392
Views
26
CrossRef citations to date
0
Altmetric
Reviews

Peptide deformylase – a promising therapeutic target for tuberculosis and antibacterial drug discovery

, & , PhD
Pages 753-765 | Published online: 17 Jun 2009

Bibliography

  • Gomez JE, Mckinney JD. M. tuberculosis persistence, latency, and drug tolerance. Tuberculosis 2004;84:29-44
  • Centers for Disease Control and Prevention (CDC). Emergence of Mycobacterium tuberculosis with extensive resistance to second-line drugs-worldwide, 2000-2004. MMWR Morb Mortal Wkly Rep 2006;55:301-5
  • Balganesh TS, Furr BJ. Molecular approaches to target discovery:–evaluating targets for anti-tuberculosis drug discovery programmes. Infect Disord Drug Targets 2007;7:120-6
  • Barry CE, Crick DC, Mcneil MR. Targeting the formation of the cell wall core of M. tuberculosis. Infect Disord Drug Targets 2007;7:182-202
  • Crane CM, Hirsch AK, Alphey MS, et al. Synthesis and characterization of cytidine derivatives that inhibit the kinase IspE of the non-mevalonate pathway for isoprenoid biosynthesis. Chem Med Chem 2008;3:91-101
  • Eoh H, Brennan PJ, Crick DC. The Mycobacterium tuberculosis MEP (2C-methyl-D-erythritol 4-phosphate) pathway as a new drug target. Tuberculosis (Edinb) 2009;89(1):1-11
  • Sanki AK, Boucau J, Srivastava P, et al. Synthesis of methyl 5-S-alkyl-5-thio-D-arabinofuranosides and evaluation of their antimycobacterial activity. Bioorg Med Chem 2008;16:5672-82
  • Purohit HJ, Cheema S, Lal S, et al. In search of drug targets for Mycobacterium tuberculosis. Infect Disord Drug Targets 2007;7245-50
  • Lu H, Tonge PJ. Inhibitors of FabI, an enzyme drug target in the bacterial fatty acid biosynthesis pathway. Acc Chem Res 2008;41:11-20
  • De Souza MV, Ferreira Mde L, Pinheiro AC, et al. Synthesis and biological aspects of mycolic acids: an important target against Mycobacterium tuberculosis. Sci World J 2008;8:720-51
  • Teh JS, Yano T, Rubin H. Type II NADH: menaquinone oxidoreductase of Mycobacterium tuberculosis. Infect Disord Drug Targets 2007;7(2):169-81
  • Amaral L, Martins M, Viveiros M. Phenothiazines as anti-multi-drug resistant tubercular agents. Infect Disord Drug Targets 2007;7(3):257-65
  • Bhave DP, Muse WB 3rd, Carroll KS. Drug targets in mycobacterial sulfur metabolism. Infect Disord Drug Targets 2007;7(2):140-58
  • Arcuri HA, Borges JC, Fonseca IO, et al. Structural studies of shikimate 5-dehydrogenase from Mycobacterium tuberculosis. Proteins 2008;72(2):720-30
  • Murphy DJ, Brown JR. Identification of gene targets against dormant phase Mycobacterium tuberculosis infections. BMC Infect Dis 2007;7:84; published online 26 July 2007
  • Monfeli RR, Beeson C. Targeting iron acquisition by Mycobacterium tuberculosis. Infect Disord Drug Targets 2007;7:213-20
  • Stirrett KL, Ferreras JA, Jayaprakash V, et al. Small molecules with structural similarities to siderophores as novel antimicrobials against Mycobacterium tuberculosis and Yersinia pestis. Bioorg Med Chem Lett 2008;18:2662-8
  • Rustomjee R, Diacon AH, Allen J, et al. Early bactericidal activity and pharmacokinetics of the diarylquinoline TMC207 in treatment of pulmonary tuberculosis. Antimicrob Agents Chemother 2008;52(8):2831-5
  • Kurabachew M, Lu SH, Krastel P, et al. Lipiarmycin targets RNA polymerase and has good activity against multidrug-resistant strains of Mycobacterium tuberculosis. J Antimicrob Chemother 2008;62(4):713-9
  • Hunter JH, Gujjar R, Pang CK, Rathod PK. Kinetics and ligand-binding preferences of Mycobacterium tuberculosis thymidylate synthases, ThyA and ThyX. PLoS ONE 2008;3(5):e2237 [published online 21 May 2008]
  • Cynamon MH, Alvirez-freites E, Yeo AE. BB-3497, a peptide deformylase inhibitor, is active against Mycobacterium tuberculosis. J Antimicrob Chemother 2004;53:403-5
  • Coates AR, Hu Y. Novel approaches to developing new antibiotics for bacterial infections. Br J Pharmacol 2007;152:1147-54
  • Clements JM, Ayscough AP, Keavey K, East SP. Peptide deformylase inhibitors, potential for a new class of broad spectrum antibacterials. Curr Med Chem AntiInfect Agents 2002;1:239-49
  • Mazel D, Coic E, Blanchard S, et al. A survey of polypeptide deformylase functions throughout the eubacterial lineage. J Mol Biol 1997;266:939-49
  • Adams JM, Capecchi M. N-formyl-methionine-tRNA as the initiator of protein synthesis. Proc Natl Acad Sci USA 1966;55:147-55
  • Lucchini G, Bianchetti R. Initiation of protein synthesis in isolated mitochondria and chloroplasts. Biochim Biophys Acta 1980;608:54-61
  • Lee MD, Antczak C, Li Y, et al. A new human peptide deformylase inhibitable by actinonin. Biochem Biophys Res Commun 2003;312:309-15
  • Nguyen KT, Hu X, Colton C, et al. Characterization of a human peptide deformylase: Implications for antibacterial drug design. Biochemistry 2003;42:9952-8
  • Serero A, Giglione C, Sardini A, et al. An unusual peptide deformylase features in the human mitochondrial N-terminal methionine excision pathway. J Biol Chem 2003;278:52953-63
  • Chen D, Hackbarth C, Ni ZJ, 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. Antimicrob Agents Chemother 2004;48:250-61
  • Hackbarth CJ, Chen DZ, Lewis JG, et al. N-alkyl urea hydroxamic acids as a new class of peptide deformylase inhibitors with antibacterial activity. Antimicrob Agents Chemother 2002;46:2752-64
  • Roblin PM, Hammerschlag MR. In vitro activity of a new antibiotic, NVP-PDF386 (VRC4887), against Chlamydia pneumoniae. Antimicrob Agents Chemother 2003;47:1447-8
  • Pei D. Peptide deformylase: a target for novel antibiotics? Exp Opin Ther Targets 2001;5:23-40
  • Chen D, Yuan Z. Therapeutic potential of peptide deformylase inhibitors. Exp Opin Investig Drugs 2005;14:1107-16
  • Pichota A, Duraiswamy J, Yin Z, et al. Peptide deformylase inhibitors of Mycobacterium tuberculosis: synthesis, structural investigations, and biological results. Bioorg Med Chem Lett 2008;18:6568-72
  • Jain R, Chen D, White RJ, et al. Bacterial peptide deformylase inhibitors: a new class of antibacterial agents. Curr Med Chem 2005;12:1607-21
  • Johnson KW, Lofland D, Moser HE. PDF inhibitors: an emerging class of antibacterial drugs. Curr Drug Targets Infect Disord 2005;5:39-52
  • Clements JM, Beckett RP, Brown A, et al. Antibiotic activity and characterization of BB-3497, a novel peptide deformylase inhibitor. Antimicrob Agents Chemother 2001;45:563-70
  • Marcker K, Sanger F. N-formyl-methionyl-S-RNA. J Mol Biol 1964;8:835-40
  • Kozak M. Comparison of initiation of protein synthesis in procaryotes, eucaryotes and organelles. Microbiol Rev 1983;47:1-45
  • Fry KT, Lamborg MR. Amidohydrolase activity of Escherichia coli extracts with formylated amino acids and dipeptides as substrates. J Mol Biol 1967;28:423-33
  • Chang SY, Mcgary EC, Chang S. Methionine aminopeptidase gene of Escherichia coli is essential for cell growth. J Bacteriol 1989;171:4071-4072
  • Ben-bassat A, Baur K, Chang SY, et al. Processing of the initiation methionine from proteins: properties of the Escherichia coli methionine aminopeptidase and its gene structure. J Bacteriol 1987;169:751-7
  • Xiao C, Zhang Y. Catalytic mechanism and metal specificity of bacterial peptide deformylase: a density functional theory QM/MM study. J Phys Chem B 2007;111:6229-35
  • Mazel D, Pochet S, Marliere P. Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation. EMBO J 1994;13:914-23
  • Bingel-Erlenmeyer R, Kohler R, Kramer G, et al. A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing. Nature 2008;452:108-11
  • Guilloteau JP, Mathieu M, Giglione C, et al. The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents. J Mol Biol 2002;320:951-62
  • Selmer M, Liljas A. Exit biology: battle for the nascent chain. Structure 2008;16(4):498-500
  • Wu XH, Quan JM, Wu YD. Theoretical study of the catalytic mechanism and metal-ion dependence of peptide deformylase. J Phys Chem B 2007;111(22):6236-44
  • Dirk LM, Schmidt JJ, Cai Y, et al. Insights into the substrate specificity of plant peptide deformylase, an essential enzyme with potential for the development of novel biotechnology applications in agriculture. Biochem J 2008;413(3):417-27
  • Fieulaine S, Juillan-Binard C, Serero A, et al. The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms. J Biol Chem 2005;280(51):42315-24
  • Leeds JA, Dean CR. Peptide deformylase as an antibacterial target: a critical assessment. Curr Opin Pharmacol 2006;6:445-52
  • Haas M, Beyer D, Gahlmann R, Freiberg C. YkrB is the main peptide deformylase in Bacillus subtilis, a eubacterium containing two functional peptide deformylases. Microbiology 2001;147:1783-91
  • Park JK, Kim KH, Moon JH, Kim EE. Characterization of peptide deformylase2 from B. cereus. J Biochem Mol Biol 2007;40(6):1050-7
  • Margolis P, Hackbarth C, Lopez S, et al. Resistance of Streptococcus pneumoniae to deformylase inhibitors is due to mutations in defB. Antimicrob Agents Chemother 2001;45:2432-5
  • Dong M, Liu H. Origins of the different metal preferences of Escherichia coli peptide deformylase and Bacillus thermoproteolyticus thermolysin: a comparative quantum mechanical/molecular mechanical study. J Phys Chem B 2008;112(33):10280-90
  • Meinnel T, Blanquet S. Enzymatic properties of Escherichia coli peptide deformylase. J Bacteriol 1995;177:1883-7
  • Rajagopalan PT, Datta A, Pei D. Purification, characterization and inhibition of peptide deformylase from Escherichia coli. Biochemistry 1997;36:13910-8
  • Groche D, Becker A, Schlichting I, et al. Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site. Biochem Biophys Res Commun 1998;246:342-6
  • Rajagopalan PT, Grimme S, Pei D. Characterization of cobalt (II)-substituted peptide deformylase: function of the metal ion and the catalytic residue Glu-133. Biochemistry 2000;39:779-90
  • Nguyen KT, Wu JC, Boylan JA, et al. Zinc is the metal cofactor of Borrelia burgdorferi peptide deformylase. Arch Biochem Biophys 2007;468:217-25
  • Dardel F, Ragusa S, Lazennec C, et al. Solution structure of nickel-peptide deformylase. J Mol Biol 1998;280:501-13
  • Becker A, Schlichting I, Kabsch W, et al. Structure of peptide deformylase and identi?cation of the substrate binding site. J Biol Chem 1998;273:11413-6
  • Chan MK, Gong W, Rajagopalan PT, et al. Crystal structure of the Escherichia coli peptide deformylase. Biochem 1997;36:13904-9
  • Becker A, Schlichting I, Kabsch W, et al. Iron center, substrate recognition and mechanism of peptide deformylase. Nat Struct Biol 1998;5:1053-8
  • Apfel CM, Banner DW, Bur D, et al. Hydroxamic acid derivatives as potent peptide deformylase inhibitors and antibacterial agents. J Med Chem 2000;43:2324-31
  • Berg AK, Manokaran S, Eiler D, et al. Energetic rationale for an unexpected and abrupt reversal of guanidinium chloride-induced unfolding of peptide deformylase. Protein Sci 2008;17:11-5
  • Nam KH, Ham JI, Priyadarshi A, et al. Insight into the antibacterial drug design and architectural mechanism of peptide recognition from the E. faecium peptide deformylase structure. Proteins 2008;74:261-5
  • Giglione C, Pierre M, Meinnel T. Peptide deformylase as a target for new generation, broad spectrum antimicrobial agents. Mol Microbiol 2000;36:1197-205
  • Meinnel T. Peptide deformylase of eukaryotic protists: a target for new antiparasitic agents? Parasitol Today 2000;16:165-8
  • Feldman F, Mahler HR. Mitochondrial biogenesis. Retention of terminal formylmethionine in membrane proteins and regulation of their synthesis. J Biol Chem 1974;249:3702-9
  • Velours J, Esparza M, Hoppe J, et al. Amino acid sequence of a new mitochondrially synthesized proteolipid of the ATP synthase of Saccharomyces cerevisiae. EMBO J 1984;3:207-12
  • Tuschen G, Sackman U, Nehls U, et al. Assembly of NADH: ubiquinone reductase (complex I) in Neurospora mitochondria. Independent pathways of nuclear-encoded and mitochondrially encoded subunits. J Mol Biol 1990;213:845-57
  • Polz G, Kreil G. Presence of N-formyl- and N-acetyl-methionine in the proteins of honeybee thorax. Biochem Biophys Res Comm 1970;39:516-21
  • Fearnley IM, Walker JF. Two overlapping genes in bovine mitochondrial DNA encode membrane components of ATP synthase. EMBO J 1986;5:2003-8
  • Yagi T, Hatefi Y. Identification of the dicyclohexylcarbodiimide-binding subunit of NADH-ubiquinone oxidoreductase (Complex I). J Biol Chem 1988;263:16150-5
  • Hauska G, Nitschke W, Herrmann RG. Amino acid identities in the three redox center-carrying polypeptides of cytochrome bc1/b6f complexes. J Bioenerg Biomemb 1988;20:211-28
  • Schmidt J, Herfuth E, Subramanian AR. Purification and characterization of seven chloroplast ribosomal proteins: evidence that organelle ribosomal protein genes are functional and that NH2-terminal processing occurs via multiple pathways in chloroplasts. Plant Mol Biol 1992;20:459-65
  • Shanklin J, Dewitt ND, Flanagan JM. The stroma of higher plant plastids contains ClpP and ClpC, functional homologs of Escherichia coli ClpP and ClpA: an archetypal two-component ATP-dependent protease. Plant Cell 1995;7:1713-22
  • Giglione C, Serero A, Pierre M, et al. Identification of eukaryotic peptide deformylases reveal universality of N-terminal protein processing mechanisms. EMBO J 2000;19:5916-29
  • Moon S, Giglione C, Lee DY, et al. Rice peptide deformylase PDF1B is crucial for development of chloroplasts. Plant Cell Physiol 2008;49(10):1536-46
  • Bouzaidi-Tiali N, Giglione C, Bulliard Y, et al. Type 3 peptide deformylases are required for oxidative phosphorylation in Trypanosoma brucei. Mol Microbiol 2007;65:1218-28
  • Hou CX, Dirk LM, Pattanaik S, et al. Plant peptide deformylase: a novel selectable marker and herbicide target based on essential cotranslational chloroplast protein processing. Plant Biotechnol J 2007;5:275-81
  • Bracchi-Ricard V, Nguyen KT, Zhou Y, et al. Characterization of an eukaryotic peptide deformylase from Plasmodium falciparum. Arch Biochem Biophys 2001;396:162-70
  • Lee MD, She Y, Soskis MJ, et al. Human mitochondrial peptide deformylase, a new anticancer target of actinonin-based antibiotics. J Clin Invest 2004;114:1107-16
  • Escobar-Alvarez S, Goldgur Y, Yang G, et al. Structure and activity of human mitochondrial peptide deformylase, a novel cancer target. J Mol Biol 2009;387:1211-28
  • Hou C, Conn HM, Brightwell R, et al. Engineered tolerance to peptide deformylase inhibitors in Nicotiana tabacum. Plant Biology 2004. Lake Buena Vista, FL, 2004 [Abstract #36]
  • Yuan Z, Trias J, White RJ. Deformylase as a novel antibacterial target. Drug Discov Today 2001;6:954-61
  • Leung D, Abbenante G, Fairlie DP. Protease inhibitors: current status and future prospects. J Med Chem 1999;43:305-41
  • Chikhi A, Bensegueni A, Boulahrouf A, Bencharif M. Theoretical study of Escherichia coli peptide deformylase inhibition by several drugs. In Silico Biol 2006;6:459-66
  • Jain R, Sundram A, Lopez S, et al. α-substituted hydroxamic acids as novel bacterial deformylase inhibitor-based antibacterial agents. Bioorg Med Chem Lett 2004;13:4223-8
  • Lee J, Doddareddy M, Cho Y, et al. Comparative QSAR studies on peptide deformylase inhibitors. J Mol Model 2007;13:543-58
  • Davies SJ, Ayscough AP, Beckett RP, et al. Structure–activity relationships of the peptide deformylase inhibitor BB-3497: modification of the P2′ and P3′ side chains. Bioorg Med Chem Lett 2003;13:2715-8
  • Meinnel T, Patiny L, Ragusa S, Blanquet S. Design and synthesis of substrate analogue inhibitors of peptide deformylase. Biochem 1999;38:4287-95
  • Wang Q, Wang J, Cai Z, Xu W. Prediction of the binding modes between BB-83698 and peptide deformylase from Bacillus stearothermophilus by docking and molecular dynamics simulation. Biophys Chem 2008;134:178-84
  • Wu XH, Quan JM, Wu YD. Theoretical study of the catalytic mechanism and metal-ion dependence of peptide deformylase. J Phys Chem B 2007;111:6236-44
  • Kosowska-Shick K, Credito KL, Pankuch GA, et al. Multistep resistance selection and postantibiotic-effect studies of the antipneumococcal activity of LBM415 compared to other agents. Antimicrob Agents Chemother 2007;51:770-3
  • Antczak C, Shum D, Escobar S, et al. High-throughput identification of inhibitors of human mitochondrial peptide deformylase. J Biomol Screen 2007;12:521-35
  • Boularot A, Giglione C, Petit S, et al. Discovery and refinement of a new structural class of potent peptide deformylase inhibitors. J Med Chem 2007;50:10-20
  • Ednie LM, Pankuch G, Appelbaum PC. Antipneumococcal activity of LBM415, a new peptide deformylase inhibitor, compared with those of other agents. Antimicrob Agents Chemother 2004;48:4027-32
  • Bandow JE, Brotz H, Leichert LIO, et al. Proteomic approach in understanding antibiotic action. Antimicrob Agents Chemother 2003;47:948-55
  • Wang W, White R, Yuan Z. Proteomic study of peptide deformylase inhibition in Streptococcus pneumoniae and Staphylococcus aureus. Antimicrob Agents Chemother 2006;50:1656-63
  • Zheng CJ, Lee S, Lee CH, Kim WG. Macrolactins O-R, glycosylated 24-membered lactones from Bacillus sp. AH159-1. J Nat Prod 2007;70(10):1632-5
  • Kwon YJ, Sohn MJ, Zheng CJ, Kim WG. Fumimycin: a peptide deformylase inhibitor with an unusual skeleton produced by Aspergillus fumisynnematus. Org Lett 2007;9(13):2449-51
  • Shen G, Zhu J, Simpson AM, Pei D. Design and synthesis of macrocyclic peptidyl hydroxamates as peptide deformylase inhibitors. Bioorg Med Chem Lett 2008;18:3060-3
  • East SP, Beckett RP, Brookings DC, et al. Peptide deformylase inhibitors with activity against respiratory tract pathogens. Bioorg Med Chem Lett 2004;14:59-62
  • Bowker KE, Noel AR, Macgowan AP. In vitro activities of nine peptide deformylase inhibitors and five comparator agents against respiratory and skin pathogens. Int J Antimicrob Agents 2003;22:557-61
  • Teo JW, Thayalan P, Beer D, et al. Peptide deformylase inhibitors as potent antimycobacterial agents. Antimicrob Agents Chemother 2006;50:3665-73
  • Wiesner J, Reichenberg A, Heinrich S, et al. The plastid-like organelle of apicomplexan parasites as drug target. Curr Pharm Des 2008;14:855-71
  • Broughton BJ, Chaplen P, Freeman WA, et al. Studies concerning the antibiotic actinonin. Part VIII. Structure-activity relationships in the actinonin series. Chem Soc 1975;9:857-60
  • Gross M, Clements J, Beckett RP, et al. Oral anti-pneumococcal activity and pharmacokinetic profiling of a novel peptide deformylase inhibitor. J Antimicrob Chemother 2004;53:487-93
  • Dean CR, Narayan S, Richards J, et al. Reduced susceptibility of Haemophilus influenzae to the peptide deformylase inhibitor LBM415 can result from target protein overexpression due to amplified chromosomal def gene copy number. Antimicrob Agents Chemother 2007;51:1004-10
  • Hasan S, Daugelat S, Rao PS, Schreiber M. Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis. PLoS Comput Biol 2006;2:540-50
  • Sassetti CM, Boyd DH, Rubin EJ. Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 2003;48:77-84
  • Meinnel T, Lazennec C, Villoing S, Blanquet S. 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. J Mol Biol 1997;267:749-61
  • Kreusch A, Spraggon G, Lee CC, 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. J Mol Biol 2003;30:309-21
  • Saxena R, Chakraborti PK. The carboxy-terminal end of the peptide deformylase from Mycobacterium tuberculosis is indispensable for its enzymatic activity. Biochem Biophys Res Commun 2005;332:418-25
  • Saxena R, Kanudia P, Datt M, et al. Three consecutive arginines are important for the mycobacterial peptide deformylase enzyme activity. J Biol Chem 2008;283:23754-64
  • Saxena R, Chakraborti PK. Identification of regions involved in enzymatic stability of peptide deformylase of Mycobacterium tuberculosis. J Bacteriol 2005;187:8216-20
  • Pichota A, Duraiswamy J, Yin Z, et al. Peptide deformylase inhibitors of Mycobacterium tuberculosis: synthesis, structural investigations, and biological results. Bioorg Med Chem Lett 2008;18:6568-72
  • Sharma A, Sharma S, Khuller GK, Kanwar AJ. In vitro and ex vivo activity of peptide deformylase inhibitors against Mycobacterium tuberculosis H37Rv. Int J Antimicrob Agents 2009 [Epub ahead of print, doi: 10.1o16/ijantimicag.2009.04.005]
  • Zhang Y, Mitchison D. The curious characteristics of pyrazinamide: a review. Int J Tubercle Lung Dis 2003;7:6-21

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.