of 470 as a white solid.

LRMS (ES+) m/z392. 9(C2oHi6N405 + H requires 393.11) ; RP-HPLC (300nm, 30 min run) 14.9 min.

Synthesis of4'-Benzamide Diacetylene Dap Hydroxamic Acid Example 21:N- ( (2S)-amino-1-hydroxycarbamoyl-ethyl)-4- {4- [4- (2-amino-ethylcarbamoyl)- phenyl]-buta-1, 3-diynyl} -benzamide (3)
EMI121.1
Preparation of N- ( (2S)-amino-l-hydroxycarbamoyl-ethyl)-4-14- [4- (2-amino-ethylearbamoyl)- phenyl]-buta-1, 3-diynyl}-benzamide (3)
Reagent MW Eq. g/mL mmol
Alkyne on resin (1) 0. 77mmol/g 1.0 145 mg 0.111
4-Ethynylbenzamide (2) 430.54 2.6 124 mg 0.288
PdCl2 (PPh3)2 701.89 0.321 mg 0.030
Cul 190.44 1.022 mg 0.110
Et3N 101.19 6. 5 100 L 0.72
DMF 2.0mL
Resin 1 (145 mg, 0.111 mmol) was swelled in DCM (2mL) for 1 h and drained. A solution of
4-ethynylbenzamide 2 (124mg, 0.288 mmol) and Et3N (1001L, 0.72 mmol) in DMF (2.0 mL) was added and the resin agitated for 5 min. A mixtureof PdCl2 (PPh3)2 (21 mg, 0.030 mmol) and CuI (22 mg, 0.110 mmol) was added and the resin was agitated for 60 h. The resin was drained, washed with
DMF (3 x 2 mL), DCM(3 x 2 mL) and cleaved with 10%TFA/DCM (1.5mL) for 20 min. The solution was collected and the resin was rinsed with additional 10% TFA/DCM (1.0 mL). The cleavage fractions were combined, treated with neat TFA (2 : 0 mL), stirred for 1 h at rt and concentrated by rotary evaporation to give a crude brown residue. Purification by RP-HPLC(Cl8 column,CH3CN gradient5-55%, 0. 1% TFA, UV analysis 300nm, 26 min) and lyophilization of the collected fractions afforded 2.6 mg (5% yield) of N-((2S)-amino-1-hydroxycarbamoyl-ethyl)-4-{4-[4-

(2-amino-ethylcarbamoyl)-phenyl]-buta-1,3-diynyl}-benzamide. LRMS (ES+) m/z 434.0(C23H23N504 + H requires 434.19) ; RP-HPLC (300 nm,26 min run) 15.3 min.

Synthesisof N- [4-Butadiynyl-benzoyl]-Thr (tBu) on Resin (Continued to make Examples 22 and 23)
EMI122.1
i. 20% piperidine/DMF FmocHN., Fmoc-Thr (OtBu)-OH FmocHN$fNsos 2
HATU, DIEA, DMF O i. 20% piperidine/DMF O O ii. EDCI, HOBt, DIEA JLXX N
DCM, DMF, 36 h i H O
0
H 3 H
3
3 Preparation of (2S,3R)-2-N-Fmoc-amino-3-tert-butoxy-N-hydroxy-butyramide on hydroxylamine 2-chlorotrityl resin(2).
EMI122.2
i. 20% piperidine/DMF 9 FmocHN,, Fmoc-Thr (OtBu)-OH FmocHN NO
I HATU, DIEA, DMF . Reagent MW Eq.g/mL mmol Hydroxylamine resin (1) 0.77 mmoUg 1.0 3. 188 g 2.45Fmoc-Thr (tBu)-OH 397.50 3. 0 2.927 g 7.36 HATU 380.25 3.0 2.798 g 7.36 DIEA 129.25 10.0 4.3mL 24.6 DMF 40 mL

A suspension of N-Fmoc-hydroxylamine 2-chlorotrityl resin (3.188 g, 2.45 mmol, 0.77'mmol/g, Novabiochem) in DCM (40 mL) was shaken for 2 h and drained. The resin was treated with 20% piperidine in DMF (40 mL) for 1 hour, washed with DMF (2 x 40 mL), treated a second time with 20% piperidine in DMF (40 mL), washed with DMF (3 x 40 mL) and DCM (3 x40 mL) and drained completely. In a separate flask, Fmoc-Thr (tBu) -OH (2.927 g, 7.36 mmol), HATU (2.798 g, 7.36 mmol) and DIEA (4.3 mL, 24.6 mmol) were dissolved in DMF (40 mL), stirred three minutes and added to the resin. After shaking for 24 h, the mixture was drained, washed with DMF (4 x 40mL) and DCM (4 x 40 mL) and dried in vacuo to give 3.500 g of a yellow resin.

Preparation of4-buta-1,3-diynyl-N- (2-tert-butoxy-l-hydroxycarbamoyl-propyl)-benzamide on hydroxylamine 2-chlorotrityl resin (4).
EMI123.1
i. 20% piperidine/DMF ii. EDCI, HOBT, DIEA 0 H
H DCM, DMF, 36 h FmocHN Np' \ N /\ O s H O
2 1-1 4 oh/. 4
HReagent MW Eq.g/mL mmolFmoc-threonine/resin (2) 0.77 mmol/g 1.0 2.030 g 1.56
Butadiynyl benzoic acid (3) 170.16. 2.3 0.617 g 3.63
EDCI 191.71 2.8 0. 834 g 4.35
HOBt 135.13 2.8 0.588 g 4.35
DIEA 129.25 3.7 1. 0 mL 5.7
DCM.15 mL
DMF4 mL
The resin 2 (2.030 g, 1.56 mmol, 0.77mmol/g) was swelled in DCM (20 mL) for 2 h and drained. The resin was treated with 20% piperidine in DMF (20 mL) for 1 hour, washed with DMF (4x 20 mL) and DCM (4 x 20 mL) and drained completely. In a separate flask,4-buta-1, 3-diynyl- benzoic acid 3 (0.617 g, 3.63mmol), EDCI (0.834 g, 4.35mmol), HOBt (0.588 g, 4.35 mmol) and
DIEA (1.0 mL, 5.7 mmol) were dissolved in DCM (15 mL) and DMF (4 mL), stirred 45 min and

dded to the resin. After shaking for 36 h, the mixture was drained, washed with DMF (4 x 20 mL) and DCM (4 x 20 mL) and driediii vacuo to give 1.900 g of a pale brown resin.

Synthesis of Diacetylenic Threonine Hydroxamic Acids Example 22: (2S,3R)-4- [4- (3-aminomethyl-phenyl)-buta-1, 3-diynyl]-N- (2-hydroxy-1- hydroxycarbamoyl-propyl) -benzamide (3).
EMI124.1


Reagent MW Eq.g/mL mmol
Diacetylene on resin (1) 0. 77mmol/g 1.0100 mg 0.0773-Iodobenzylamine HCI (2) 269.51 4.0 83.0 mg 0.308
PdCI2 (PPh3)2 701.89 0.2 11. 0 mg 0.016
Cul 190.44 0.5 7.0mg, 0.037
Et3N 101.19 23 250liL 1.80 DMF 1.5mL
Resin 1 (obtained from previous synthesis) (100mg, 0. 077 mmol) was swelled in DCM (2 mL) for 1 h and drained. A solution of 3-iodobenzylamine hydrochloride 2 (83.0 mg, 0.308 mmol) and
Et3N (250uL, 1.80 mmol) in DMF (1.5 mL) was purged with a stream of N2 bubbles for two minutes and added to the resin. After mixing for 5 min,PdCl2(PPh3) 2(11. 0 mg, 0.016 mmol) and CuI (7.0 mg,
0.037 mmol) were added and the mixture shaken for 36 h. The resin was drained, washed with DMF(4 x 2 mL), DCM(4 x 2 mL) and cleaved with 10% TFA/DCM (1.5 mL) for 20 min. The solution was collected and the resin was rinsed with additional 10% TFA/DCM (1.5mL). The cleavage fractions were combined, treated with neat TFA (3.0 mL), stirred for 1 h at rt and concentrated by rotary evaporation to give a crude brown residue. Purification by RP-HPLC (Cis column, CH3CN gradient 5-65%, 0.1% TFA, UV analysis 300nm, 28 min) and lyophilization of the collected fractions afforded 4.3 mg (14%) of(2S, 3R)-4- [4- (3-aminomethyl-phenyl)-buta-l, 3-diynyl]-N- (2-hydroxy-l-

hydroxycarbamoyl-propyl)-benzamide as a white solid. LRMS (ES+) m/z 392.0(C22H2tN304 + H requires 392.15) ; RP-HPLC (300nm, 28 min run) 10.0 min.

Synthesis of Diacetylenic Benzylamine Analogues Example 23:(IS,2R)-N-2-hydroxy-1-hydroxycarbamoyl-propyl)-4- [4- (4-morpholin-4-ylmethyl-phenyl)-buta-1, 3-diynyl]-benzamide (4)
EMI125.1
Preparation of threonine diacetylenic benzaldehyde on resin (3).
EMI125.2


Reagent MW Eq.g/mL mmol
Diacetylene on resin (1) 0.77 mmol/g 1.0 1. 00 g 0.770
4-Iodobenzaldehyde 232.00 4.0 715 mg 3.081 PdCl2 (PPh3)2 701.89 0.07 40.0 mg 0.057
Cul 190.44 0.1319. 0 mg 0.100
Et3N 101.19 9.3 1.00 mL 7.17
DMF 20.0 mL

Resin1 (1.00 g, 0.77 mmol) was pre-swelled in DCM (25 mL) for 14 h and drained. A solution of 4-iodobenzaldehyde 2 (715 mg, 3.08 mmol) and Et3N (1.00 mL, 7.17 mmol) in DMF (20 mL) was purged with N2 for two minutes and added to the resin. After mixing for 5 min,PdCl2(PPh3) 2 (40.0 mg, 0.057 mmol) and CuI (19.0 mg, 0.100 mmol) were added and the reaction shaken for 48 h. The resin was drained, washed with DMF (4 x 20 mL), DCM (4 x 20 mL) and dried in vacuo to give 1.100 g of a dark yellow resin.

Preparation of (1S, 2R)-N-2-hydroxy-1-hydroxycarbamoyl-propyl)-4- [4- (4-morpholin-4ylmethyl-phenyl)-buta-1, 3-diynyl]-benzamide (4).
EMI126.1


Reagent MWEq. mg/ l mmolBenzaldehyde on resin (3) 0. 77 mmol/g 1.0 188 mg 0.141 Morpholine 87.12 6.075, uL 0.860NaCNBH3 62.84 4.5 40 mg 0.637Trimethyl orthoformate 106.12 6.5100 4L 0.914 Acetic acid 60.0512 : 3 100 L 1. 750
THF 3.0 mLMeOH 1. 0 mL
A solution of morpholine (75 L, 0.860 mmol) and trimethyl orthoformate (100juL, 0. 914 mmol) in THF (3.0 mL) was added to a Teflon-lined screw-capped vial containing the resin-bound diacetylenic benzaldehyde 3. The resin was agitated for 10 min, treated successively with acetic acid (100 L, 1.75 mmol) and a solution of NaCNBH3 (40.0 mg, 0.637 mmol) in MeOH (1.0 mL) and shaken for 44 h. The resin was filtered, washed with DMF(3 x 3 mL) and DCM (3 x 3 mL) and drained. Cleavage from the resin was achieved by treatment with 10% TFA/DCM (2.0 mL) and shaking 20 min. The solution was collected and the resin was rinsed with additional 10%TFA/DCM

(2.0 mL). The cleavage fractions were combined, treated with neat TFA (3.0 mL), stirred for 1 h at rt and concentrated by rotary evaporation to give a crude yellow residue. Purification by RP-HPLC(C18 column,CH3CN gradient 5-35%, 0.1% TFA, UV analysis 300nm, 18 min) and lyophilization of the collected fractions afforded 19.0 mg (29%) of 472 as a fluffy yellow. solid. LRMS(ES+)inlz 462.0(C26H27N30s + H requires 462.10) ; HPLC (300nm, 18 min run) 10.3 min.

Synthesis of4'-Benzamide Diacetylene Threonine Hydroxamic Acid Example 24 : (1S,2R)-N- (2-hydroxy-1-hydroxycarbamoyl-propyl)-4- {4- [4- (2-amino-ethylcarbamoyl)-phenyl]-buta-1, 3-diynyl3-benzamide (5)
EMI127.1
Preparationof N- (2-trityl-amino-ethyl)-4-ethynyl-benzamide (3).

Reagent MW Eq.g/mL mmol 4-Ethynylbenzoic acid (1) 146: 14 1.0 0.292 g 2.00 N-Trityl ethylenediamine 302.41 1.3 0.810 g 2.67 EDCI 191.71 1.0 0.382 g 2.00 HOBt 135.13 3.0 0.270 g 2.00 DIEA 129.25 4.0 1.40 mL 8.00 DMF. 10.0mL

To a solution of 4-ethynylbenzoic acid 1 (292 mg, 2.00 mmol), EDCI (382 mg, 2.00mmol), and HOBt (270 mg, 2.00 mmol) in DMF (10 mL) was added N-trityl ethylenediamine 2 (810 mg, 2.67 mmol) and DIEA (1.4 mL, 8.0 mmol). The reaction mixture was stirred 24 h, diluted with EtOAc (200mL), washed with 0.5 M HCl (60 mL), saturated NaHCO3 (2 x 60 mL), H20 (4 x 60 mL), dried overMgS04 and concentrated to give 836 mg (97% yield) of N-(2-trityl-amino-ethyl)-4-ethynyl-benzamide
3 as a white solid, mp 50-51 C. Rf = 0.40(1 :1Hexanes/EtOAc).

Preparation of (lS,2R)-N- (2-hydroxy-1-hydroxycarbamoyl-propyl)-4- {4- [4- (2-amino- ethylcarbamoyl)-phenyl]-buta-1,3-diynyl}-benzamide (5).

Reagent MW Eq. g/mL mmol
Alkyne on resin (4) 0.77 mmol/g 1.00 150 mg 0.116
4-Ethynylbenzamide (3) 430.54 3.00 151 mg 0.350PdCl2 (PPh3)2701. 89 0.25 21 mg 0.030
Cul 190.44 1.25 28 mg 0.147
Et3N 101.19 9.50 1501L 1.10
DMF 2.0mL
Resin 4 (150 mg, 0.116 mmol) was swelled in DCM (2 mL) for 1h and drained. A solution of4-ethynylbenzamide 3 (151 mg, 0.350 mmol) and Et3N (150uL, 1.10 mmol) in DMF (2.0mL) was added and the resin agitated for 5 min. A mixtureof PdCl2 (PPh3) 2 (21 mg, 0.030 mmol) and Cul (28 mg, 0.147 mmol) was added and the resin was agitated for 60 h. The resin was drained, washed with
DMF(3 x 2 mL), DCM (3 x 2 mL) and cleaved with 10% TFA/DCM (1.5mL) for 20 min. The solution was collected and the resin was rinsed with additional 10%TFA/DCM (1.0 mL). The cleavage fractions were combined, treated with neat TFA (2.0 mL), stirred for 1 h at rt and concentrated by rotary evaporation to give a crude brown residue. Purification by RP-HPLC (Cl8 column, CH3CN gradient 5-65%, 0.1% TFA, UV analysis 300nm, 26 min) and lyophilization of the collected fractions afforded 2.0 mg (4% yield) of(lS,2R)-N-(2-hydroxy-1-hydroxycarbamoyl-propyl),4-f 4- [4- (2-amino-ethylcarbamoyl)-phenyl]-buta-1, 3-diynyl}-benzamide. LRMS (ES+) m/z 449.1(C24H24N405 + H requires 449.18) ; RP-HPLC (300 nm, 26 min run) 17.0 min.

Synthesis of 3'-Pyridine Diacetylene Threonine Hydroxamic Acid Example 25:N-((2R)-hydroxy-(lS)-hydroxycarbamoyl-propyl)-4-(4-pyridin-3-yl-buta-1, 3- diynyl) -benzamide (3)
EMI129.1

Preparation ofN-((2R)-hydroxy-(lS)-hydroxycarbamoyl-propyl)-4-(4-pyridin-3-yl-buta-1, 3- diynyl)-benzamide (3).

ReagentMW Eq.glmL mmol
Alkyne on resin(1) 0. 77 mmol/g 1.0 142 mg 0.109
3-Ethynylpyridine (2) 103.12 3. 4 38 mg 0.368PdCl2 (PPh3)2 701.89 0. 3 22 mg 0.031
Cul 190.44 1.2 25 mg 0. 131 Et3N 101.19 13200 jus 1.40
DMF 2.0 mL
Resin 1 (142 mg, 0.109 mmol) was swelled in DCM (2mL) for 1 h and drained. A solution of3-ethynylpyridine 2 (38 mg, 0.368 mmol) and Et3N(200 L, 1. 4 mmol) in DMF (2 mL) was added and the resin agitated for 5 min. A mixture of PdCl2(PPh3)2 (22 mg, 0.031 mmol) and Cul (25 mg, 0.131 mmol) was added and the resin was agitated for 72 h. The resin was drained, washed with DMF (3 x 2 mL), DCM(3 x 2 mL) and cleaved with10% TFA/DCM (1.5mL) for 20 min. The solution was collected and the resin was rinsed with additional10% TFA/DCM (1.0 mL). The cleavage fractions were combined, treated with neat TFA (2.0rnL), stirred for 1 h at rt and concentrated by rotary evaporation to give a crude brown residue. Purification byRP-HPLC(Cl8column, CH3CN gradient 5-
65%, 0.1% TFA, UV analysis 300 nm, 24 min) and lyophilization of the collected fractions afforded
4.4 mg (11% yield) of N-((2R)-hydroxy-(1S)-hydroxycarbamoyl-propyl)-4-(4-pyridin-3-yl-buta-1, 3-

diynyl)-benzamide. LRMS (ES+) m/z 364.0(C2oHl7N304 + H requires364. 13) ; RP-HPLC (300 nm, 24 min run) 11. 2 min.

Example 26: Synthesis ofN- (l- (N-hydroxycarbamoyl) (lS, 2R)-2-hydroxy propyl){4- [4- (6-morpholin-4-yl (3-pyridyl) ) buta-1, 3-diynyl] phenyl} carboxamide (5)
EMI130.1

0
Br 2 H Thr-NH-0-Trt- [Rink], DIC, HOBT, DIEA, DMF
1. Pd2dba3,
I. Pdzdbaa,
PdC12 (PPh3) 2,
Et3N, DMF 3
2. NaOH, MeOH
OH
OtBu H zozo
O 1. Morpholine, NMP HO'N
N 90 c 0 H
0 H 2. TFA, water
ZON
4 N N ci (DO
Cl Reagent MW EQg/ml mmol Dibromovinylbenzoic acid (1) 320 1.0 9.6 g 30.0 2-Chloro-5-ethynyl-pyridine 138 1.3 5.43 g 39.0Pd2dba3915 0.01 274 mg 0.3(1% cat. ) TMPP 352 0.04422 mg 1.2 (4%) TEA 101 3.0 12. 5 ml 90.0 DMF 90 mldegassed with argon Preparation. of 4-[4-(6-Chloro-pyridin-3-yl)-buta-1,3-diynyl]-benzoic acid methyl ester.

EMI131.1


4- [4- (6-Chloro-pyridin-3-yl)-buta-1, 3-diynyl]-benzoic acid was made according to the method of Wang Shen and Sheela A. Thomas in Org. Lett. 2000,2 (18), 2857-2860.

A solution of 4- (2, 2-dibromo-vinyl) -benzoic acid methyl ester (1) (9.6g,30. Ommol), ethynyl- pyridine (2) (5.43g,39. Ommol), Pd2dba3 (274mg, 0.3mmol), tris (4-methoxyphenyl) phosphine(TMPP) (422mg,1.2mmol) were dissolved in argon sparged(5 min. ) DMF (60ml). The reaction was sparged with argon for 1 min. TEA(12.5ml, 90.0mmol) was added to the stirred reaction mixture that was then heated under argon at 85 C for 3 hours. The reaction was found complete by LCMS. The reaction was cooled to rt and diluted with EtOAc/hexane(1 :1) (500ml). The organic phase was washed with1M NaOH (2x80ml), water(2x80m1), sat. brine(80ml), dried withNa2S04, filtered and concentrated under reduced pressure to give crude product. The residue was filtered through a filter plug of silica eluting with EtOAc/hexane(1 :1). The fractions with product were evaporated to give 9.06 g of product in good purity(-96% pure). The material was taken on without further purification.

Preparation of4- [4- (6-Chloro-pyridin-3-yl)-buta-1, 3-diynyll-benzoic acid (3)
A 6M aq. solution ofNaOH(15ml) was added to a stirred solution of 4- [4- (6-Chloro-pyridin-3-yl)-buta-1, 3-diynyl] -benzoic acid methyl ester. (9.06g, 30mmol) in MeOH(350ml) at rt. The reaction solution was heated to refluxfor 3 hours. The reaction stayed a mixture and did not turn clear. HPLC and LCMS indicated that the reaction was forming side products. The reaction was cooled to rt and some MeOH(-200ml) was removed by evaporation under reduced pressure. Water(400ml) was added to the mixture. Conc.HC1 was added dropwise to the stirred solution until acidic by pH paper (pH2). The yellow precipitate that formed was collected by suction filtration. The solid was washed with water(3x20ml) and hexane(2x20ml) to give the crude product. HPLC indicated that there was approximately 40% product in the mixture. The crude reaction product was purified by flash

chromatography using EtOAc (8-10%) /hexane as eluant. The pure fractions were evaporated and driedin vacuo to give 4.2 g of product 3 in 50% yield.

Preparation of[4- [4- (6-chloro-pyridin-3-yl)-buta-1, 3-diynyl]-benzoyl]-HN-Thr (OtBu) hydroxamic acid trityl resin (4)
EMI132.1
4- [4- (6-Chloro-pyridin-3-yl)-buta-1, 3-diynyl] -benzoic acid (3) was coupled to a tert-butyl protectedthreonine pre-loaded on hydroxylamine 2-chlorotrityl resin following the same procedure as used for Example 26. The coupling employed DIC and HOBT. [N-Fmoc-hydroxylamine 2- chlorotrityl resin was purchased from Novabiochem cat. #01-64-0165.] Preparation ofN- (2-Hydroxy-l-hydroxycarbamoyl-propyl)-4- [4- (6-morpholin-4-yl-pyridin-3-yl)-buta-1, 3-diynyl]-benzamide (5)
EMI132.2

OH
OtBu H W 0
H > 1. Morpholine, NMP HO' NJA /O
N-IN 90 c 3-0 0 H I 0 H 1 2. TFA, water
N \N I/N
4 /5 O cl
A solution of morpholine(300uL) in NMP(lml) was added to a vial containing the 2- cloropyridine resin (4) (150mg, 0.12mmol). The reaction mixture was purged with argon and heated to 85-90 C for 24 hours. The resin was drained and washed with DMF and DCM alternately several times. The product was cleaved from the resin through treatment with a TFA/water solution (80:20)

(1.5ml) for 45 min. The resin was filtered and washed with fresh TFA/water solution (80: 20)(0.5ml).

The combined TFA and organic fractions were diluted with CH3CN/water (1: 1) (lOml), water(2ml) and lyophilized. The crude product was purified by prep. HPLC. The crude product was dissolved in DMSO(lml), passed through a Teflon syringe filter, and the clear filtrate was injected on a preparative HPLC. The purification used a20x50 mm Ultro 120C18 column running a 22 ml/min 2% gradient (AcCN/water, 0.1% TFA) for 16 min. The purified fractions were lyophilized to dryness to give 2.2 mg of pure product as the TFA salt(-32% yield).

Example 27: Synthesis of4- [4- (4-Amino-phenyl)-buta-1, 3-diynyl]-N- (2-hydroxy-1-hydroxycarbamoyl-propyl)-benzamide (4)
EMI133.1

0
OtBu vOH
H > . tJ DIC, HOBT,
N DIEA, DMF
0 NH2
2
1 Jt J 2
H2N
OH
OtBu H 0
O TFA, water HO / o'N N H oh
3 4 NH2 nu2
NH Preparation of2-4- [4- (4-Amino-phenyl)-buta-1, 3-diynyl]-benzoylamino}-3-tert-butoxycarbonyloxy-butyric hydroxamic acid trityl resin (3).

EMI134.1


Reagent MW EQg/ml mmol H-Thr(Boc)-NHO-Trt Resin (1) 1.0 5.8 g 4.47 1,3-diynyl benzoic acid (2) 261.3 1.4 1.64 g 6.25 HOBT 135. 1 1.4 0.85 g 6.25 DIC 126.2 1.4 0.98 ml 6.25 DIEA 129.25 3.5 2. 7 ml 15.6 DMF 50 ml
DIEA (2.7ml, 15.6mmol) was added to a stirred solutionof 4- [4- (4-Amino-phenyl)-buta-1, 3- diynyl]-benzoic acid (2) (1.64g, 6.3mmol), HOBT (0.85g, 6.3mmol), DIC (0.98ml, 6.3mmol) in DMF (50ml). After 2 min. , the Thr hydroxylamine resin (5.8g, 4.5mmol) was added in one portion. [N- Fmoc-hydroxylamine2-chlorotrityl resin was purchased from Novabiochem cat. #01-64-0165.] After 12 hours at rt, the reaction was found complete by LCMS. The resin was drained and washed with DMF and DCM alternately 3 times each. The product on resin3 was used as is in subsequent reactions without further treatment.

Preparation of4- [4- (4-Amino-phenyl)-buta-1, 3-diynyl]-N- (2-hydroxy-1-hydroxy carbamoyl-propyl)-benzamide (4)
EMI134.2
Reagent MW EQg/ml mmol

1,3-diynyl benzoic Thr Resin (3) 1.0 120 mg 0.09 TFA/water (80: 20) 1.5 ml
The product (4) (120mg, 0.09mmol) was cleaved from the resin through treatment with a TFA/water solution (80: 20)(1. 5ml) for 45 min. The resin was filtered and washed with fresh TFA/water solution (80: 20) (0.5ml). The combined TFA and organic fractions were diluted with CH3CN/water (1: 1) (lOml), water(2ml) and lyophilized. The crude product was purified by prep.

HPLC. The crude product was dissolved in DMSO(lml), passed through a Teflon syringe filter, and the clear filtrate was injected on a preparative HPLC. The purification used a20x50 mm Ultro 120 C18 column running a 22mUmin 2% gradient (AcCN/water, 0. 1% TFA) for16 min. The purified fractions were lyophilized to dryness to give 2.2 mg of pure product as the TFA salt. The product (4) was lyophilized again from CH3CN/water with 10 equivalents of HCl to remove most of the TFA to yield 2 mg of product as the HCl salt(-53% yeild).

Example 28: Synthesisof 4-f 4- [4- (2-Dimethylamino-acetylamino)-phenyl]-buta-1, 3-diynyl}-N- (2-hydroxy-l-hydroxycarbamoyl-propyl)-benzamide (6) (Continued from compound 3 of Example 27 above)
EMI135.1

0 tBu
OtBu OtBu
O Ci ~. N.

. N'4 O I N/ ol N Lutidine, Dcm 0 H
0 H
5 Br zon
NH- H '-NH2 H
OH
H 0
HO'N
1. Me2NH, NMP O H WJIX
2. TFA, water
6 \Nt
H
H

Preparation of2- (4- {4- [4- (2-Bromo-acetylamino)-phenyl]-buta-1, 3-diynyl}-benzoylamino)-3-tert-butoxycarbonyloxy-butyric acid hydroxamate trityl resin (5).
EMI136.1


0 OtBu
OtBu Br H o
H cri N ou H 'M'u.

\ \ zozo
W 5 s Br
5 N)-,/Br
NH2 H "NH2" Reagent MW EQg/ml mmol Amino 1,3-diynyl benzoic Thr Trt Resin (3) 1.0 0.75 g 0.578 Bromo-acetyl chloride 157.4 8.0 0.728 g 4.62 Lutidine 107 10.0 1. 07 ml 9.24 DMF 6 ml
A solution of bromo-acetyl chloride (0.75g, 0.58mmol) in DCM (2ml) was added to a mixture of2-f 4- [4- (4-Amino-phenyl)-buta-l, 3-diynyl]-benzoylamino}-3-tert-butoxycarbonyloxy-butyric acid hydroxamate Trt Resin (3) (0.75g, 0.58mmol), lutidine(l. lml, 9.2mmol) and DCM (4ml) atrt with shaking. After shaking for 1.5 hours, the reaction was found complete by LCMS. The resin was drained and washed with DCM(2xlOml), DMF(3xlOml) and DCM(3xlOml) again. The resin was drained and dried in vacuo. The product on resin 5 was used as is in subsequent reactions without further treatment.

Preparation of 4-{4-[4-(2-Dimethylamino-acetylamino)-phenyl]-buta-1,3-diynyl}-N-(2-hydroxyl-hydroxycarbamoyl-propyl)-benzamide (6).
EMI136.2


OtBu OH
H 0 1. Me2NH, NMP H *T0
N, O p H (. 2. TFA, water HO/N H
O H 1. 2. TFA, I'
I
1-11
H H
N
H H

Reagent MW EQg/ml mmol Bromo acetic Thr Trt Resin (5) 1.0 125 mg 0.093 Dimethyl amine 45.08 0.2 ml excess NMP 1.2 ml
A solution of dimethyl amine (0.2ml) in NMP(1. 2ml) was added to bromo acetic Thr Trt Resin (5) (125 mg, 0.09mmol) at rt with shaking. After shaking for 12 hours, the reaction was found complete by LCMS. The resin was drained and washed with DCM(2xlOml), DMF (3xlOml) and DCM(3xlOml) again. The product (6) was cleaved from the resin through treatment with aTFA/water solution (80: 20)(1.5ml) for 45 min. The resin was filtered and washed with fresh TFA/water solution (80: 20)(0.5ml). The combined TFA and organic fractions were diluted withCH3CN/water (1: 1) (10ml), water (2ml) and lyophilized. The crude product was purified by prep.

HPLC. The crude product was dissolved in DMSO(lml), passed through a Teflon syringe filter, and the clear filtrate was injected on a preparative HPLC. The purification used a20x50 mm Ultro 120 C18 column running a 22 ml/min 2% gradient(AcCN/water, 0.1%TFA)'for 16 min. The purified fractions were lyophilized to dryness to give 2 mg of pure product as the TFA salt(~37% yeild).

Example 29: Synthesis of4- {4- [4- (2-Amino-4-methyl-pentanoylamino)-phenyl]-buta-1, 3-diynyl}-N-(2-hydroxy-1-hydroxycarbamoyl-propyl)-benzamide (7) (Continued from compound 3 of Example 27 above)
EMI137.1

OH
H 0
OtBu 1. FmooL-Leu, HATU, HO) N) + H 0 DIEA, DMF 0 H
N 2. Piperldine,
0 H 3. TFA, water 0 NH2
N \
3 \ 7 H \+NH2) ReagentMW EQg/ml mmol Amino 1,3-diynyl benzoic Thr Trt Resin (3) 1.0 125 mg 0.093

Fmoc-L-leucine 353.42 4.0 0.135 g 0.384
HATU 380 4.0 0. 146g 0.384
DIEA 129.25 8.0 133 ul 0.768
DMF 1. 5 ml
A solution of Fmoc-L-leucine (0.135g, 0.38mmol), HATU (0.146g, 0.38mmol) in DMF (1.5ml) was made. After 2 min. of shaking, the activated acid was added to the amino 1,3-diynyl benzoic Thr Trt Resin (3) (125 mg, 0.09mmol) at rt with shaking. After shaking for 36 hours, the reaction was drained and washed with DCM(2x4ml), DMF(3x4ml) and DCM(3x4ml) again. The resin was treated with 20% piperizine in DMF (4ml) for 2 hours twice. The resin was drained and washed with DMF and DCM alternately several times. The product was cleaved from the resin through treatment with a TFA/water solution (80: 20) (1.5ml) for 45 min. The resin was filtered and washed with freshTFA/water solution (80: 20)(0. 5ml). The combined TFA and organic fractions were diluted with CH3CN/water (1: 1)(lOml), water(2ml) and lyophilized. The crude product was purified by prep. HPLC. The crude product was dissolved in DMSO(lml), passed through a Teflon syringe filter, and the clear filtrate was injected on a preparative HPLC. The purification used a20x50 mm Ultro 120C18 column running a 22mUmin 2% gradient (AcCN/water, 0.1% TFA) for 16 min. The purified fractions were lyophilized to dryness to give 1.7 mg of pure product (7) as the TFA salt(-30% yield).


* Examples 30-1307 of Table 1 were synthesized according to the synthetic schemes described above.

Biological protocols and dataP. aeruginosa LpxC Inhibition Assay
The assay followed the general method of Hyland et al (Journal of Bacteriology 1997 179,
2029-2037: Cloning, expression and purificationof UDP-3-O-acyl-GlcNAc deacetylase from
Pseudomonas aeruginosa : a metalloamidase of the lipidA biosynthesis pathway) and the radiolabeling procedure is according to Kline et al. supra. Briefly, samples were incubated with 2 nM P. aeruginosa
LpxC and 150 nM[3H-Ac]-UDP-3-0-(R-3-hydroxydecanoyl)-GlcNAc in a total volume of 50 uL for
90 min at room temperature. Reactions were carried out in 96-well polypropylene plates in 50 mM sodium phosphate buffer, pH 7.5, containing 1 mg/mL BSA. Reactions were stopped by the addition of
180 uL of a 3% suspension of activated charcoal powder in 100 mM sodium acetate, pH 7.5.

Supernatants were clarified by centrifugation. A portion of the clarified supernatant, containing the enzymatically released [3H] -acetate, was transferred to opaque white 96-well plates containing scintillation fluid. The radioactivity was measured in a Perkin-Elmer/WallacTrilux Microbeta counter.

Control reactions to which 5 mM EDTA had been added were included with each run to determine nonspecific tritium release.

Bacterial Screens and Cultures
Bacterial isolates were cultivatedfrom-70 C frozen stocks by two consecutive overnight passages at35 C in ambient air on 5% blood agar(Remel, Lenexa, KS). Clinical isolates tested were from a collection composed of isolates collected during clinical trials and recent clinical isolates obtained from various geographically diverse hospitals in the US. Quality control and primary panel strains were from the American Type Culture Collection (ATCC; Rockville, MD), with the exception of P. aeruginosa PA0200, a strain with a deletion of the mexABoprM genes that was received from
Dr. H. Schweizer. This strain does not express the principalmultidrug efflux pump and is hypersusceptible to many antibacterials. Strain Z61 (ATCC 35151) is also hypersusceptible to antibacterials. It is thought that thehypersusceptibility of this strain is the result of increased permeability of its outer membrane (Angus BL et al, Antimicrobial Agents and Chemotherapy 1982
21,299-309 : Outer membrane permeability in Pseudomonas aeruginosa : Comparison of a wild-type with anantibacterial-supersusceptible mutant).

Susceptibility Testing
Minimum Inhibitory Concentrations(MICs) were determined by the broth microdilution method in accordance with the National Committee for Clinical Laboratory Standards (NCCLS) guidelines. In brief, organism suspensions were are adjusted to a 0.5 McFarland standard to yield a finalinoculum between3x105 and7x105 colony-forming units(CFU)/mL. Drug dilutions and inocula were made in sterile, cation adjustedMueller-Hinton Broth (Remel). An inoculum volume of100 was added to wells containing 1001 of broth with 2-fold serial dilutions of drug. All inoculated microdilution trays were incubated in ambient air at35 C for 18-24 hours. Following incubation, the lowest concentration of the drug that prevented visible growth was recorded as the MIC. Performance of the assay was monitored by the use of laboratory quality-control strains againsttobramycin, that has a defined MIC spectrum, in accordance with NCCLS guidelines.

Efficacy in mouse model of systemic Pseudomonas aeruginosa infection
Female Balb/c mice were injected intraperitoneally with 0.5 ml of a bacterial suspension containing approximately 100 times the dose that would kill 50% of animals(LDso) of P. aeruginosa strain PAO1 or E. coli ATCC 25922. At one and five hours post infection, the test compound was injected intravenously in doses ranging from 5mg/kg to 100mg/kg, five mice per group. Mice were observed for 5 days, and the dose of compound resulting in survival of50% of mice(EDso) was calculated.

Drug Combination (Synergy) StudiesI. Principle
Checkerboard experiments can be performed to assess potential interactions between primary drug of interest(#1) and other related antibacterials (#2). P.aerugi71osa ATCC 27853, S. aureus ATCC 29213 and other organisms can be used as challenge strains as well as selected clinical isolates. Brothmicrodilution format can be used to assess the activity of drug #1 and test compound alone and in combination. Two-fold dilutions of the two compounds to be tested (each bracketing the expected MIC value) are used. The fractional inhibitory concentration (FIC) was calculated as the MIC of compound #1 in combination with a second compound, divided by the MIC of compound #1 alone. A summation FIC (EFIC) was computed for each drug combination as the sum of the individual FICs of compound #1 and #2. Synergy was defined as anzFICzu 0.5, indifference as anEFIC between 0.5 and

4, and antagonism as EPIC > 4. The lowest EFIC was used for the final interpretation of drug combination studies., Interpretation of summation (EFIC) a) Synergism, x#0. 5 b) Indifference, 0.5 4 Table 2: Demonstration of Antibacterial activity of Select Compounds from Table 1 Enzyme inhibitory activity
EMI141.1


Compound ICgo (nM)





Example #




12 100 nM




572 100 nM




481 100 nM





19 100 nM




516 100 nM




280 100 nM




366 100 nM





777 100 nM




315



779 100 nM




860 100 nM





801 100 nM





13 100 nM



Table 3: Antibacterial activity vs standard panel of organisms (MIC, g/ml).

MIC Key
MIC's of 6.25 ug/ml or less = A
MIC's of greater than 6.25 ug/ml to 50 ug/ml = B . MIC's of greater than 50 ug/ml = C
EMI142.1


Bacterial strain: P. aeruginosa E. coli S. aureus hyper-permeable P. aeruginosa




27853 25922 29213 P. aerug. 35151 PA0200 mexAB







Compound




Example #





12 A A C A A





572 A A C A A





481 A A C A





19 A A B A A





516 A A C A A





. 280 A A C A A





366 A A C A A

Documents:

01343-kolnp-2005-abstract.pdf

01343-kolnp-2005-claims.pdf

01343-kolnp-2005-description complete.pdf

01343-kolnp-2005-form 1.pdf

01343-kolnp-2005-form 3.pdf

01343-kolnp-2005-form 5.pdf

01343-kolnp-2005-international publication.pdf

1343-KOLNP-2005-(13-08-2012-)-CORRESPONDENCE.pdf

1343-KOLNP-2005-(13-08-2012-)-FORM-1.pdf

1343-KOLNP-2005-(13-08-2012-)-FORM-13.pdf

1343-KOLNP-2005-(13-08-2012-)-FORM-5.pdf

1343-KOLNP-2005-(13-08-2012-)-OTHERS.pdf

1343-kolnp-2005-assignment.pdf

1343-kolnp-2005-correspondence-1.1.pdf

1343-KOLNP-2005-CORRESPONDENCE.pdf

1343-kolnp-2005-examination report.pdf

1343-kolnp-2005-form 13.pdf

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1343-kolnp-2005-form 3.pdf

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1343-kolnp-2005-granted-abstract.pdf

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1343-kolnp-2005-granted-description (complete).pdf

1343-kolnp-2005-granted-form 1.pdf

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Patent Number 250653
Indian Patent Application Number 1343/KOLNP/2005
PG Journal Number 03/2012
Publication Date 20-Jan-2012
Grant Date 16-Jan-2012
Date of Filing 12-Jul-2005
Name of Patentee NOVARTIS VACCINES AND DIAGNOSTICS INC.
Applicant Address 1209 ORANGE STREET CITY OF WILMINGTON, COUNTY OF NEW CASTLE
Inventors:
# Inventor's Name Inventor's Address
1 ANDERSON NEIL H 6529 GREENWOOD AVENUE N., SEATTLE WA 98103
2 ERWIN ALICE NOVARTIS VACCINES AND DIAGNOSTICS INC. 1209 ORANGE STREET CITY OF WILMINGTON, COUNTY OF NEW CASTLE
3 HARWOOD ERIC NOVARTIS VACCINES AND DIAGNOSTICS INC. 1209 ORANGE STREET CITY OF WILMINGTON, COUNTY OF NEW CASTLE
4 KLINE TONI NOVARTIS VACCINES AND DIAGNOSTICS INC. 1209 ORANGE STREET CITY OF WILMINGTON, COUNTY OF NEW CASTLE
5 MDLULI KHISIMUZI NOVARTIS VACCINES AND DIAGNOSTICS INC. 1209 ORANGE STREET CITY OF WILMINGTON, COUNTY OF NEW CASTLE
6 NG SIMON NOVARTIS VACCINES AND DIAGNOSTICS INC. 1209 ORANGE STREET CITY OF WILMINGTON, COUNTY OF NEW CASTLE
7 PFISTER KEITH B NOVARTIS VACCINES AND DIAGNOSTICS INC. 1209 ORANGE STREET CITY OF WILMINGTON, COUNTY OF NEW CASTLE
8 SHAWAR RIBHI NOVARTIS VACCINES AND DIAGNOSTICS INC. 1209 ORANGE STREET CITY OF WILMINGTON, COUNTY OF NEW CASTLE
9 WAGMAN ALLAN NOVARTIS VACCINES AND DIAGNOSTICS INC. 1209 ORANGE STREET CITY OF WILMINGTON, COUNTY OF NEW CASTLE
10 YABANNAVAR ASHA NOVARTIS VACCINES AND DIAGNOSTICS INC. 1209 ORANGE STREET CITY OF WILMINGTON, COUNTY OF NEW CASTLE
11 BOWMAN JASON 4810 ELM STREET, QUINCY, IL 62305
PCT International Classification Number A61K
PCT International Application Number PCT/US2004/000433
PCT International Filing date 2004-01-08
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/520,211 2003-11-13 U.S.A.
2 60/438,523 2003-01-08 U.S.A.
3 60/466,974 2003-04-30 U.S.A.