Antibacterial agents

This application claims benefit of priority to the following U.S. Provisional Patent Applications, Ser. No. 60/438,523, filed Jan. 8, 2003; Ser. No. 60/466,974, filed Apr. 30, 2003; and Ser. No. 60/520,211 filed Nov. 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 activity of UDP-3-O—(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, β-lactam-resistant and multidrug-resistant pneumococci, and vancomycin-resistant enterococci. Important causes of Gram-negative resistance include extended-spectrum β-lactamases (ESBLS) in Klebsiella pneumoniae, Escherichia coli, and Proteus mirabilis, high-level third-generation cephalosporin (Amp C) β-lactamase resistance among Enterobacter species and Citrobacter freundii, and multidrug-resistance genes observed in Pseudomonas aeruginosa, Acinetobacter, and Stenotrophomonas maltophilia. (Jones R N 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 (Sahm D F 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-negative multidrug 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 enzyme uridyldiphospho-3-O—(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 to multidrug 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:

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, Apr. 14, 2000, pps. 11002-11009), discuss the mechanism of lipid A biosynthesis in the context of gram-negative bacteria and discloses a new class of hydroxamate-containing inhibitors of LpxC. Wyckoff et al., in Trends in Microbiology (vol. 6, no. 4, April 1998, 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 Ser. No. 08/958,638) published Dec. 20, 2001, corresponding to WO 98/18754 published May 7, 1998 discloses a combinatorial library of hydroxylamine, hydroxamic acid, hydroxyurea and hydroxylsulfonamide compounds purported to be potentially useful as inhibitors of metalloproteases. U.S. Pat. No. 6,281,245, a continuation in part of U.S. Ser. No. 08/958,638 claims a method of inhibiting a deformylase enzyme by administering one of the hydroxylamine compounds from the combinatorial library as disclosed 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 Nov. 11, 1999, that discloses a method of solid phase synthesis of the hydroxylamine library of compounds. WO 00/61134 (to British Biotech Pharmaceuticals Limited), published Oct. 19, 2000, discloses compounds of the formula below:

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

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

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

Recently, De Novo Pharmaceuticals LTD disclosed in WO 02/50081, published Jun. 27, 2002, antibacterial and antiprotozoal agents having the formulae shown below:

The patent publication discusses that the antibacterial activity is due, at least in part to intracellular inhibition of bacterial polypeptide deformylase.

SUMMARY OF THE INVENTION

The present invention provides novel compounds, pharmaceutical formulations including the compounds, methods of inhibiting UDP-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 formula 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 unsubstituted C₁-C₆-alkyl,
  • (3) substituted or unsubstituted C₂-C₆-alkenyl,
  • (4) substituted or unsubstituted C₂-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 unsubstituted C₁-C₆-alkyl,
  • (2) —(NH)_0-1—(CH₂)_j—NR^3L—(CH₂)_k,
  • (3) —(NH)_0-1—C(R^1L,R^2L)—NR^3L—C(R^1L,R^2L)—,
  • (4) —C(R^1L,R^2L)—O—C(R^1L,R^2L)—,
  • (5) —(CH₂)_j—NR^3L—C(R^1L,R^2L)—CONH—(CH₂)_k—,
  • (6) —CO—C(R^1L,R^2L)—NHCO—,
  • (7) —CONH—,
  • (8) —NHCO—,
  • wherein
  • R^1L, R^2L, and R^3L are independently selected from the group consisting of

    • (a) H,
    • (b) substituted or unsubstituted C₁-C₆-alkyl,
    • (c) C₁-C₆-alkyl substituted with aryl,
    • (d) C₁-C₆-alkyl substituted with heterocyclyl, and
    • (e) C₁-C₆-alkyl substituted with heteroaryl

  • or R^1L and R^3L, 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 unsubstituted C₃-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)_i—,
  • (2) —(CH₂)_i—S—(CH₂)_i—,
  • (3) —(CH₂)_i—NR⁸—(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 unsubstituted C₁-C₆-alkyl;
  • i is an integer of 0-4;

    
    
    

    Y is selected from the group consisting of

  • (1) substituted or unsubstituted C₃-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-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 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

• • wherein R^1b and R^2b, are independently selected from the group consisting of

    • (a) H,
    • (b) substituted or unsubstituted C₁-C₆-alkyl,
    • (c) substituted or unsubstituted C₂-C₆-alkenyl,
    • (d) substituted or unsubstituted C₂-C₆-alkynyl,
    • (e) substituted or unsubstituted aryl,
    • (f) substituted or unsubstituted heterocyclyl,
    • (g) substituted or unsubstituted heteroaryl,
    • (h) C₁-C₆-alkyl substituted with aryl,
    • (i) C₁-C₆-alkyl substituted with heterocyclyl, and
    • (j) C₁-C₆-alkyl substituted with heteroaryl,

  • or R^1b and R^2b, 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 unsubstituted C₁-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,
  • (2) —(CH₂)_rC(R^1a,R^2a)(CH₂)_sOR^3a,
  • (3) —(CH₂)_rC(R^1a,R^2a)N(R^4a,R^5a),
  • (4) —(CH₂)_rC(R^1aR^2a)N(R^4a)COR^3a,
  • (5) —(CH₂)_rC(R^1a,R^2a)NHCON(R^4a,R^5a),
  • (6) —(CH₂)_r(R^1a,R^2a)NHC(═NH)N(R^4a,R^5a),
  • (7) —CH(R^1a,R^2a),
  • (8) —C≡CH,
  • (9) —(CH₂)_rC(R^1a,R^2a)CN,
  • (10) —(CH₂)_rC(R^1a,R^2a)CO₂R^3a, and
  • (11) —(CH₂)_rC(R^1a,R^2a)CON(R^4a,R^5a),
  • wherein R^1a, R^2a, R^3a, R^4a, and R^5a 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) C₁-C₆-alkyl substituted with aryl,
    • (g) C₁-C₆-alkyl substituted with heterocyclyl, and
    • (h) C₁-C₆-alkyl substituted with heteroaryl,
    • or R^4a and R^5a together with the N atom 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;

  • 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(R₁,R₂),
  • (3) —N(OH)C(═O)N(R₁,R₂),
  • (4) —CH(OH)C(═O)N(R₁,R₂),
  • (5) —CH[N(R^2q,R^3q)]C(═O)N(R₁,R₂),
  • (6) —CHR_1qC(═O)N(R₁,R₂),
  • (7) —CO₂H,
  • (8) —C(═O)NHSO₂R^4q,
  • (9) —SO₂NH₂,
  • (10) —N(OH)C(═O)R^1q,
  • (11) —N(OH)SO₂R^4q,
  • (12) —NHSO₂R^4q,
  • (13) —SH,
  • (14) —CH(SH)(CH₂)_0-1C(═O)N(R₁,R₂),
  • (15) —CH(SH)(CH₂)_0-1CO₂H,
  • (16) —CH(OH)(CH₂)_0-1CO₂H,
  • (17) —CH(SH)CH₂CO₂R^1q,
  • (18) —CH(OH)(CH₂)SO₂NH₂,
  • (19) —CH(CH₂SH)NHCOR^1q,
  • (20) —CH(CH₂SH)NHSO₂R^4q,
  • (21) —CH(CH₂SR^5q)CO₂H,
  • (22) —CH(CH₂SH)NHSO₂NH₂,
  • (23) —CH(CH₂OH)CO₂H,
  • (24) —CH(CH₂OH)NHSO₂NH₂,
  • (25) —C(═O)CH₂CO₂H,
  • (26) —C(═O)(CH₂)_0-1CONH₂,
  • (27) —OSO₂NHR^5q,
  • (28) —SO₂NHNH₂,
  • (29) —P(═O)(OH)₂,

• • wherein
  • R¹ is selected from the group consisting of

    • (1) H,
    • (2) —OH,
    • (3) —OC₁-C₆-alkyl,
    • (4) —N(R^2q,R^3q), and
    • (5) substituted or unsubstituted C₁-C₆-alkyl;

  • R₂ is selected from the group consisting of

    • (1) H,
    • (2) substituted or unsubstituted C₁-C₆-alkyl,
    • (3) substituted or unsubstituted C₂-C₆-alkenyl,
    • (4) substituted or unsubstituted C₂-C₆-alkenyl,
    • (5) substituted or unsubstituted aryl,
    • (6) substituted or unsubstituted heterocyclyl,
    • (7) substituted or unsubstituted heteroaryl,
    • (8) C₁-C₆-alkyl substituted with aryl,
    • (9) C₁-C₆-alkyl substituted with heterocyclyl, and
    • (10) C₁-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, O and S,
    • or R² and R⁴, 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;

  • R^1q, R^2q, R^3q, R^4q, and R^5q are selected from H or C₁-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 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 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 with a 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 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, 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 for UDP-3-O—(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 atom is/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, and hexadienyl 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 limited to —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 “substituted alkynyl” 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.

The phrase “heterocyclyl” refers to both aromatic and nonaromatic ring compounds including monocyclic, 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 the phrase “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 as 2-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, 1H-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 to 3 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, dihydrodithionyl, 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 tetrahydrothiophene 1,1-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 “substituted heterocyclyl” 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, naphthenyl by way of example. Although the phrase “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, the phrase “substituted aryl” includes, but is not limited to tolyl, and hydroxyphenyl among others. Preferred substituents include straight and branched chain alkyl groups, —CH₃, —C₂H₅, —CH₂OH, —OH, —OCH₃, —OC₂H₅, —OCF₃, —CN, —NO₂, —CO₂H, —CO₂CH₃, —CONH₂, —NH₂, —F, —Cl, Br, —CF₃, —N(CH₃)₂, —NHSO₂CH₃, —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, O 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.

The term “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 with Cl, Br, F, I, OH, CN, C₁-C₃-alkyl, C₁-C₆-alkoxy, C₁-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. Preferred substituents include straight and branched chain alkyl groups, —CH₃, —C₂H₅, —CH₂OH, —OH, —OCH₃, —OC₂H₅, —OCF₃, —CN, —NO₂, —CO₂H, —CO₂CH₃, —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-1-methoxy-4-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, N-[4-(2-phenylethynyl)phenyl]pyrrolidin-2-ylcarboxamide, 2-amino-3-methyl-N-[4-(2-phenylethynyl)phenyl]butanamide, 4-(4-phenylbuta-1,3-diynyl)phenylamine, 2-(dimethylamino)-N-[4-(4-phenylbuta-1,3-diynyl)phenyl]acetamide, 2-(ethylamino)-N-[4-(4-phenylbuta-1,3-diynyl)phenyl]acetamide, 4-ethyl-1-phenylbenzene, 1-[4-(2-phenylethynyl)phenyl]ethan-1-one, N-(1-carbamoyl-2-hydroxypropyl)[4-(4-phenylbuta-1,3-diynyl)phenyl]carboxamide, N-[4-(2-phenylethynyl)phenyl]propanamide, 4-methoxyphenyl phenyl ketone, phenyl-N-benzamide, (tert-butoxy)-N-[(4-phenylphenyl)methyl]carboxamide, 2-(3-phenylphenoxy)ethanehydroxamic acid, 3-phenylphenyl propanoate, 1-(4-ethoxyphenyl)-4-methoxybenzene, and [4-(2-phenylethynyl)phenyl]pyrrole.

The term “heteroarylaryl” refers to a biaryl group where one of the aryl groups is a heteroaryl group. Exemplary heteroarylaryl groups include, for example, 2-phenylpyridine, phenylpyrrole, 3-(2-phenylethynyl)pyridine, phenylpyrazole, 5-(2-phenylethynyl)-1,3-dihydropyrimidine-2,4-dione, 4-phenyl-1,2,3-thiadiazole, 2-(2-phenylethynyl)pyrazine, 2-phenylthiophene, phenylimidazole, 3-(2-piperazinylphenyl)furan, 3-(2,4-dichlorophenyl)-4-methylpyrrole, and the like. Preferred optionally substituted heteroarylaryl groups include: 5-(2-phenylethynyl)pyrimidine-2-ylamine, 1-methoxy-4-(2-thienyl)benzene, 1-methoxy-3-(2-thienyl)benzene, 5-methyl-2-phenylpyridine, 5-methyl-3-phenylisoxazole, 2-[3-(trifluoromethyl)phenyl]furan, 3-fluoro-5-(2-furyl)-2-methoxy-1-prop-2-enylbenzene, (hydroxyimino)(5-phenyl(2-thienyl))methane, 5-[(4-methylpiperazinyl)methyl]-2-phenylthiophene, 2-(4-ethylphenyl)thiophene, 4-methylthio-1-(2-thienyl)benzene, 2-(3-nitrophenyl)thiophene, (tert-butoxy)-N-[(5-phenyl(3-pyridyl))methyl]carboxamide, hydroxy-N-[(5-phenyl(3-pyridyl))methyl]amide, 2-(phenylmethylthio)pyridine, and benzylimidazole.

The term “heteroarylheteroaryl” refers to a biaryl group where both of the aryl groups is a heteroaryl group. Exemplary heteroarylheteroaryl groups include, for example, 3-pyridylimidazole, 2-imidazolylpyrazine, and the like. Preferred optionally substituted heteroarylheteroaryl groups include: 2-(4-piperazinyl-3-pyridyl)furan, diethyl(3-pyrazin-2-yl(4-pyridyl))amine, and dimethyl{2-[2-(5-methylpyrazin-2-yl)ethynyl](4-pyridyl)}amine.

“Optionally substituted” refers to the optional replacement of hydrogen with one or more monovalent or divalent radicals. Optionally substituted groups include those described herein, for each group in which a distinct definition for substitution is supplied. Additionally, suitable substitution groups include, for example, hydroxyl, nitro, amino, imino, cyano, halo, thio, thioamido, amidino, 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 and heterocycloamidino groups include, for example, those shown below. These amidino and heterocycloamidino 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.

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.

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. Preferred 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-[1-(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-(1-formylpyrrolidin-3-yl)acetamide,

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.

The term “protected” with respect to hydroxyl groups, amine groups, and sulfhydryl 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, N.Y., (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, methylthiomethyl 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 protected sulfhydryl groups include, but are not limited to, thioethers 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 acceptable salt” 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, the term “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, particularly alkanoic, alkenoic, cycloalkanoic and alkanedioic acids, in which each alkyl or alkenyl moiety 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.

The term “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 reasonable benefit/risk ratio, and effective for their intended use, as well as the zwitterionic forms, where possible, of the compounds of the invention. The term “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 “antibacterial agent” 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 the growth” 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 ³H, ¹³C, ¹⁴C, ¹⁵N, ¹⁸O, ¹⁷O, ³¹P, ³²P, ³⁵S, ¹⁸F and ³⁶Cl, 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 and ¹⁴C are incorporated, are useful in drug and/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 a non-isotopically labeled reagent.

The present invention provides novel compounds, pharmaceutical formulations including the compounds, methods of inhibiting UDP-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 formula 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 unsubstituted C₁-C₆-alkyl,
  • (3) substituted or unsubstituted C₂-C₆-alkenyl,
  • (4) substituted or unsubstituted C₂-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 unsubstituted C₁-C₆-alkyl,
  • (2) —(NH)_0-1—(CH₂)_j—NR^3L—(CH₂)_k—,
  • (3) —(NH)_0-1—C(R^1L,R^2L)—NR^3L—C(R^1L,R^2L)—,
  • (4) —C(R^1L,R^2L)—O—C(R^1L,R^2L)—,
  • (5) —(CH₂)_j—NR^3L—C(R^1L,R^2L)—CONH—(CH₂)_k—,
  • (6) —CO—C(R^1L,R^2L)—NHCO—,
  • (7) —CONH—,
  • (8) —NHCO—,
  • wherein
  • R^1L, R^2L, and R^3L are independently selected from the group consisting of

    • (a) H,
    • (b) substituted or unsubstituted C₁-C₆-alkyl,
    • (c) C₁-C₆-alkyl substituted with aryl,
    • (d) C₁-C₆-alkyl substituted with heterocyclyl, and
    • (e) C₁-C₆-alkyl substituted with heteroaryl,

  • or R^1L and R^3L, 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 unsubstituted C₃-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)_i—,
  • (2) —(CH₂)_i-—S—(CH₂)_i—,
  • (3) —(CH₂)_i—NR^g—(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 unsubstituted C₁-C₆-alkyl;
  • i is an integer of 0-4;

    
    
    

    Y is selected from the group consisting of

  • (1) substituted or unsubstituted C₃-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-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 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

• • wherein R^1b and R^2b, are independently selected from the group consisting of

    • (a) H,
    • (b) substituted or unsubstituted C₁-C₆-alkyl,
    • (c) substituted or unsubstituted C₂-C₆-alkenyl,
    • (d) substituted or unsubstituted C₂-C₆-alkynyl,
    • (e) substituted or unsubstituted aryl,
    • (f) substituted or unsubstituted heterocyclyl,
    • (g) substituted or unsubstituted heteroaryl,
    • (h) C₁-C₆-alkyl substituted with aryl,
    • (i) C₁-C₆-alkyl substituted with heterocyclyl, and
    • (j) C₁-C₆-alkyl substituted with heteroaryl,

  • or R^1b and R^2b, 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 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 0-2;

    
    
    

    A is selected from the group consisting of

  • (1) H,
  • (2) —(CH₂)_rC(R^1a,R^2a)(CH₂)_sOR^3a,
  • (3) —(CH₂)_rC(R^1a,R^2a)N(R^4a,R^5a),
  • (4) —(CH₂)_rC(R^1a,R^2a)N(R^4a)COR^3a,
  • (5) —(CH₂)_rC(R^1a,R^2a)NHCON(R^4a,R^5a),
  • (6) —(CH₂)_r(R^1a,R^2a)NHC(═NH)N(R^4a,R^5a),
  • (7) —CH(R^1a,R^2a),
  • (8) —C≡CH,
  • (9) —(CH₂)_rC(R^1aR^2a)CN,
  • (10) —(CH₂)_rC(R^1a,R^2a)CO₂R^3a, and
  • (11) —(CH₂)_rC(R^1a,R^2a)CN(R^4a,R^5a),
  • wherein R^1a, R^2a, R^3a, R^4a, and R^5a 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) C₁-C₆-alkyl substituted with aryl,
    • (g) C₁-C₆-alkyl substituted with heterocyclyl, and
    • (h) C₁-C₆-alkyl substituted with heteroaryl,
    • or R^4a and R^5a 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(R₁,R₂),
  • (3) —N(OH)C(═O)N(R₁,R₂),
  • (4) —CH(OH)C(═O)N(R₁,R₂),
  • (5) —CH[N(R^2q,R^3q)]C(═O)N(R₁,R₂),
  • (6) —CHR^1qC(═O)N(R₁,R₂),
  • (7) —CO₂H,
  • (8) —C(═O)NHSO₂R^4q,
  • (9) —SO₂NH₂,
  • (10) —N(OH)C(═O)R^1q,
  • (11) —N(OH)SO₂R^4q,
  • (12) —NHSO₂R^4q,
  • (13) —SH,
  • (14) —CH(SH)(CH₂)_0-1C(═O)N(R₁,R₂),
  • (15) —CH(SH)(CH₂)_0-1CO₂H,
  • (16) —CH(OH)(CH₂)_0-1CO₂H,
  • (17) —CH(SH)CH₂CO₂R^1q,
  • (18) —CH(OH)(CH₂)SO₂NH₂,
  • (19) —CH(CH₂SH)NHCOR^1q,
  • (20) —CH(CH₂SH)NHSO₂R^4q,
  • (21) —CH(CH₂SR^5q)CO₂H,
  • (22) —CH(CH₂SH)NHSO₂NH₂,
  • (23) —CH(CH₂OH)CO₂H,
  • (24) —CH(CH₂OH)NHSO₂NH₂,
  • (25) —C(═O)CH₂CO₂H,
  • (26) —C(═O)(CH₂)_0-1CONH₂,
  • (27) —OSO₂NHR^5q,
  • (28) —SO₂NHNH₂,
  • (29) —P(═O)(OH)₂,

R₁ is selected from the group consisting of

• • (1) —H,
  • (2) —OH,
  • (3) —OC₁-C₆-alkyl,
  • (4) —N(R^2q,R^3q), and
  • (5) substituted or unsubstituted C₁-C₆-alkyl;

    
    
    

    R₂ is selected from the group consisting of

  • (1) H,
  • (2) substituted or unsubstituted C₁-C₆-alkyl,
  • (3) substituted or unsubstituted C₂-C₆-alkenyl,
  • (4) substituted or unsubstituted C₂-C₆-alkenyl,
  • (5) substituted or unsubstituted aryl,
  • (6) substituted or unsubstituted heterocyclyl,
  • (7) substituted or unsubstituted heteroaryl,
  • (8) C₁-C₆-alkyl substituted with aryl,
  • (9) C₁-C₆-alkyl substituted with heterocyclyl, and
  • (10) C₁-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, O and S,
  • R^1q, R^2q, R^3q, R^4q, and R^5q are selected from H or C₁-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:

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;

    
    
    

    L is absent or selected from the group consisting of

  • (1) —(CH₂)_j—NR^3L—(CH₂)_k—,
  • (2) —C(R^1L,R^2L)_j—NR^3L—C(R^1L,R^2L)_k—,
  • (3) —C(R^1L,R^2L)_j—O—C(R^1L,R^2L)_k—,
  • (4) —(CH₂)_j—NR^3L—C(R^1L,R^2L)_k—CONH—(CH₂)_k—,
  • (5) —CO—C(R^1L,R^2L)—NHCO—,
  • (6) —CONH—, and
  • (7) —NHCO—,
  • wherein
  • R^1L, R^2L, R^3L are independently selected from the group consisting of

    • (a) H,
    • (b) substituted or unsubstituted C₁-C₆-alkyl,
    • (c) C₁-C₆-alkyl substituted with aryl,
    • (d) C₁-C₆-alkyl substituted with heterocyclyl,
    • (e) C₁-C₆-alkyl substituted with heteroaryl,

  • or R^1L and R^3L, 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 of 0-4;

    
    
    

    D is absent or selected from the group consisting of

  • (1) substituted or unsubstituted C₃-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)—,
  • (3) —C(═O)NH—,
  • (4) —(CH₂)_iNHCH₂C(═O)NH—,
  • (5) —C≡C—, and
  • (6) —C≡C—C≡C—,
  • wherein i is an integer of 0-4;

    
    
    

    Y is selected from the group consisting of

  • (1) substituted or unsubstituted C₃-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-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 to 8 ring atoms, wherein 1-2 ring atoms of the heterocyclic ring system are selected from N, O and S;

    
    
    

    B is absent or

• • wherein R^1b and R^2b are independently selected from the group consisting of

    • (a) H
    • (b) substituted or unsubstituted C₁-C₆-alkyl,
    • (c) substituted or unsubstituted C₂-C₆-alkenyl,
    • (d) substituted or unsubstituted C₂-C₆-alkenyl,
    • (e) substituted or unsubstituted aryl,
    • (f) substituted or unsubstituted heterocyclyl,
    • (g) substituted or unsubstituted heteroaryl,
    • (h) C₁-C₆-alkyl substituted with aryl,
    • (i) C₁-C₆-alkyl substituted with heterocyclyl, and
    • (j) C₁-C₆-alkyl substituted with heteroaryl,
    • or R^1b and R^2b, 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 C₁-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 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(R^1a,R^2a)(CH₂)_sOR^3a,
  • (3) —(CH₂)_rC(R^1a,R^2a)N(R^4a,R^5a),
  • (4) —(CH₂)_rC(R^1a,R^2a)N(R^4a)COR^3a,
  • (5) —(CH₂)_rC(R^1a,R^2a)NHCON(R^4a,R^5a),
  • (6) —(CH₂)_rC(R^1a,R^2a)NHC(═NH)N(R^4a,R^5a),
  • (7) —CH(R^1a,R^2a),
  • (8) —C≡CH,
  • (9) —(CH₂)_rC(R^1a,R^2a)CN, and
  • (10) —(CH₂)_rC(R^1a,R^2a)CO₂R^3a,
  • wherein R^1a, R^2a, R^3a, R^4a, and R^5a, are independently selected from the group consisting of

    • (a) H,
    • (b) substituted or unsubstituted C₁-C₆-alkyl,
    • (c) C₁-C₆-alkyl substituted with aryl,
    • (d) C₁-C₆-alkyl substituted with heterocyclyl, and
    • (e) C₁-C₆-alkyl substituted with heteroaryl,
    • or R^4a and R^5a, together with the N atom 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;

  • r 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(R₁,R₂),
  • (3) —N(OH)C(═O)N(R₁,R₂),
  • (4) —CH(OH)C(═O)N(R₁,R₂),
  • (5) —CH[N(R^2q,R^3q)]C(═O)N(R₁,R₂), and
  • (6) —CHR^1qC(═O)N(R₁,R₂),

    
    
    

    R¹ is selected from the group consisting of

  • (1) H,
  • (2) OH,
  • (3) OC_1-6-alkyl,
  • (4) N(R^2q,R^3q), and
  • (5) substituted or unsubstituted C_1-4-alkyl;

    
    
    

    R₂ is 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,
  • (5) substituted or unsubstituted heteroaryl,
  • (6) C₁-C₆-alkyl substituted with aryl,
  • (7) C₁-C₆-alkyl substituted with heterocyclyl, and
  • (8) C₁-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, O and S,
  • R^1q, R^2q, and R^3q are selected from H or C₁-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 II:

or stereoisomer, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein D-G-Y taken together, is selected from the group consisting of

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 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 formula III:

or stereoisomer, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein D-G-Y taken together, is selected from the group consisting of

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) —C₁-C₆-alkyl-(C═O)—, and
  • (3) —C₂-C₆-alkenyl-(C═O)—.

    
    
    

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

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

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) —C₁-C₆-alkyl-(C═O)—, and
  • (3) —C₂-C₆-alkenyl-(C═O)—.

    
    
    

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

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

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) —C₁-C₆-alkyl-(C═O)—, and
  • (3) —C₂-C₆-alkenyl-(C═O)—.

    
    
    

    In another embodiment, the present invention provides compounds of formula 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,
  • or E and R^3L, 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,

    
    
    

    R^1L, R^3L are independently selected from the group consisting of

  • (1) H,
  • (2) substituted or unsubstituted C₁-C₆-alkyl,
  • (3) C₁-C₆-alkyl substituted with aryl,
  • (4) C₁-C₆-alkyl substituted with heterocyclyl, and
  • (5) C₁-C₆-alkyl substituted with heteroaryl,
  • or R^1L and R^3L, 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 VII:

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 and R^3L, 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;

    
    
    

    R^1L, R^3L are independently selected from the group consisting of

  • (1) H,
  • (2) substituted or unsubstituted C₁-C₆-alkyl,
  • (3) C₁-C₆-alkyl substituted with aryl,
  • (4) C₁-C₆-alkyl substituted with heterocyclyl, and
  • (5) C₁-C₆-alkyl substituted with heteroaryl,
  • or R^1L and R^3L, 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 VIII:

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 and R^3L, 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;

    
    
    

    R^1L, R^3L are independently selected from the group consisting of

  • (1) H,
  • (2) substituted or unsubstituted C₁-C₆-alkyl,
  • (3) C₁-C₆-alkyl substituted with aryl,
  • (4) C₁-C₆-alkyl substituted with heterocyclyl, and
  • (5) C₁-C₆-alkyl substituted with heteroaryl,
  • or R^1L and R^3L, 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:

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 and R^3L, 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;

    
    
    

    R^1L, R^3L are independently selected from the group consisting of

  • (1) H,
  • (2) substituted or unsubstituted C₁-C₆-alkyl,
  • (3) C₁-C₆-alkyl substituted with aryl,
  • (4) C₁-C₆-allyl substituted with heterocyclyl, and
  • (5) C₁-C₆-alkyl substituted with heteroaryl,
  • or R^1L and R^3L, 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 X:

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 and R^3L, 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;

    
    
    

    R^1L, R^3L are independently selected from the group consisting of

  • (1) H,
  • (2) substituted or unsubstituted C₁-C₆-alkyl,
  • (3) C₁-C₆-alkyl substituted with aryl,
  • (4) C₁-C₆-alkyl substituted with heterocyclyl, and
  • (5) C₁-C₆-alkyl substituted with heteroaryl,
  • or R^1L and R^3L, 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:

or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein Y-X taken together, is selected from the group consisting of

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

or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein R^1b and R^2b are independently selected from the group consisting of

• • (1) H,
  • (2) substituted or unsubstituted C₁-C₆-alkyl,
  • (3) substituted or unsubstituted C₂-C₆-alkenyl,
  • (4) substituted or unsubstituted C₂-C₆-alkenyl,
  • (5) substituted or unsubstituted aryl,
  • (6) substituted or unsubstituted heterocyclyl,
  • (7) substituted or unsubstituted heteroaryl,
  • (8) C₁-C₆-alkyl substituted with aryl,
  • (9) C₁-C₆-alkyl substituted with heterocyclyl, and
  • (10) C₁-C₆-alkyl substituted with heteroaryl;

    
    
    

    q is an integer of 0-2;

    
    
    

    In another embodiment, the present invention provides compounds of formula XI

or stereoisomers, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein

R₄ is selected from the group consisting of

• • (1) H,
  • (2) substituted or unsubstituted C₁-C₆-alkyl,
  • (3) C₁-C₆-alkyl substituted with aryl,
  • (4) C₁-C₆-alkyl substituted with heterocyclyl, and
  • (5) C₁-C₆-alkyl substituted with heteroaryl;

A is H or —CH(CH₃)OH—;

R₁ is H or substituted or unsubstituted C_1-6-alkyl;

R₂ is 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,
  • (5) substituted or unsubstituted heteroaryl,
  • (6) C₁-C₆-alkyl substituted with aryl,
  • (7) C₁-C₆-alkyl substituted with heterocyclyl,
  • (8) C₁-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 formula XIV:

or stereoisomer, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein D-G-Y taken together is selected from the group consisting of

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;

R₄ is selected from the group consisting of

• • (1) H,
  • (2) substituted or unsubstituted C₁-C₆-alkyl,
  • (3) C₁-C₆-alkyl substituted with aryl,
  • (4) C₁-C₆-alkyl substituted with heterocyclyl, and
  • (5) C₁-C₆-alkyl substituted with heteroaryl.

    
    
    

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

or stereoisomer, pharmaceutically acceptable salts, esters, and prodrugs thereof, wherein D-G-Y taken together, is selected from the group consisting of

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;

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

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

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;

R₄ is selected from the group consisting of

• • (1) H,
  • (2) substituted or unsubstituted C₁-C₆-alkyl,
  • (3) C₁-C₆-alkyl substituted with aryl,
  • (4) C₁-C₆-alkyl substituted with heterocyclyl, and
  • (5) C₁-C₆-alkyl substituted with heteroaryl;

    
    
    

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

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

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;

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 formula I.

In some embodiments of the method of inhibiting LpxC using a compound of formula I, the IC₅₀ value of the compound is less than or equal to 10 μM with respect to LpxC. In other such embodiments, the IC₅₀ value is less than or equal to 1 μM, is less than or equal to 0.1 μM, is less than or equal to 0.050 μM, is less than or equal to 0.030 μM, is less than or equal to 0.025 μM, or is less than or equal to 0.010 μM.

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 of a 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, and vancomycin.

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 antibodies antilipopolysaccharide-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, bronchodilators, mucolytics, anti-asthma therapeutics and lung fluid surfactants. In particular, the non-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, bronchodilators, mucolytics, calfactant, beractant, poractant alfa, surfaxin and pulmozyme (also called dornase 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, Stenotrophomonas maltophilia, Pseudomonas aeruginosa, Burkholderia cepacia, Acinetobacter calcoaceticus, Alcaligenes xylosoxidans, Flavobacterium meningosepticum, Providencia stuartii and Citrobacter freundi, 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, Helicobacter pylori, Vibrionaceae and Bordetella species as well as the infections is caused by a Brucella species, Francisella tularensis and/or Yersinia Pestis.

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, meziocillin, 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 and sulfathalidine;
  • (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 and rifaximin;
  • (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 and colymycin;
  • (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 containing a 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 consisting of tobramycin, gentamicin, aztreonam, ciprofloxacin, polymyxin, colistin, colymycin, azithromycin and clarithromycin.

Pharmaceutical Compositions

Pharmaceutical compositions of the present invention comprise a therapeutically 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- or diglycerides. 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 absorption of a parenterally administered drug form may be accomplished by dissolving or suspending the drug in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the drug in biodegradable polymers such as polylactide-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 or dicalcium-phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, acetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid 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 other tableting 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 or transdermal 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 to 5 μM. 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 from 1-5 μm. Predominantly in this application means that at least 70% but preferably more than 90% of all generated aerosol particles are 1 to 5 μm 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, Calif.), Sidestream7 nebulizers (Medic-Aid Ltd., West Sussex, England), Pari LC7 and Pari LC Star7 jet nebulizers (Pari Respiratory Equipment, Inc., Richmond, Va.), and Aerosonic (DeVilbiss Medizinische Produkte (Deutschland) GmbH, Heiden, Germany) and UltraAire7 (Omron Healthcare, Inc., Vernon Hills, Ill.) 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 of a 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 reasonable benefit/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, in Remington: 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 tam 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 tablets and/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 “daily dose” 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 taken and/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 and oxazolidinones. 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 Millennium chromatography system with a 2690 Separation Module (Milford, Mass.). The analytical columns were Alltima C-18 reversed phase, 4.6×250 mm from Alltech (Deerfield, Ill.). A gradient elution was used, typically starting with 5% acetonitrile/95% water and progressing to 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 254 nm. HPLC solvents were from Burdick and Jackson (Muskegan, Mich.), or Fisher Scientific (Pittsburgh, Pa.). In some instances, purity was assessed by thin layer chromatography (TLC) using glass or plastic backed silica gel plates, such as, for example, Baker-Flex Silica Gel 1B2-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: Eclipse XDB-C18, 2.1×50 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 temperature 40° C.) or a Hewlett Packard System (Series 1100 HPLC; Column: Eclipse XDB-C18, 2.1×50 mm; solvent system: 1-95% acetonitrile in water with 0.05% TFA; flow rate 0.4 mL/min; molecular weight range 150-850; cone Voltage 50 V; column temperature 30° 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: 1 μL; initial column temperature: 50° C.; final column temperature: 250 C; ramp time: 20 minutes; gas flow rate: 1 mL/min; column: 5% phenyl methyl siloxane, Model #HP 190915-443, dimensions: 30.0 m×25 m×0.25 m).

Nuclear magnetic resonance (NMR) analysis was performed with a Varian 300 Mhz NMR (Palo Alto, Calif.). 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, Ariz.)

Melting points were determined on a Laboratory Devices Mel-Temp apparatus (Holliston, Mass.).

Preparative separations were carried out using a Flash 40 chromatography system and KP-Sil, 60A (Biotage, Charlottesville, Va.), 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 hydroxamic acids or similar scaffolds having a wide variety of substituents are comprehensively reviewed in Kline T, Andersen N H, Harwood E A, Bowman J, Malanda A, Endsley S, Erwin A L, Doyle M, Fong S, Harris A L, Mendelsohn B, Mdluli K, Raetz C R, Stover C K, Witte P R, Yabannavar A, Zhu S., “Potent, novel in vitro inhibitors of the Pseudomonas aeruginosa deacetylase LpxC,” J Med Chem 2002 Jul. 4; 45(14):3112-29; Patchett, A. A., Nargund, R., Chen, M.-H., Nishi, H. R., U.S. Pat. No. 5,925,659, 1999; Pirrung, M. C., Chau, J. H., “A Convenient Procedure for the Preparation of Amino Acid Hydroxamates from Esters,” J. Org. Chem. 1995, 60, 8084-8085; Nhu, K., Patel, D. V., “A New and Efficient Solid Phase Synthesis of 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 WO 98/18754, 1998, Mellor, S. L., McGuire, C., Chan, W. C., “N-Fmoc-aminoxy-2-chlortrityl Polystyrene Resin: A Facile Solid-phase Methodology for the Synthesis of Hydroxamic Acids,” Tetrahedron Lett., 1997, 38, 3311-3314; Khan, S. I., Grinstaff; M. W., “A Facile and Convenient Solid-phase Procedure for Synthesizing Nucleoside Hydroxamic Acids,” 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 Gelatinase Inhibitors,” 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 Method of Heterocycle Synthesis,” J. Am. Chem. Soc., 1973, 95, 4447-4448; Ito, Y., Ito, L, Hirao, T., Saegus, T., “Synthetic Reactions by Complex Catalysts XXXV,” Syn. Commun. 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 Synthesis of Thiangazole, A Novel Naturally Occurring HIV-1 Inhibitor from Polyangium sp.” Tetrahedron, 1995, 51, 7321-7330; Galeotti, N., Plagnes, E., Jouin, P., “Synthesis of Peptidyl Aldehydes from Thiazolines,” Tetrahedron. Lett. 1997, 38, 2459-2462; Charette, A. B., Chua, P., “Mild Method for the Synthesis of Thiazolines from Secondary and Tertiary Amides,” 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 C4′ Hydroxylation on the Iron Clearing Efficiency and Toxicity of Desferrithiocin 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: Biomimetic Synthesis of Thiazoline- and Thiazole-containing Heterocycles,” Org. Lett., 2000, 2, 3289-3292; Fernandez, X., Fellous, R, Dunach, E., “Novel Synthesis of 2-Thioazolines,” Tetrahedron Lett., 2000, 41, 3381-3384. Wipf, P., Miller, C. P., Venkatraman, S., Fritch, P., “C. Thiolysis of Oxazolinenes: A New, Selective Method for the Direct Conversion of Peptide Oxazolines into. Thiazolines,” Tetrahedron Lett., 1995, 36, 6395-6398, which are incorporated herein by reference.

The synthesis of other non-hydroxamates compounds or more generally zinc binding groups are reviewed in Pirrung, M. C., Tumey, L. N., Raetz, C. R. H., Jackman, J. E., Snehalatha, K, McClerren, A. L., Fierke, C. A., Gantt, S. L., Rusche, K. M., “Inhibition of the Antibacterial Target UDP-(3-O-acyl)-N-acetylglucosamine Deacetylase (LpxC): Isoxazoline Zinc Amidase Inhibitors Bearing Diverse Metal Binding Groups,” Journal of Medicinal Chemistry (2002), 45(19), 4359-4370; Jackman, J. E., Fierke, C. A., Tumey, L. N., Pirrung, M., Uchiyama, T., Tahir, S. H., Hindsgaul, O., Raetz, C. R. H., “Antibacterial agents that target lipid A biosynthesis in gram-negative bacteria: inhibition of diverse UDP-3-O—(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylases by substrate analogs containing zinc binding motifs,” Journal of Biological Chemistry (2000), 275(15), 11002-11009; Brooks, C. D. W., Summers, J. B., “Modulators of Leukotriene Biosynthesis and Receptor Activation,” Journal of Medicinal Chemistry (1996), 39(14), 2629-2654; Jeng, A. Y., De Lombaert, S., “Endothelin converting enzyme inhibitors,” Current Pharmaceutical Design (1997), 3(6), 597-614; Zask, A., Levin, J. L., Killar, L. M., Skotnicki, J. S., “Inhibition of matrix metalloproteinases: structure based design,” Current Pharmaceutical Design (1996), 2(6), 624-661; Skotnicki, J. S., DiGrandi, M. J., Levin, J. L., Chemical and Screening Sciences, Wyeth Research, New York, N.Y., USA. Current Opinion in Drug Discovery & Development (2003), 6(5), 742-759.

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)-OH 3-(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: Diisopropylethylamine
  • DME: 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 acetate
  • EtOH: Ethanol
  • Fmoc: 9-fluorenylmethoxycarbonyl
  • Gly-OH: glycine
  • HATU: O-(7-azabenzotriaazo-1-yl)-N,N,N′N′=tetramethyluronium hexafluorophosphate
  • HBTU: 2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate
  • Hex: hexane
  • HOBt: butyl alcohol
  • HOBT: 1-Hydroxybenzotriazole
  • HPLC: High Pressure Liquid Chromatography
  • IC₅₀ 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 methoxide
  • nm: Nanometer
  • NMP: N-Methylpyrrolidone
  • PPh₃: triphenyl phosphine
  • RP-HPLC: Reversed-phase high-pressure liquid chromatography
  • RT: 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 (Nov. 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

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

Reagent

MW

Eq.

g/ml

mmol

Benzoic acid (1)

219.02

1.0

2.152

g

9.83

L-Thr-OMe—HCl

169.61

1.2

1.968

g

11.6

EDCI

191.71

1.2

2.218

g

11.6

HOBt

135.13

1.1

1.410

g

10.4

DIEA

129.25

4.0

6.8

ml

39.0

DMF

60

ml

Preparation of (2S,3R)-2-(3-bromo-4-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 (2.152 g, 9.83 mmol), L-threonine methyl ester hydrochloride (1.968 g, 11.6 mmol), EDCI (2.218 g, 11.6 mmol) and HOBt (1.410 g, 10.4 mmol) in anhydrous DMF (60 mL) at 0° C. under N₂. The solution was stirred at 0° C. for 1 h and at room temperature for 20 h. The solution was diluted with EtOAc (300 mL) and washed with 1.0 M HCl (2×80 mL), saturated NaHCO₃ (2×80 mL), H₂O (4×80 mL), dried over MgSO₄, 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 (C₁₂H₁₃BrFNO₄+H requires 334.00).

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

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 M HCl (10 mL) was added and the solution extracted with 4:1 chloroform/isopropyl alcohol (4×20 mL). The organic layers were combined, dried over Na₂SO₄ and concentrated to give a pink foam. The crude solid was triturated with diethyl ether (2×8 mL) and dried in vacuo to give 3-bromo-4-fluoro-N-{(1S,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

Synthesis of 4-benzoyl-N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino) carbonyl]propyl}benzamide

Procedure:

To a solution of hydroxylamine hydrochloride (121 mg, 1.74 mmol) in anhydrous MeOH (2.0 mL) at 0° C. under N2 atmosphere was added sodium methoxide (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 at 0° 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 5:1 chloroform/isopropyl alcohol (4×40 mL). The organic layers were combined, dried over Na₂SO₄ and concentrated to give an orange foam. Purification by silica gel chromatography (increasing eluant polarity from 30:1 CH₂Cl₂/MeOH to 15:1 CH₂Cl₂/MeOH) 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)

Procedure:

To a solution of (2R,3R-3-hydroxy-1-{[4-(trifluoromethoxy)phenyl]carbonyl}pyrrolidine-2-carboxylic acid (1) (405 mg, 1.27 mmol), benzylhydroxylamine hydrochloride (243 mg, 1.52 mmol), HATU (556 mg, 1.46 mmol), and HOBt (178 mg, 1.32 mmol) in DMF (10 mL) at 0° C. was added diisopropylethylamine (710 μL, 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 (2×60 mL), sat. NaHCO₃ (2×60 mL) and H₂O (5×60 mL), dried over MgSO₄ 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 (25:1 CH₂Cl₂/MeOH)=0.35.

Preparation of (2R,3R-3-hydroxy-1-{[4-(trifluoromethoxy)phenyl]carbonyl}pyrrolidine-2-carbohydroxamic acid (2)

Procedure:

To a solution of ((2R,3R)-3-hydroxy-1-{[4-(trifluoromethoxy)phenyl]carbonyl}pyrrolidin-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 (10 mL) and filtered through celite, washing with 20:1 EtOAc/EtOH (50 mL). The solution was concentrated and dried in vacuo to afford 90 mg (80%) of (2R,3R)-3-hydroxy-1-{[4-(trifluoromethoxy)phenyl]carbonyl}pyrrolidine-2-carbohydroxamic acid (2) as a sticky white foam: mp 64-65° C. Rf (10:1 CH₂Cl₂/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)

Reagent

MW

Eq.

g/ml

mmol

4-biphenylcarboxaldehyde

182.22

1.0

1.104

g

6.06

L-Tbr-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

25

mL

Triethylamine (1.70 mL, 12.1 mmol) was added to a stirred suspension of 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 (50:1 DCM/MeOH, R_f=0.4). The reaction mixture was quenched with saturated NaHCO₃ (50 mL), extracted with EtOAc (2×120 mL), dried over MgSO₄, 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 addition of NH₂OH in MeOH/NaOMe at 0° C., warming to ambient temperature 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)

Suzuki Procedures Using Pd(dppf)Cl₂-DCM Catalyst and a THF/H₂O Mixture

Reagent

MW

EQ

g/ml

mmol

BromoArene #1

~300

1

 100 mg

~0.33

Boronic Acid #2

—

  1.2

—

~0.40

Na₂CO₃

105.99

3

 104 m 

~0.99

Pd(dppf)Cl₂

816.63

0.1-0.2

27-54 mg

~0.033-0.066

THF (3) (sparged with argon for 5 min.)

 0.75 ml

water(1) (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 (1 ml). The organic layer is separated and washed with NaHCO₃ (2×3 ml), water (1×3 ml), brine (1×3 ml), dried with Na₂SO₄, 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

Reagent

MW

EQ

g/ml

mmol

BromoArene #1

~500

1

20

mg

~0.04

Boronic Acid #2

~200

2

~14

mg

~0.08

Pd(dppf)Cl₂

816.63

0.25

10

mg

~0.01-0.02

TEA

101.19

5

28

μL

~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 Analogue

Example 5

3-(R)-Amino-2-(S)-[(4′-ethyl-biphenyl-4-carbonyl)-amino]butyl-hydroxamic acid (8)

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

Reagent

MW

EQ

g/ml

mmol

H-allo-Thr-OMe•HCl (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 (3.2 g, 10.0 mmol) in CHCl₃ (40 ml) was added dropwise to a stirred solution of allo-threonine methyl ester HCl salt (1) (2.0 g, 12.0 mmol) and DIEA (5.2 ml, 30.0 mmol) in CHCl₃ (60 ml) at rt under N₂. The reaction could be followed by TLC eluting with EtOAc/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 (170 ml) and washed with 0.2 N citric acid (2×50 ml), water (2×50 ml), brine (50 ml), dried (Na₂SO₄), filtered and concentrated under reduced pressure to yield 3.73 g (85% yield, 95% pure) of a yellow solid.

HPLC (220 nm, 41 min. run) 30.90 min.; HPLC (220 nm, 17 min. run) 14.86 min.; LCMS: LC (214 nm) 3.06 min., MS (ES+) m/z 376.2 (C₂₄H₂₅NO₃+H requires 376.18).

Preparation of 3-(R)-Azido-2-(S)-trityl-amino)-butyric acid methyl ester (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)

174.16

1.6

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 (2.9 ml, 17.8 mmol) in THF (5 ml) was added slowly dropwise to a stirred solution of trt-allo-threonine methyl ester (2) (4.1 g, 10.9 mmol) and PPh₃ (2.9 g, 10.9 mmol) in THF (40 ml) at 0° C. under N₂. After 3 min., a solution of DPPA (6.4 ml, 29.7 mmol) in THF (5 ml) was added to the orange-yellow reaction solution at 0° C. After 1 h, the reaction was allowed to warm to rt. After 40 h, 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 18 g of crude material that was purified by column chromatography eluting with Hexane/EtOAc (88:12) giving 3.5 g 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 with Hexane/DCM/EtOAc (76:20:4) giving 1.65 g (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 5.44 g (14.5 mmol) of trt-allo-threonine methyl ester (2) in DCM (100 ml) with PPh₃ (3.8 g, 14.5 mmol), pure DEAD (3.4 ml, 21.8 mmol) in DCM (5 ml) and DPPA (6.3 ml, 24.0 mmol) in DCM (10 ml) were combined following the procedure above. After 3 days, the reaction did not progress further by TLC and LCMS. After the same work up, 2.97 g of the product was obtained in 51% yield.

HPLC (220 nm, 41 min. run) 40.5 min.; HPLC (220 nm, 17 min. run) 16.32 min.; LCMS: LC (214 nm) 3.7 min., MS (ES+) m/z 401.2 (C₂₄H₂₅N₃O₂+H requires 401.15).

Preparation of 2-(S)-Amino-3-(R)-azido-butyric acid methyl ester HCl Salt (4)

Reagent

MW

EQ

g/ml

mmol

Trt-Azido-Thr-OMe (3)

400.47

1.0

4.79

g

11.98

TFA

57

ml

CHCl₃ (dry)

3

ml

A solution of Trt-Azido-Thr-OMe (3) (4.8 g, 12.0 mmol) was dissolved in a 95% TFA/DCM solution (60 ml) at rt with stirring. After 2.5 h, the reaction was complete by LCMS. The bright yellow solution was diluted with 0.5 N aq. HCl (300 ml). The aqueous layer was extracted with DCM (2×30 ml) and then lyophilized to dryness. The white solid was dissolved in AcCN/water (50:50) (100 ml) and again lyophilized to dryness to produce a consistent powder and remove as much of the TFA as possible. The azido-Thr product (4), 2.26 g (97% yield, 95% pure) of a white solid, was obtained as the HCl salt.

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

Preparation of 3-(R)-Azido-2-(S)-[(4′-ethyl-biphenyl-4-carbonyl)-amino]-butyric acid methyl ester (6)

Reagent

MW

EQ

g/ml

mmol

Azido-Thr-OMe•HCl (4)

194.62

1.0

195

mg

1.0

Biphenyl Acid (5)

226.27

1.0

226

mg

1.0

HOBT

153

1.0

158

mg

1.0

EDC•HCl

191.17

1.3

249

mg

1.3

DIEA

129.25

2.5

0.44

ml

2.5

DCM (dry)

10

ml

A EDC.HCl (249 mg, 1.3 mmol) was added to a stirred colorless solution of azido-Thr-OMe.HCl (4) (195 mg, 11.0 mmol), HOBT (158 mg, 1.0 mmol), 4′-Ethyl-biphenyl-4-carboxylic acid (5) (226 mg, 1.0 mmol) and DIEA (0.44 ml, 2.5 mmol) in DCM (10 ml) at rt under N₂. After 24 h, the reaction had reached completion by TLC (Hexane/EtOAc (60:40) (Rf=0.3)) and LCMS. The reaction was evaporated under reduced pressure to a brown tar. The crude product was dissolved in EtOAc (100 ml) and washed with 0.2N aq. HCl (2×50 ml), aq. sat. NaHCO₃ (50 ml), brine (50 ml), dried (Na₂SO₄), filtered and concentrated under reduced pressure to yield a crude brown solid. The crude material was further purified by column chromatography eluting with Hexane/EtOAc (70:30) giving 245 mg (67% yield) of pure product after evaporation and drying in vacuo.

HPLC (220 nm, 41 min. run) 33.87 min.; HPLC (220 nm, 17 min. run) 15.61 min; LCMS: LC (214 nm) 3.25 min., MS (ES+) m/z 367.2 (C₂₀H₂₂N₄O₃+H requires 367.17).

Preparation of 3-(R)-Amino-2-(S)-[(4′-ethyl-biphenyl-4-carbonyl)-amino]-butyric acid methyl ester (7)

Reagent

MW

EQ

g/ml

mmol

Biphenyl Azido-Thr (6)

366.41

1.0

244 mg

0.67

10% Pd/C

200 mg

H₂ (gas)

12” balloon

MeOH (dry)

10 ml

A solution of biphenyl azido-Thr methyl ester (6) (244 mg, 0.67 mmol) in MeOH (10 ml) was made by sonicating until the milky precipitate cleared. After bubbling nitrogen through the reaction solution for 30 sec., 10% Pd/C was added in one portion. The reaction was stirred under nitrogen at RT. The reaction was exposed to aspirator vacuum to remove the nitrogen and then opened to the hydrogen gas at balloon pressure (˜1 atm). The reaction stirred for 3 h 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 (30 ml). The combined fractions of MeOH were evaporated under reduced pressure and dried in vacuo to give 225 mg (99% yield) of pure produce (7) as a white solid.

HPLC (220 nm, 17 min. run) 10.79 min.; LCMS: LC (214 nm) 2.21 min., MS (ES+) m/z 341.2 (C₂₀H₂₄N₂O₂+H requires 341.18).

Preparation of 3-(R)-Amino-2-(S)-[(4′-ethyl-biphenyl-4-carbonyl)-amino]-butyl-hydroxamic acid (8)

Reagent

MW

EQ

g/ml

mmol

Amino-Thr-OMe (7)

340.42

1.0

225

mg

0.66

H₂NOH•HCl

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) (225 mg, 0.6 mmol) and hydroxylamine HCl salt (460 mg, 6.6 mmol) in MeOH (7 ml) and DCM (5 ml) was added fresh solid NaOMe powder (430 mg, 7.92 mmol) 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 (50-10 mg) 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 (250 mg 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 Büchner funnel. The white residue was washed with MeOH (15 ml). The organic fractions were collected and concentrated under reduced pressure to give crude product (750 mg). The crude product (only one 150 mg portion) was dissolved in DMSO (1 ml), AcCN (100 μl) and water (100 μl), passed through a Teflon syringe filter, and the clear filtrate was injected on a preparative HPLC. The purification used a 20×50 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. The product as the TFA salt was dissolved in AcCN/water (50:50) (5 ml), 1N aq. HCl (1 equivalent) and lyophilized again to give 11.5 mg of white powder as an HCl salt (23% yield).

HPLC (220 nm, 41 min. run) 19.31 min.; HPLC (220 nm, 17 min. run) 9.39 min; LCMS: LC (214 nm) 1.98 min., MS (ES+) m/z 342.2 (C₁₉H₂₃N₃O₃+H requires 342.17).

Synthesis of 4′Benzamide Biphenyl Threonine Hydroxamic Acid

Example 6

Biphenyl-4,4′-dicarboxylic acid 4′-[(3-Boc-amino-propyl)-amide]4-[((2R)-hydroxy-(1S)-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)

Synthesis of (2S,3R)-2-amino-3-(phenylmethoxy)butanamide (1)

Procedure:

To a suspension of benzylhydroxylamine hydrochloride (8.310 g, 52.06 mmol), Boc-Thr(OBn)-OH (14.01 g, 45.28 mmol), 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 with CH₂Cl₂ (300 mL). The organic layer was washed with 1.0) M HCl (2×200 mL), sat. NaHCO₃ (2×200 mL) and brine (200 mL), dried over MgSO₄ and concentrated to give 14.5 g of a white solid. The crude solid was treated with a solution of trifluoroacetic acid (90 mL) in CH₂Cl₂ (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 (2×200 mL), dried over MgSO₄ and concentrated to give a dark orange oil. Purification by silica gel chromatography (50:1 CH₂Cl₂/MeOH) afforded (2S,3R)-2-amino-3-(phenylmethoxy)-N-(phenylmethoxy) butanamide (A) (8.9 g) as a pale yellow oil. Rf (50:1 CH₂Cl₂/MeOH on silica gel)=0.2.

Preparation of (1S,2R)-4′-(2-benzyloxy-1-benzyloxycarbamoyl-propylcarbamoyl)biphenyl-4-carboxylic acid (3)

Reagent

MW

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

200

mL

To a suspension of 4,4′-biphenyldicarboxylic acid 2 (1.360 g, 5.61 mmol) in DMF (180 mL) was added BOP (2.007 g, 4.54 mmol) and DIEA (1.7 ml, 9.8 mmol). A solution of (1S,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 18 h. The solution was diluted with EtOAc (250 mL) and washed with 1.0 M HCl (500 mL). The aqueous layer was extracted with EtOAc (250 mL) and the organic layers combined. The organic layer was washed with 1.0 M HCl (250 mL), dried over MgSO₄, and concentrated to give a crude yellow solid. Purification by silica gel chromatography (60:1 CH₂Cl₂/MeOH) gave 210 mg (1S,2R)-4′-(2-benzyloxy-1-benzyloxycarbamoyl-propylcarbamoyl)-biphenyl-4-carboxylic acid 3. (13% yield) as a yellow solid. R_f=0.80 (10:1 CH₂Cl₂/MeOH); LRMS (ES+) m/z 539.1 (C₃₂H₃₀N₂O₆+H requires 539.22).

Preparation of biphenyl-4,4′-dicarboxylic acid 4′-[(3-(Boc)-amino-propyl)-amide]-4-[(2R)-benzyloxy-(1S)-benzyloxycarbamoyl-propyl)-amide] (5)

Reagent

MW

Eq.

g/mL

mmol

Biphenylcarboxylic 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

μL

1.0

DMF

2

mL

To a solution of biphenylcarboxylic acid 3 (200 mg, 0.371 mmol), EDCI (78 mg, 0.407 mmol), and HOBt (52 mg, 0.385 mmol) in DF (2 mL) was added t-Butyl N-(3-aminopropyl)carbamate 4 (71 mg, 0.407 mmol) and DIEA (180 μL, 1.0 mmol). The reaction mixture was stirred 24 h, diluted with EtOAc (150 mL), washed with 1.0 M HCl (2×60 mL), saturated NaHCO₃ (2×60 mL), H₂O (3×60 mL), dried over MgSO₄ and concentrated to give a crude white solid. Purification by silica gel chromatography (25:1 CH₂Cl₂/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. R_f 0.15 (50:1 CH₂Cl₂/MeOH); LRMS (ES+) m/z 695.2 (C₄₀H₄₆N₄O₇+H requires 695.35).

Preparation of 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-protected 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) for 16 h. The crude mixture was filtered through a plug of celite eluting with 2:1 MeOH/THF (15 mL) and concentrated to give an orange syrup. Purification by silica gel chromatography (5:1:1 THF/MeOH/CH₂Cl₂ afforded 110 mg (78% yield) of biphenyl-4,4′-dicarboxylic acid 4′-[(3-Boc-amino-propyl)-amide]4-[((2R)-hydroxy-(1S)-hydroxycarbamoyl-propyl)-amide] as a white foam, mp 75-77° C. R_f=0.20 (10:1 CH₂Cl₂/MeOH); LRMS (ES+) m/z 515.4 (C₂₆H₃₄N₄O₇+H requires 515.26).

Preparation of Biphenyl-4,4′-dicarboxylic acid 4′-[(3-amino-propyl)-amide]4-[((2R)-hydroxy-(1S)-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

CH₂Cl₂

3.0

mL

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 by RP-HPLC (C₁₈ column, CH₃CN gradient 5-70%, 0.1% TFA, UV analysis 300 nm, 36 min) and lyophilization of the collected fractions afforded 14 mg (21% yield) of biphenyl-4,4′-dicarboxylic acid 4′-[(3-amino-propyl)-amide]4-[((2R)-hydroxy-(1S)-hydroxycarbamoyl-propyl)-amide] as a white solid. LRMS (ES+) m/z 415.3 (C₂₁H₂₆N₄O₅+H requires 415.20); RP-HPLC (300 mm, 36 min run) 18.2 min.

Example 8

Synthesis of N-(2-(N-hydroxycarbamoyl)(2S)-2-{[4-(4-ethylphenyl)phenyl]carbonylamino}ethyl)acetamide (4)

Preparation of 3-Acetylamino-2-(9H-fluoren-9-ylmethoxycarbonylamino)-propionic acid (2)