Structure-based design of a macrocyclic inhibitor for peptide deformylase

Journal of Medicinal Chemistry

Volumn 46, Issue 18, 2003, Pages 3771-3774

  Hu, Xubo ^a   Nguyen, Kiet T ^a   Verlinde, Christophe L M J ^b   Hol, Wim G J ^b   Pei, Dehua ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MACROCYCLIC COMPOUND; PEPTIDE DEFORMYLASE;

AMINO TERMINAL SEQUENCE; ANTIBACTERIAL ACTIVITY; ANTIBIOTIC RESISTANCE; ARTICLE; CATALYSIS; COVALENT BOND; CROSS LINKING; DRUG DESIGN; ENZYME INHIBITION; HYDROLYSIS; MITOCHONDRIAL MEMBRANE; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

AMIDOHYDROLASES; AMINOPEPTIDASES; ANTI-BACTERIAL AGENTS; CHELATING AGENTS; DRUG DESIGN; ENZYME INHIBITORS; GRAM-NEGATIVE BACTERIA; GRAM-POSITIVE BACTERIA; METALLOENDOPEPTIDASES; MICROBIAL SENSITIVITY TESTS; MODELS, MOLECULAR; MOLECULAR MIMICRY; PEPTIDES, CYCLIC; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0041418430     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm034113f     Document Type: Article

References (32)

1. Giglione, C.; Pierre, M.; Meinnel, T. Peptide deformylase as a target for new generation, broad spectrum antimicrobial agents. Mol. Microbiol. 2000, 36, 1197-1205.
2. Pei, D. Peptide deformylase: a target for novel antibiotics? Emerging Ther. Targets 2001, 5, 23-40.
3. Yuan, Z.; Trias, J.; White, R. J. Deformylase as a novel antibacterial target. Drug Discovery Today 2001, 6, 954-961.
4. Meinnel, T.; Mechulam, Y.; Blanquet, S. Methionine as translational start signal: a review of the enzymes of the pathway in Escherichia coli. Biochimie 1993, 75, 1061-1075.
5. Mazel, D.; Pochet, S.; Marliere, P. Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation. EMBO J. 1994, 13, 914-923.
6. Meinnel, T.; Blanquet, S. Characterization of the Thermus thermophilus locus encoding peptide deformylase and methionyl-tRNA(fMet) formyltransferase. J. Bacteriol. 1994, 176, 7387-7390.
7. Margolis, P. S.; Hackbarth, C. J.; Young, D. C.; Wang, W.; Chen, D.; Yuan, Z.; White, R.; Trias, J. peptide deformylase in S. aureus: resistance to inhibition is mediated by mutations in the formyltransferase gene. Antimicrob. Agents Chemother. 2001, 44, 1825-1831.
8. Nguyen, K. T.; Hu, X.; Colton, C.; Chakratarti, R.; Zhu, M. X.; Pei, D. Characterization of a human peptide deformylase: Implications for antibacterial drug design. Biochemistry (in press).
9. Rajagopalan, P. T. R.; Yu, X. C.; Pei, D. Peptide deformylase: a new type of mononuclear iron protein. J. Am. Chem. Soc. 1997, 119, 12418-12419.
10. Groche, D.; Becker, A.; Schlichting, I.; Kabasch, W.; Schultz, S.; Wagner, A. F. V. 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, 342-346.
11. Rajagopalan, P. T. R.; Pei, D. Oxygen-mediated inactivation of peptide deformylase. J. Biol. Chem. 1998, 273, 22305-22310.
12. Meinnel, T.; Patiny, L.; Ragusa, S.; Blanquet, S. Design and synthesis of substrate analogue inhibitors of peptide deformylase. Biochemistry 1999, 38, 4287-4295.
13. Huntington, K. M.; Yi, T.; Wei, Y.; Pei, D. Synthesis and antibacterial activity of peptide deformylase inhibitors. Biochemistry 2000, 39, 4543-4551.
14. Wei, Y.; Yi, T.; Huntington, K. M.; Chaudhury, C.; Pei, D. Identification of a potent peptide deformylase inhibitor from a rationally designed combinatorial library. J. Comb. Chem. 2000, 2, 650-657.
15. Chen, D. Z.; Patel, D. V.; Hackbarth, C. J.; Wang, W.; Dreyer, G.; Young, D.; Margolis, P. S.; Wu, C.; Ni, Z.-J.; Trias, J.; White, R.; Yuan, Z. Actinonin, a naturally occurring antibacterial agent, is a potent deformylase inhibitor. Biochemistry 2000, 39, 1256-1262.
16. Apfel, C.; Banner, D. W.; Bur, D.; Dietz, M.; Hirata, T.; Hubschwerlen, C.; Locher, H.; Page, M. G. P.; Pirson, W.; Rosse, G.; Specklin, J.-L. Hydroxamic acid derivatives as potent peptide deformylase inhibitors and antibacterial agents. J. Med. Chem. 2000, 43, 2324-2331.
17. Jayasekera, M. M. K.; Kendall, A.; Shammas, R.; Dermyer, M.; Tomala, M.; Shapiro, M. A.; Holler, T. P. Novel nonpeptidic inhibitors of peptide deformylase. Arch. Biochem. Biophys. 2000, 381, 313-316.
18. Thorarensen, A.; Douglas, M. R., Jr.; Rohrer, D. C. et al. Identification of novel potent hydroxamic acid inhibitors of peptidyl deformylase and the importance of the hydroxamic acid functionality on inhibition. Bioorg. Med. Chem. Lett. 2001, 11, 1355-1358.
19. Roblin, P. M.; Hammerschlag, M. R. In vitro activity of a new antibiotic, NVP-PDF386 (VRC4887), against Chlamydia pneumoniae. Antimicrob. Agents Chemother. 2003, 47, 1447-1448.
20. Clements, J. M.; Beckett, R. P.; Brown, A.; Catlin, G.; Lobell, M.; Palan, S.; Thomas, W.; Whittaker, M.; Wood, S.; Salama, S.; Baker, P. J.; Rodgers, H. F.; Barynin, V.; Rice, D. W.; Hunter, M. G. Antibiotic activity and characterization of BB-3497, a novel peptide deformylase inhibitor. Antimicrob. Agents Chemother. 2001, 45, 563-570.
21. Smith, H. K.; Beckett, R. P.; Clements, J. M.; Doel, S.; East, S. P.; Launchbury, S. B.; Pratt, L. M.; Spavold, Z. M.; Thomas, W.; Todd, R. S.; Whittaker, M. Structure-activity relationship of the peptide deformylase inhibitor BB-3497: modification of the metal binding group. Bioorg. Med. Chem. Lett. 2002, 12, 3595-3599.
22. Xue, C.-B.; He, X.; Roderick, J. et al. Design and synthesis of cyclic inhibitors of matrix metalloproteases and TNF-α production. J. Med. Chem. 1998, 41, 1745-1748.
23. Wei, C.-Q.; Gao, Y.; Lee, K. et al. Macrocyclization in the design of Grb2 SH2 domain-binding ligands exhibiting high potency in whole-cell systems. J. Med. Chem. 2003, 46, 244-254.
24. Hao, B.; Gong, W.; Rajagopalan, P. T. R.; Zhou, Y.; Pei, D.; Chan, M. K. Structural basis for the design of antibiotics targeting peptide deformylase. Biochemistry 1999, 38, 4712-4719.
25. Guilloteau, J.-P.; Mathieu, M.; Giglione, C.; Blanc, V.; Dupuy, A.; Chevrier, M.; Gil, P.; Famechon, A.; Meinnel, T.; Mikol, V. 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, 951-962.
26. Evans, D. A.; Rieger, D. L.; Bilodeau, M. T.; Urpi, F. Stereoselective aldol reactions of chlorotitanium enolates. An efficient method for the assemblage of polypropionate-related synthons. J. Am. Chem. Soc. 1991, 113, 1047-1049.
27. Mitsunobu, O. The use of diethyl azodicarboxyalte and triphenylphosphane in synthesis and transformation of natural products. Synthesis 1981, 1-28.
28. Miller, S. J.; Blackwell, H. E.; Grubbs, R. H. Application of ringclosing metathesis to the synthesis of rigidified amino acids and peptides. J. Am. Chem. Soc. 1996, 118, 9606-9614.
29. Furstner, A. Olefin metathesis and beyond. Angew. Chem., Int. Ed. 2000, 39, 3012-3043.
30. Rajagopalan, P. T. R.; Datta, A.; and Pei, D. Purification, characterization, and inhibition of peptide deformylase from Escherichia coli. Biochemistry 1997, 36, 13910-13918.
31. Lazennec, C.; Meinnel, T. Formate dehydrogenase-coupled spectrophotometric assay of peptide deformylase. Anal. Biochem. 1997, 244, 180-182.
32. Bertini, I.; Luchinat, C. The reaction pathways of zinc enzymes and related biological catalysts. In Bioinorganic Chemistry; Bertini, I., Gray, H. B., Lippard, S. J., Valentine, J. S., Eds.; University Science Books: Sausalito, CA, 1994; pp 37-106.