Peptide Deformylase Inhibitors for Addressing the Issue of Bacterial Resistance

Tripti Kumari(1*), Richa Arora(2), Rita Kakkar(3)

(1) Department of Chemistry, University of Delhi, India
(2) Department of Chemistry, University of Delhi, India
(3) Department of Chemistry, University of Delhi, India
(*) Corresponding author


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Abstract


Peptide Deformylase (PDF) is an attractive antibacterial target, and is gaining much momentum in contemporary research because of its remarkable features. This article reviews the bacterial PDF structure and criteria required for designing novel PDF inhibitors. It also presents a summary of the known and recently explored classes of PDF inhibitors, both peptidic and non-peptidic
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Keywords


Non-Peptidic Inhibitors; Peptide Deformylase (PDF); Peptidic Inhibitors

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References


Y. Balabanova, M. Ruddy, et al., Multidrug-Resistant Tuberculosis in Russia: Clinical characteristics, analysis of second-line drug resistance and development of standardized therapy, European Journal of Clinical Microbiology and Infectious Diseases, Volume 24, (Issue 2), January 2005, Pages 136-139.

Centers for Disease Control and Prevention (CDC), Emergence of Mycobacterium tuberculosis with extensive resistance to second-line drugs-worldwide, 2000-2004, Morbidity and Mortality Weekly Reports (MMWR), Volume 55, (Issue 11), March 2006, Pages 301-305.

T.G. Chandrashekarappa, S. Suresh, Challenges facing antitubercular therapy: New drugs and delivery systems, Clinical Research and Regulatory Affairs, Volume 24, (Issue 2-4), January 2007, Pages 95-109.

G. Lamichhane, Novel targets in M. tuberculosis: Search for new drugs, Trends in Molecular Medicine, Volume 17, (Issue 1), January 2011, Pages 25-33.

S. Sarkar, M.R. Suresh, An overview of tuberculosis chemotherapy – a literature review, Journal of Pharmacy and Pharmaceutical Science, Volume 14, (Issue 2), April 2011, Pages 148-161.

E.L. Corbett, C.J. Watt, et al., The growing burden of tuberculosis: Global trends and interactions with the HIV epidemic, Archives of Internal Medicine, Volume 163, (Issue 9), May 2003, Pages 1009-1021.

E. Marris, Extreme TB strain threatens HIV victims worldwide, Nature, Volume 443, (Issue 7108), September 2006, Page 131.

K.A. Sepkowitz, J. Raffali, et al., Tuberculosis in AIDS era, Clinical Microbiology Reviews, Volume 8, (Issue 2), April 1995, Pages 180-199.

World Health Organisation. Stop TB annual report. W.H.O/CDS/STB/2002.17. World Health Organisation, Geneva, Switzerland.

S.J. Aarons, I.W. Sutherland, et al., A novel gene, algK, from the alginate biosynthetic cluster of Pseudomanas aeruginosa, Microbiology, Volume 143, (Issue 2), February 1997, Pages 641-652.

J. Davies, Inactivation of antibiotics and the dissemination of resistance genes, Science, Volume 264, (Issue 5157), April 1994, Pages 375-382.

H. Nikaido, Prevention of drug access to bacterial targets: Permeability barriers and active efflux, Science, Volume 264, (Issue 5157), April 1994, Pages 382-388.

B.G. Spratt, Resistance to antibiotics mediated by target alterations, Science, Volume 264, (Issue 5157), April 1994, Pages 388-393.

D.Z. Chen, D.V. Patel, et al., Actinonin, a naturally occurring antibacterial agent, is a potent deformylase inhibitor, Biochemistry, Volume 39, (Issue 6), February 2000, Pages 1256-1262.

D. Groche, A. Becker, et al., Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site, Biochemical and Biophysical Research Communications, Volume 246, (Issue 2), May 1998, Pages 342-346.

C.J. Hackbarth, D.Z. Chen, et al., N-alkyl urea hydroxamic acids as a new class of peptide deformylase inhibitors with antibacterial activity, Antimicrobial Agents and Chemotherapy, Volume 46, (Issue 9), September 2002, Pages 2752-2764.

R. Jain, D. Chen, et al., Bacterial peptide deformylase inhibitors: A new class of antibacterial agents, Current Medicinal Chemistry, Volume 12, (Issue 14), July 2005, Pages 1607-1621.

S.-Y. P. Chang, E.C. McGary, et al., Methionine aminopeptidase gene of Escherichia coli is essential for cell growth, Journal of Bacteriology, Volume 171, (Issue 7), July 1989, Pages 4071-4072.

P.S. Margolis, C.J. Hackbarth, et al., Peptide deformylase in Staphylococcus aureus: Resistance to inhibition is mediated by mutations in the formyltransferase gene, Antimicrobial Agents and Chemotherapy, Volume 44, (Issue 7), July 2000, Pages 1825-1831.

D. Mazel, S. Pochet, et al., Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation, The EMBO Journal, Volume 13, (Issue 4), February 1994, Pages 914-923.

C. Giglione, T. Meinnel, Peptide deformylase as an emerging target for antiparasitic agents, Expert Opinion on Therapeutic Targets, Volume 5, (Issue 1), February 2001, Pages 41-57.

J.-P. Guilloteau, M. Mathieu, et al., The crystal structure of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: A platform for the structure-based design of antibacterial agents, Journal of Molecular Biology, Volume 320, (Issue 5), July 2002, Pages 951-962.

M.F. Browner, W.W. Smith, et al., Crystal structure of matrilysin-inhibitor complexes, Biochemistry, Volume 34, (Issue 20), May 1995, Pages 6602-6610.

M.K. Chan, W. Gong, et al., Crystal structure of the Escherichia coli peptide deformylase, Biochemistry, Volume 36, (Issue 45), November 1997, Pages 13904-13909 [Erratum published Biochemistry, Volume 37, (Issue 37), September 1998, Page 13042.]

F. Dardel, S. Ragusa, et al., Solution structure of nickel-peptide deformylase, Journal of Molecular Biology, Volume 280, (Issue 3), July 1998, Pages 501-513.

B. Hao, W. Gong, et al., Structural basis for the design of antibiotics targeting peptide deformylase, Biochemistry, Volume 38, (Issue 15), April 1999, Pages 4712-4719.

T. Meinnel, S. Blanquet, et al., A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase, Journal of Molecular Biology, Volume 262, (Issue 3), September 1996, Pages 375-386.

M.A. Holmes, B.W. Matthews, Structure of thermolysin refined at 1.6 Å resolution, Journal of Molecular Biology, Volume 160, (Issue 4), October 1982, Pages 623-639.

P.R. Gooley, J.F. O'Connell, et al., The NMR structure of the inhibited catalytic domain of human stromelysin-1, Nature Structural Biology, Volume 1, (Issue 2), February 1994, Pages 111-118.

K.T. Nguyen, X. Hu, et al., Characterization of a human peptide deformylase: Implications for antibacterial drug design, Biochemistry, Volume 42, (Issue 33), August 2003, Pages 9952-9958.

S. Fieulaine, A. Boularot, et al., Trapping conformational states along ligand-binding dynamics of peptide deformylase: The impact of induced fit on enzyme catalysis, PLoS Biology, Volume 9, (Issue 5), May 2011, Pages 1-17.

C. Giglione, A. Serero, et al., Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms, The EMBO Journal, Volume 19, (Issue 21), November 2000, Pages 5916-5929.

J.A. Leeds, C.R. Dean, Peptide deformylase as an antibacterial target: A critical assessment, Current Opinion in Pharmacology, Volume 6, (Issue 5), October 2006, Pages 445-452.

M.D. Lee, C. Antczak, et al., A new human peptide deformylase inhibitable by actinonin, Biochemical and Biophysical Research Communications, Volume 312, (Issue 2), December 2003, Pages 309-315.

M.D. Lee, Y. She, et al., Human mitochondrial peptide deformylase, a new anticancer target of actinonin-based antibiotics, The Journal of Clinical Investigation, Volume 114, (Issue 8), October 2004, Pages 1107-1116.

A. Serero, C. Giglione, et al., An unusual peptide deformylase features in the human mitochondrial N-terminal methionine excision pathway, The Journal of Biological Chemistry, Volume 278, (Issue 52), December 2003, Pages 52953-52963.

S. Escobar-Alvarez, Y. Goldgur, et al., Structure and activity of human mitochondrial peptide deformylase, a novel cancer target, Journal of Molecular Biology, Volume 387, (Issue 5), April 2009, Pages 1211-1228.

C. Antczak, D. Shum, et al., High-throughput identification of inhibitors of human mitochondrial peptide deformylase, Journal of Biomolecular Screening, Volume 12, (Issue 4), June 2007, Pages 521-535.

C. Antczak, D. Shum, et al., Identification of benzofuran-4,5-diones as novel and selective non-hydroxamic acid, non-peptidomimetic based inhibitors of human peptide deformylase, Bioorganic and Medicinal Chemistry Letters, Volume 21, (Issue 15), August 2011, Pages 4528-4532.

S. Fieulaine, C. Juillan-Binard, et al., The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms, The Journal of Biological Chemistry, Volume 280, (Issue 51), December 2005, Pages 42315-42324.

P.S. Charifson, T.H. Grossman, et al., The use of structure-guided design to discover new anti-microbial agents: Focus on antibacterial resistance, Anti-Infective Agents in Medicinal Chemistry, Volume 8, (Issue 1), January 2009, Pages 73-86.

V. Singh, P. Somvanshi, Targeting the peptide deformylase of Mycobacterium tuberculosis leads to drug discovery, Letters in Drug Design and Discovery, Volume 6, (Issue 7), October 2009, Pages 487-493.

M. Kozak, Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles, Microbiological Reviews, Volume 47, (Issue 1), March 1983, Pages 1-45.

T. Meinnel, Y. Mechulam, et al., Methionine as translation start signal: A review of the enzymes of the pathway in Escherichia coli, Biochimie, Volume 75, (Issue 12), December 1993, Pages 1061-1075.

E. Goemaere, A. Melet, et al., New peptide deformylase inhibitors and cooperative interaction: A combination to improve antibacterial activity, Journal of Antimicrobial Chemotherapy, Volume 67, (Issue 6), June 2012, Pages 1392-1400.

K. Aubart, M. Zalacain, Progress in Medicinal Chemistry (Elsevier, 2006, pp. 109-143).

T. Meinnel, S. Blanquet, Characterization of the Thermus thermophilus locus encoding peptide deformylase and methionyl-tRNAfMet formyltransferase, Journal of Bacteriology, Volume 176, (Issue 23), December 1994, Pages 7387-7390.

J.M. Clements, A.P. Ayscough, et al., Peptide deformylase inhibitors, potential for a new class of broad spectrum antibacterials, Current Medicinal Chemistry - Anti-Infective Agents, Volume 1, (Issue 3), July 2002, Pages 239-249.

C. Giglione, M. Pierre, et al., Peptide deformylase as a target for new generation, broad spectrum antimicrobial agents, Molecular Microbiology, Volume 36, (Issue 6), June 2000, Pages 1197-1205.

D. Pei, Peptide deformylase: A target for novel antibiotics, Expert Opinion on Therapeutic Targets, Volume 5, (Issue 1), February 2001, Pages 23-40.

Z. Yuan, J. Trias, et al., Deformylase as a novel antibacterial target, Drug Discovery Today, Volume 6, (Issue 18), September 2001, Pages 954-961.

H. Fu, C. Dahlgren, et al., Subinhibitory concentrations of the deformylase inhibitor actinonin increase bacterial release of neutrophil-activating peptides: A new approach to antimicrobial chemotherapy, Antimicrobial Agents and Chemotherapy, Volume 47, (Issue 8), August 2003, Pages 2545-2550.

D. Mader, M.-J. Rabiet, et al., Formyl peptide receptor-mediated proinflammatory consequences of peptide deformylase inhibition in Staphylococcus aureus, Microbes and Infection, Volume 12, (Issue 5), May 2010, Pages 415-419.

M.R. Capecchi, Initiation of E. coli proteins, Proceedings of the National Academy of Sciences of The United States of America, Volume 55, (Issue 6), June 1966, Pages 1517-1524.

J.M. Adams, On the release of the formyl group from nascent protein, Journal of Molecular Biology, Volume 33, (Issue 3), May 1968, Pages 571-589.

P.T.R. Rajagopalan, X.C. Yu, et al., Peptide deformylase, a new type of mononuclear iron protein, Journal of the American Chemical Society, Volume 119, (Issue 50), December 1997, Pages 12418-12419.

R. Jain, B. Hao, et al., Structures of E. coli peptide deformylase bound to formate: Insight into the preference for Fe2+ over Zn2+ as the active site metal, Journal of the American Chemical Society, Volume 127, (Issue 13), April 2005, Pages 4558-4559.

P.T.R. Rajagopalan, S. Grimme, et al., Characterization of cobalt(II)-substituted peptide deformylase: Function of the metal ion and the catalytic residue Glu-133, Biochemistry, Volume 39, (Issue 4), February 2000, Pages 779-790.

A. Becker, I. Schlichting, et al., Iron center, substrate recognition and mechanism of peptide deformylase, Nature Structural and Molecular Biology, Volume 5, (Issue 12), December 1998, Pages 1053-1058.

B. Hao, W. Gong, et al., Structural basis for the design of antibiotics targeting peptide deformylase, Biochemistry, Volume 38, (Issue 15), April 1999, Pages 4712-4719.

G.S.V. Aller, R. Nandigama, et al., Mechanism of time-dependent inhibition of polypeptide deformylase by actinonin, Biochemistry, Volume 44, (Issue 1), January 2005, Pages 253-260.

A. Pichota, J. Duraiswamy, et al., Peptide deformylase inhibitors of Mycobacterium tuberculosis: Synthesis, structural investigations, and biological results, Bioorganic and Medicinal Chemistry Letters, Volume 18, (Issue 24), December 2008, Pages 6568-6572.

E.T. Baldwin, M.S. Harris, et al., Crystal Structure of Type II Peptide Deformylase from Staphylococcus aureus, The Journal of Biological Chemistry, Volume 277, (Issue 34), August 2002, Pages 31163-31171.

K.J. Smith, C.M. Petit, et al., Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species, Protein Science, Volume 12, (Issue 2), February 2003, Pages 349-360.

A. Kreusch, G. Spraggon, et al., Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: Snapshots of the oxygen sensitivity of peptide deformylase, Journal of Molecular Biology, Volume 330, (Issue 2), July 2003, Pages 309-321.

J.K. Park, J.H. Moon, et al., Crystallization and preliminary X-ray crystallographic analysis of peptide deformylase (PDF) from Bacillus cereus in ligand-free and actinonin-bound forms, Acta Crystallographica Section F Structural Biology and Crystallization Communications, Volume 61, (Issue 1), January 2005, Pages 150-152.

J. Cai, C. Han, et al., Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: Reverse docking, enzymatic assay, and X-ray crystallography validation, Protein Science, Volume 15, (Issue 9), September 2006, Pages 2071-2081.

K.H. Nam, J.I. Ham, et al., Insight into the antibacterial drug design and architectural mechanism of peptide recognition from the E. faecium peptide deformylase structure, Proteins, Volume 74, (Issue 1), September 2008, Pages 261-265.

A. Sharma, G.K. Khuller, et al., Peptide deformylase – a promising therapeutic target for tuberculosis and antibacterial drug discovery, Expert Opinion on Therapeutic Targets, Volume 13, (Issue 7), July 2009, Pages 753-765.

L.-C. Song, S.-T. Ma, Recent progress in peptide deformylase and its inhibitors, Chinese Journal of Antibiotics, Volume 34, (Issue 1), 2009, Pages 1-6,29.

S.K. Verma, R.K. Jat, et al., A novel antibacterial target: Peptide deformylase, Pharmacophore, Volume 2, (Issue 2), 2011, Pages 114-123.

A. Becker, I. Schlichting, et al., Structure of peptide deformylase and identification of the substrate binding site, The Journal of Biological Chemistry, Volume 273, (Issue 19), May 1998, Pages 11413-11416.

W. Kabsch, C. Sander, Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, Volume 22, (Issue 12), December 1983, Pages 2577-2637.

T. Meinnel, S. Blanquet, Enzymatic properties of Escherichia coli peptide deformylase, Journal of Bacteriology, Volume 177, (Issue 7), April 1995, Pages 1883-1887.

T. Meinnel, C. Lazennec, et al., Structure-function relationships within the peptide deformylase family. Evidence for a conserved architecture of the active site involving three conserved motifs and a metal ion, Journal of Molecular Biology, Volume 267, (Issue 3), April 1997, Pages 749-761.

D.W. Byerly, C.A. McElroy, et al., Mapping the surface of Escherichia coli peptide deformylase by NMR with organic solvents, Protein Science, Volume 11, (Issue 7), July 2002, Pages 1850-1853.

J.M. Clements, R.P. Beckett, et al., Antibiotic activity and characterization of BB-3497, a novel peptide deformylase inhibitor, Antimicrobial Agents and Chemotherapy, Volume 45, (Issue 2), February 2001, Pages 563-570.

Y.-J. Hu, Y. Wei, et al., Determination of substrate specificity for peptide deformylase through the screening of a combinatorial peptide library, Biochemistry, Volume 38, (Issue 2), January 1999, Pages 643-650.

Q. Wang, D. Zhang, et al., Docking studies of nickel-peptide deformylase (PDF) inhibitors: Exploring the new binding pockets, Biophysical Chemistry, Volume 122, (Issue 1), June 2006, Pages 43-49.

R. Ménard, A.C. Storer, Oxyanion hole interactions in serine and cysteine proteases, Biological Chemistry Hoppe-Seyler, Volume 373, (Issue 7), July 1992, Pages 393-400.

D. Groche, Charakterisierung des Eisenzentrums und des Katalysemechanismus von Peptid-Deformylase aus Escherichia coli, Ph.D. dissertation, Ruprecht-Karls-Universität Heidelberg., Germany, 1995.

Y. Wei, D. Pei, Continuous spectrophotometric assay of peptide deformylase, Analytical Biochemistry, Volume 250, (Issue 1), July 1997, Pages 29-34.

D. Chen, C. Hackbarth, et al., Peptide deformylase inhibitors as antibacterial agents: Identification of VRC3375, a proline-3-alkylsuccinyl hydroxamate derivative, by using an integrated combinatorial and medicinal chemistry approach, Antimicrobial Agents and Chemotherapy, Volume 48, (Issue 1), January 2004, Pages 250-261.

J. Trias, The role of combichem in antibiotic discovery, Current Opinion in Microbiology, Volume 4, (Issue 5), October 2001, Pages 520-525.

M. Whittaker, C.D. Floyd, et al., Design and therapeutic application of matrix metalloproteinase inhibitors, Chemical Reviews, Volume 99, (Issue 9), September 1999, Pages 2735-2776.

A.K. Berg, Q. Yu, et al., Solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase, Biochimica et Biophysica Acta, Volume 1804, (Issue 4), April 2010, Pages 704-713.

D.J. Durand, B.G. Green, et al., Peptide aldehyde inhibitors of bacterial peptide deformylases, Archives of Biochemistry and Biophysics, Volume 367, (Issue 2), July 1999, Pages 297-302.

Y.-J. Hu, P.T.R. Rajagopalan, et al., H-phosphonate derivatives as novel peptide deformylase inhibitors, Bioorganic and Medicinal Chemistry Letters, Volume 8, (Issue 18), September 1998, Pages 2479-2482.

T. Meinnel, L. Patiny, et al., Design and synthesis of substrate analog inhibitors of peptide deformylase, Biochemistry, Volume 38, (Issue 14), April 1999, Pages 4287-4295.

B.G. Green, J. H. Toney, et al., Inhibition of bacterial peptide deformylase by biaryl acid analogs, Archives of Biochemistry and Biophysics, Volume 375, (Issue 2), March 2000, Pages 355-358.

K.M. Huntington, T. Yi, et al., Synthesis and antibacterial activity of peptide deformylase inhibitors, Biochemistry, Volume 39, (Issue 15), April 2000, Pages 4543-4551.

A. Thorarensen, M.R. Douglas, Jr., et al., Identification of novel potent hydroxamic acid inhibitors of peptidyl deformylase and the importance of the hydroxamic acid functionality on inhibition, Bioorganic and Medicinal Chemistry Letters, Volume 11, (Issue 11), June 2001, Pages 1355-1358.

V. Madison, J. Duca, et al., Binding affinities and geometries of various metal ligands in peptide deformylase inhibitors, Biophysical Chemistry, Volume 101-102, December 2002, Pages 239-247.

H.K. Smith, R.P. Beckett, et al., Structure-activity relationships of the peptide deformylase inhibitor BB-3497: Modification of the metal binding group, Bioorganic and Medicinal Chemistry Letters, Volume 12, (Issue 24), December 2002, Pages 3595-3599.

M.K. Gupta, P. Mishra, et al., 2D-QSAR in hydroxamic acid derivatives as peptide deformylase inhibitors and antibacterial agents, Bioorganic and Medicinal Chemistry, Volume 10, (Issue 12), December 2002, Pages 3713-3716.

B. Lou, K. Yang, Molecular diversity of hydroxamic acids: Part II. Potential therapeutic applications, Mini Reviews in Medicinal Chemistry, Volume 3, (Issue 6), September 2003, Pages 609-620.

R. Jain, A. Sundram, et al., α-Substituted hydroxamic acids as novel bacterial deformylase inhibitor-based antibacterial agents, Bioorganic and Medicinal Chemistry Letters, Volume 13, (Issue 23), December 2003, Pages 4223-4228.[Erratum: Bioorganic and Medicinal Chemistry Letters, Volume 14, (Issue 9), May 2004, Pages 2373-2374]

E. Galardon, M. Giorgi, et al., Modeling the inhibition of peptide deformylase by hydroxamic acids: Influence of the sulfur donor, Dalton Transactions, (Issue 10), March 2007, Pages 1047-1052.

K.D. Dobbs, A.M. Rinehart, et al., Computational characterization of metal binding groups for metalloenzyme inhibitors, Journal of Chemical Theory and Computation, Volume 2, (Issue 4), May 2006, Pages 990-996.

D. Hesek, B.C. Noll, et al., Side reaction of significance in preparation of peptide- or peptidomimetic-based hydroxamate enzyme inhibitors, Journal of Organic Chemistry, Volume 71, (Issue 7), March 2006, Pages 2885-2887.

S.J. Davies, A.P. Ayscough, et al., Structure-activity relationships of the peptide deformylase inhibitor BB-3497: Modification of the methylene spacer and the P1' side chain, Bioorganic and Medicinal Chemistry Letters, Volume 13, (Issue 16), August 2003, Pages 2709-2713.

S. Ragusa, P. Mouchet, et al., Substrate recognition and selectivity of peptide deformylase. Similarities and differences with metzincins and thermolysin, Journal of Molecular Biology, Volume 289, (Issue 5), June 1999, Pages 1445-1457.

K.W. Johnson, D. Lofland, et al., PDF inhibitors: An emerging class of antibacterial drugs, Current Drug Targets - Infectious Disorders, Volume 5, (Issue 1), March 2005, Pages 39-52.

M. Chu, R. Mierzwa, et al., Isolation and structure elucidation of two novel deformylase inhibitors produced by Streptomyces sp., Tetrahedron Letters, Volume 42, (Issue 21), May 2001, Pages 3549-3551.

S.J. Davies, A.P. Ayscough, et al., Structure-activity relationships of the peptide deformylase inhibitor BB-3497: Modification of the P2' and P3' side chains, Bioorganic and Medicinal Chemistry Letters, Volume 13, (Issue 16), August 2003, Pages 2715-2718.

C. Apfel, D. Banner, et al., Hydroxamic acid derivatives as potent peptide deformylase inhibitors and antibacterial agents, Journal of Medicinal Chemistry, Volume 43, (Issue 12), June 2000, Pages 2324-2331.

C. Apfel, D.W. Banner, et al., 2-(2-Oxo-1,4-dihydro-2H-quinazolin-3-yl)- and 2-(2,2-Dioxo-1,4-dihydro-2H-2λ6-benzo[1,2,6]thiadiazin-3-yl)-N-hydroxy-acetamides as potent and selective peptide deformylase inhibitors, Journal of Medicinal Chemistry, Volume 44, (Issue 12), June 2001, Pages 1847-1852.

M.M.K. Jayasekera, A. Kendall, et al., Novel nonpeptidic inhibitors of peptide deformylase, Archives of Biochemistry and Biophysics, Volume 381, (Issue 2), September 2000, Pages 313-316.

B.J. Broughton, P. Chaplen, et al., Studies concerning the antibiotic actinonin. Part VIII. Structure-activity relationships in the actinonin series, Journal of the Chemical Society, Perkin Transactions 1, (Issue 9), June 1975, Pages 857-860.

S.-W. Yu, H.-Y. Lee, et al., Synthesis and biological evaluation of N-formyl hydroxylamine derivatives as potent peptide deformylase inhibitors, Bulletin of the Korean Chemical Society, Volume 27, (Issue 7), April 2006, Pages 1075-1078.

S.K. Lee, K.H. Choi, et al., Peptide deformylase inhibitors with non-peptide scaffold: Synthesis and structure-activity relationships, Bioorganic and Medicinal Chemistry Letters, Volume 21, (Issue 1), January 2011, Pages 133-136.

S.P. East, R.P. Beckett, et al., Peptide deformylase inhibitors with activity against respiratory tract pathogens, Bioorganic and Medicinal Chemistry Letters, Volume 14, (Issue 1), January 2004, Pages 59-62.

D. Lofland, S. Difuntorum, et al., In vitro antibacterial activity of the peptide deformylase inhibitor BB-83698, Journal of Antimicrobial Chemotherapy, Volume 53, (Issue 4), April 2004, Pages 664-668.

R.S. Ananthula, M. Ravikumar, et al., Insights from ligand and structure based methods in virtual screening of selective Ni-peptide deformylase inhibitors, Journal of Molecular Modelling, Volume 18, (Issue 2), February 2012, Pages 693-708.

S. Ragusa, S. Blanquet, et al., Control of peptide deformylase activity by metal cations, Journal of Molecular Biology, Volume 280, (Issue 3), July 1998, Pages 515-523.

Y. Wei, T. Yi, et al., Identification of a potent peptide deformylase inhibitor from a rationally designed combinatorial library, Journal of Combinatorial Chemistry, Volume 2, (Issue 6), November 2000, Pages 650-657.

T. Meinnel, Developing a rational strategy for new antibacterial agents, Pathologie Biologie (Paris), Volume 47, (Issue 8), October 1999, Pages 780-783.

J.J. Gordon, B.K. Kelly, et al., Actinonin: An antibiotic substance produced by an actinomycete, Nature, Volume 195, (Issue 4842), August 1962, Pages 701-702.

V. Larue, B. Seijo, et al., 1H, 13C and 15N NMR assignments of the E. coli peptide deformylase in complex with a natural inhibitor called actinonin, Biomolecular NMR Assignments, Volume 3, (Issue 1), June 2009, Pages 153-155.

C.D. Amero, D.W. Byerly, et al., Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase, Biochemistry, Volume 48, (Issue 32), August 2009, Pages 7595-7607.

A. Chikhi, A. Bensegueni, et al., Theoretical study of Escherichia coli peptide deformylase inhibition by several drugs, In Silico Biology, Volume 6, (Issue 5), August 2006, Pages 459-466.

R. Frechette, S. Davis, et al., Screening, preparation, and use of peptide deformylase iinhibitors as antibacterial agents, Patent Cooperation Treaty International Application (2001), WO 2001038561 A1 20010531.

Y.-J. Kwon, M.-J. Sohn, et al., Fumimycin: A peptide deformylase inhibitor with an unusual skeleton produced by Aspergillus fumisynnematus, Organic Letters, Volume 9, (Issue 13), June 2007, Pages 2449-2451.

P.J. Gross, S. Bräse, The total synthesis of (±)-fumimycin, Chemistry - A European Journal, Volume 16, (Issue 42), November 2010, Pages 12660-12667.

C.E. Hartmann, P.J. Gross, et al., Towards an asymmetric synthesis of the bacterial peptide deformylase (PDF) inhibitor fumimycin, Organic and Biomolecular Chemistry, Volume 7, (Issue 24), December 2009, Pages 5059-5062.

R.P. Beckett, J.M. Clements, et al., Structure-activity relationships of the peptide deformylase inhibitor BB-3497, 41st Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC), Abstract No. 350, Chicago, USA, December 2001.

J.Y. Lee, M.R. Doddareddy, et al., Comparative QSAR studies on peptide deformylase inhibitors, Journal of Molecular Modelling, Volume 13, (Issue 5), May 2007, Pages 543-558.

J. Gao, Y. Cheng, et al., 3D-QSAR and molecular docking studies of hydroxamic acids as peptide deformylase inhibitors, Medicinal Chemistry Research, Volume 21, (Issue 8), August 2012, Pages 1597-1610.

F. Meng, W. Xu, et al., Computer-aided drug design of peptide deformylase (PDF) inhibitors: A docking molecular modeling study, Internet Electronic Journal of Molecular Design, Volume 7, (Issue 1), January 2008, Pages 1-11.

S.P. East, A. Ayscough, et al., Peptidomimetic inhibitors of bacterial peptide deformylase, Bioorganic and Medicinal Chemistry Letters, Volume 21, (Issue 13), July 2011, Pages 4032-4035.

W. Shi, H. Ma, et al., Design, synthesis and antibacterial activity of 3-methylenepyrrolidine formyl hydroxyamino derivatives as novel peptide deformylase inhibitors, Bioorganic and Medicinal Chemistry Letters, Volume 21, (Issue 3), February 2011, Pages 1060-1063.

L. Yin, J. Jia, et al., Design, synthesis, and antibacterial activity of novel N-formylhydroxylamine derivatives as PDF inhibitors, Indian Journal of Chemistry, Volume 50B, (Issue 5), May 2011, Pages 695-703.

L. Yin, W.-R. Xu, et al., Synthesis and antimicrobial activities of novel peptide deformylase inhibitors, Archives of Organic Chemistry (ARKIVOC), (Issue 9), July 2010, Pages 196-205.

W. Shi, Y. Duan, et al., Design, synthesis, and antibacterial activity of 2,5-dihydropyrrole formyl hydroxyamino derivatives as novel peptide deformylase inhibitors, Bioorganic and Medicinal Chemistry Letters, Volume 20, (Issue 12), June 2010, Pages 3592-3595.

D.V. Patel, K. Ngu, K. Methods for solid-phase synthesis of hydroxylamine compounds and derivatives and combinatorial libraries, Patent Cooperation Treaty International Application (1999), WO 9957097 A2 19991111.

D. Zhang, J. Jia, et al., Synthesis and preliminary antibacterial evaluation of 2-butyl succinate-based hydroxamate derivatives containing isoxazole rings, Archives of Pharmacal Research, Volume 33, (Issue 6), June 2010, Pages 831-842.

Z.-J. Ni, J.W. Jacobs, et al., Novel heterocyclic urea compounds, particularly N-hydroxy-2-[N-substituted-N-[(2-substituted-pyrrolidin-1-yl)carbonyl]amino]acetamides, with activity as peptide deformylase inhibitors, and their compositions, methods of use as antimicrobials, and preparation, Patent Cooperation Treaty International Application (2001), WO 2001044178 A1 20010621.

J.W.P. Teo, P. Thayalan, et al., Peptide deformylase inhibitors as potent antimycobacterial agents, Antimicrobial Agents and Chemotherapy, Volume 50, (Issue 11), November 2006, Pages 3665-3673.

W. Takayama, M. Shirasaki, et al., Preparation of β-aminohydroxamic acids as peptide deformylase (PDF) inhibitors and their medical use, Japanese Kokai Tokkyo Koho (2004), JP 2004143053 A 20040520.

P. Gane, B. Porter, et al., Preparation of N-hydroxyformamide derivatives as bacterial enzyme inhibitors, Patent Cooperation Treaty International Application (2003), WO 2003048115 A1 20030612.

R.A. Coats, S.-L. Lee, et al., Stereochemical definition and chirospecific synthesis of the peptide deformylase inhibitor Sch 382583, Journal of Organic Chemistry, Volume 69, (Issue 5), January 2004, Pages 1734-1737.

S.K. Lee, K.H. Choi, et al., Peptide deformylase inhibitors with retro-amide scaffold: Synthesis and structure-activity relationships, Bioorganic and Medicinal Chemistry Letters, Volume 20, (Issue 15), August 2010, Pages 4317-4319.

X. Hu, K.T. Nguyen, et al., Structure-based design of a macrocyclic inhibitor for peptide deformylase, Journal of Medicinal Chemistry, Volume 46, (Issue 18), August 2003, Pages 3771-3774.

C.-Q. Wei, Y. Gao, et al., Macrocyclization in the design of Grb2 SH2 domain-binding ligands exhibiting high potency in whole-cell systems, Journal of Medicinal Chemistry, Volume 46, (Issue 2), January 2003, Pages 244-254.

C.-B. Xue, X. He, et al., Design and synthesis of cyclic inhibitors of matrix metalloproteinases and TNF-α production, Journal of Medicinal Chemistry, Volume 41, (Issue 11), May 1998, Pages 1745-1748.

M. Capet, A. Genevois-Borella, et al., Macrocyclic hydroxamic acid derivatives as bactericides, Patent Cooperation Treaty International Application (2001), WO 2001040198 A2 20010607.

I. Bertini, C. Luchinat, Bioinorganic Chemistry (University Science Books, 1994, pp. 37-106).

C. Lazennec, T. Meinnel, Formate dehydrogenase-coupled spectrophotometric assay of peptide deformylase, Analytical Biochemistry, Volume 244, (Issue 1), January 1997, Pages 180-182.

P.T.R. Rajagopalan, A. Datta, et al., Purification, characterization, and inhibition of peptide deformylase from Escherichia coli, Biochemistry, Volume 36, (Issue 45), November 1997, Pages 13910-13918.

K.T. Nguyen, X. Hu, et al., Slow-binding inhibition of peptide deformylase by cyclic peptidomimetics as revealed by a new spectrophotometric assay, Bioorganic Chemistry, Volume 32, (Issue 3), June 2004, Pages 178-191.

X. Hu, K.T. Nguyen, et al., Macrocyclic inhibitors for peptide deformylase: a structure-activity relationship study of the ring size, Journal of Medicinal Chemistry, Volume 47, (Issue 20), September 2004, Pages 4941-4949.

G. Shen, J. Zhu, et al., Design and synthesis of macrocyclic peptidyl hydroxamates as peptide deformylase inhibitors, Bioorganic and Medicinal Chemistry Letters, Volume 18, (Issue 10), May 2008, Pages 3060-3063.

K.M. Aubart, A.B. Benowitz, et al., Peptide deformylase inhibition and antimicrobial activity of heteroarylenes, Patent Cooperation Treaty International Application (2005), WO 2005017124 A2 20050224.

Q. Wang, J. Wang, et al., Prediction of the binding modes between BB-83698 and peptide deformylase from Bacillus stearothermophilus by docking and molecular dynamics simulation, Biophysical Chemistry, Volume 134, (Issue 3), May 2008, Pages 178-184.

R. Wise, J.M. Andrews, et al., In vitro activities of peptide deformylase inhibitors against gram-positive pathogens, Antimicrobial Agents and Chemotherapy, Volume 46, (Issue 4), April 2002, Pages 1117-1118.

K.B. Waites, N.B. Reddy, et al., Comparitive in vitro activities of investigational peptide deformylase inhibitor NVP LBM-415 and other agents against human mycoplasmas and ureaplasmas, Antimicrobial Agents and Chemotherapy, Volume 49, (Issue 6), June 2005, Pages 2541-2542.

W. Wang, R. White, et al., Proteomic study of peptide deformylase inhibition in Streptococcus pneumoniae and Staphylococcus aureus, Antimicrobial Agents Chemotherapy, Volume 50, (Issue 5), May 2006, Pages 1656-1663.

R.D. Ye, F. Boulay, Structure and function of leukocyte chemoattractant receptors, Advances in Pharmacology, Volume 39, 1997, Pages 221-289.

B. Bozdogan, D. Esel, et al., Antibacterial susceptibility of a vancomycin-resistant Staphylococcus aureus strain isolated at the Hershey Medical Center, Journal of Antimicrobial Chemotherapy, Volume 52, (Issue 5), November 2003, Pages 864-868.

R.N. Jones, T.R. Fritsche, et al., Antimicrobial spectrum and activity of NVP PDF-713, a novel peptide deformylase inhibitor, tested against 1,837 recent Gram-positive clinical isolates, Diagnostic Microbiology and Infectious Disease, Volume 49, (Issue 1), May 2004, Pages 63-65.

R.N. Jones, G.J. Moet, et al., Potential utility of a peptide deformylase inhibitor (NVP PDF-713) against oxazolidinone-resistant or streptogramin-resistant Gram-positive organism isolates, Journal of Antimicrobial Chemotherapy, Volume 53, (Issue 5), May 2004, Pages 804-807.

R.N. Jones, H.S. Sader, et al., Antimicrobial activity of LBM415 (NVP PDF-713) tested against pathogenic Neisseria spp. (Neisseria gonorrhoeae and Neisseria meningitidis), Diagnostic Microbiology and Infectious Disease, Volume 51, (Issue 2), February 2005, Pages 139-141.

M. Fonseca-Aten, C.M. Salvatore, et al., Evaluation of LBM415 (NVP PDF-713), a novel peptide deformylase inhibitor, for treatment of experimental Mycoplasma pneumoniae pneumonia, Antimicrobial Agents and Chemotherapy, Volume 49, (Issue 10), October 2005, Pages 4128-4136.

T.R. Fritsche, H.S. Sader, et al., Comparative Antimicrobial characterization of LBM415 (NVP PDF-713), a new peptide deformylase inhibitor of clinical importance, Antimicrobial Agents and Chemotherapy, Volume 49, (Issue 4), April 2005, Pages 1468-1476.

A.A. Watters, R.N. Jones, et al., Antimicrobial activity of a novel peptide deformylase inhibitor, LBM415, tested against respiratory tract and cutaneous infection pathogens: A global surveillance report (2003-2004), Journal of Antimicrobial Chemotherapy, Volume 57, (Issue 5), May 2006, Pages 914-923.

C.S. Osborne, G. Neckermann, et al., In vivo characterization of the peptide deformylase inhibitor LBM-415 in murine infection models, Antimicrobial Agents and Chemotherapy, Volume 53, (Issue 9), September 2009, Pages 3777-3781.

J. Slade, D. Parker, et al., A practical enantioselective synthesis of a novel peptide deformylase inhibitor, Organic Process Research and Development, Volume 10, (Issue 1), January 2006, Pages 78-93.

L. Yu, W. Zhou, et al., Synthesis and in vitro antibacterial activity of oxazolidine LBM-415 analogs as peptide deformylase inhibitors, Bioorganic and Medicinal Chemistry Letters, Volume 21, (Issue 5), March 2011, Pages 1541-1544.

T. Bogdanovich, K.A. Smith, et al., Activity of LBM-415 compared to those of 11 other agents against Haemophilus species, Antimicrobial Agents and Chemotherapy, Volume 50, (Issue 7), July 2006, Pages 2323-2329.

V. Molteni, X. He, et al., Identification of novel potent bicyclic peptide deformylase inhibitors, Bioorganic and Medicinal Chemistry Letters, Volume 14, (Issue 6), March 2004, Pages 1477-1481.

M. Hidalgo, S.G. Eckhardt, Development of matrix metalloproteinase inhibitors in cancer therapy, Journal of the National Cancer Institute, Volume 93, (Issue 3), February 2001, Pages 178-193.

K. Noda, Y. Saad, et al., Tetrazole and carboxylate groups of angiotensin receptor antagonists bind to the same subsite by different mechanism, The Journal of Biological Chemistry, Volume 270, (Issue 5), February 1995, Pages 2284-2289.

E.M. Naylor, P.K. Chakravarty, et al., Potent imidazole angiotensin II antagonists: Acyl sulfonamides and acyl sulfamides as tetrazole replacements, Bioorganic and Medicinal Chemistry Letters, Volume 4, (Issue 1), January 1994, Pages 69-74.

S.S. Karnik, A. Husain, et al., Molecular determinants of peptide and non-peptide binding to the AT1 receptor, Clinical and Experimental Pharmacology and Physiology Supplement, Volume 3, 1996, Pages S58-S66.

K.M. Aubart, S.B. Christensen, et al., Preparation of peptide deformylase inhibitors as antimicrobial agents, Patent Cooperation Treaty International Application (2001), WO 2001085160 A1 20011115.

S.B. Christensen, M.D. Cummings, et al., N-[2-(N-formyl-N hydroxyamino)ethyl]arylamides as peptide deformylase inhibitors with antibacterial activity, Patent Cooperation Treaty International Application (2002), WO 2002098901 A2 20021212.

W. Takayama, Y. Shirasaki, et al., Synthesis and PDF inhibitory activities of novel benzothiazolylidenehydroxamic acid derivatives, Bioorganic and Medicinal Chemistry Letters, Volume 13, (Issue 19), March 2003, Pages 3273-3276.

P. Calí, L. Nærum, et al., Isoxazole-3-hydroxamic acid derivatives as peptide deformylase inhibitors and potential antibacterial agents, Bioorganic and Medicinal Chemistry Letters, Volume 14, (Issue 24), December 2004, Pages 5997-6000.

A. Boularot, C. Giglione, et al., Discovery and refinement of a new structural class of potent peptide deformylase inhibitors, Journal of Medicinal Chemistry, Volume 50, (Issue 1), January 2007, Pages 10-20.

S. Petit, Y. Duroc, et al., Structure-activity relationship analysis of the peptide deformylase inhibitor 5-bromo-1H-indole-3-acetohydroxamic acid, ChemMedChem, Volume 4, (Issue 2), February 2009, Pages 261-275.

M.H. Howard, T. Cenizal, et al., A novel class of inhibitors of peptide deformylase discovered through high-throughput screening and virtual ligand screening, Journal of Medicinal Chemistry, Volume 47, (Issue 27), December 2004, Pages 6669-6672.

J.S. Yoo, C.-J. Zheng, et al., Macrolactin N, a new peptide deformylase inhibitor produced by Bacillus subtilis, Bioorganic and Medicinal Chemistry Letters, Volume 16, (Issue 18), September 2006, Pages 4889-4892.

Y.-J. Kwon, C.-J. Zheng, et al., Isolation and identification of FR198248, a hydroxylated 1,3-dihydroisobenzofuranfrom Aspergillus flavipes as an inhibitor of peptide deformyalse, Bioscience, Biotechnology, and Biochemistry, Volume 74, (Issue 2), February 2010, Pages 390-393.

K.M. Aubart, A.B. Benowitz, et al., Preparation of N-hydroxy-N-(3-hydrazino-3-oxopropyl)formamide derivatives as peptide deformylase inhibitors with antibacterial activity, Patent Cooperation Treaty International Application (2003), WO 2003101442 A1 20031211.

D.V. Patel, Z. Yuan, et al., Preparation of N -hydroxyamide-substituted pyrrolidine derivatives as inhibitors of peptidyl deformylase, Patent Cooperation Treaty International Application (2002), WO 2002102791 A1 20021227.

R.P. Beckett, S. Launchbury, et al., Hydroxamic acid or N-formyl hydroxylamine derivatives as inhibitors of bacterial polypeptide deformylase for treating microbial infections, Patent Cooperation Treaty International Application (2002), WO 2002041886 A1 20020530.

J.M. Karpinski, K.M. Aubart, et al., Preparation of peptide deformylase inhibitors, Patent Cooperation Treaty International Application (2003), WO 2003104209 A1 20031218.

K.M. Aubart, A. Bhat, et al., Peptide deformylase inhibitors, their preparation, and their use as antibacterial agents, Patent Cooperation Treaty International Application (2003), WO 2003077913 A1 20030925.

K.M. Aubart, J.-N. Xiang, et al., Antimicrobial peptide deformylase inhibitors, Patent Cooperation Treaty International Application (2002), WO 2002070540 A2 20020912.

S.B. Falconer, E.D. Brown, New screens and targets in antibacterial drug discovery, Current Opinion in Microbiology, Volume 12, (Issue 5), October 2009, Pages 497-504.


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