In silico study of the selective inhibition of Bacterial Peptide Deformylases by several drugs

Journal of Proteomics and Bioinformatics

Volumn 3, Issue 2, 2010, Pages 61-65

  Chikhi, Abdelouahab ^a   Bensegueni, Abderrahmane ^a  

^a Universite Mentouri Constantine   (Algeria)

Author keywords

Antibiotics; Autodock; Docking; Human homologue; Lipinski's rule; Molecular properties; Peptide deformylase

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 77149143225     PISSN: None     EISSN: 0974276X     Source Type: Journal    
DOI: 10.4172/jpb.1000122     Document Type: Article

References (28)

1. Boularot A, Giglione C, Artaud I, Meinnel T (2004) Structure-activity relationship and Therapeutic potential of peptide deformylase inhibitors Curr Opin Investig Drugs 5: 809-822.
2. Boularot A, Giglione C, Petit S, Duroc Y, Alves de Sousa R, et al. (2007) Discovery and refinement of a new structural class of potent peptide deformylase inhibitors J. Med. Chem 50: 10-20.
3. Bursulaya BD, Totrov M, Abagyan R, Brooks CL 3rd (2003) Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des 17: 755-763.
4. Bush K, Macielag M, Weidner-Wells M (2004) Taking inventory: antibacterial agents currently at or beyond phase 1. Curr Opin Microbiol 7: 466-476.
5. Chen DZ, Patel DV, Hackbarth CJ, Wang W, Dreyer G, et al. (2000) Actinonin, a naturally occurring antibacterial agent, is a potent deformylase inhibitor. Biochemistry 39: 1256-1262.
6. Chikhi A, Bensegueni A (2008) Comparative Study of the Efficiency of Three Protein-Ligand Docking Programs. J Proteomics Bioinform 1: 161-165.
7. Chikhi A, Bensegueni A, Boulahrouf A Bencharif M (2006). Theoretical study of Escherichia coli peptide deformylase inhibition by several drugs In Silico Biology 6: 459-466.
8. Fritsche TR, Sader HS, Cleeland R, Jones RN (2005) Comparative Antimicrobial Characterization of LBM415 (NVP PDF-713), a New Peptide Deformylase Inhibitor of Clinical Importance Antimicrob. Agents Chemother 49: 1468-1476.
9. Giglione C, Meinnel T (2001) Organellar peptide deformylases: universality of the N-terminal methionine cleavage mechanism. Trends Plant Sci 6: 566-572.
10. Giglione C, Pierre M, Meinnel T (2000) Peptide deformylase as a target for new generation, wide-spectrum antibiotic agents. Mol Microbiol 36: 1197-1205.
11. Giglione C, Serero A, Pierre M, Boisson B, Meinnel T (2000) Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms. EMBO J 19: 5916-5929.
12. Gordon JJ, Kelly BK, Miller GA (1962) Actinonin: an Antibiotic Substance produced by an Actinomycete Nature 195: 701-702.
13. Guilloteau JP, Mathieu M, Giglione C, Blanc V, Dupuy A, et al. (2002) 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 320: 951-962.
14. Giglione C, Vallon O, Meinnel T (2003) Control of protein life-span by N-terminal methionine excision EMBO J 22: 13-23.
15. Hao B, Gong W, Rajagopalan PT, Zhou Y, Pei D, et al. (1999) Structural basis for the design of antibiotics targeting peptide deformylase. Biochemistry 38: 4712-4719.
16. Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual screening for drug discovery: methods and applications Nature reviews. Drug discovery 3: 9350-949.
17. Kumar A, Nguyen KT, Srivathsan S, Ornstein B, Turley S, et al. (2002) Crystals of peptide deformylase from Plasmodium falciparum reveal critical characteristics of the active site for drug design. Structure 10: 357-367.
18. Lee MD, She Y, Soskis MJ, Borella CP, Gardner JR, et al. (2004) Human mitochondrial peptide deformylase, a new anticancer target of actinonin-based antibiotics. J Clin Invest 114: 1107-1116.
19. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Del Rev 23: 3-25.
20. Mazel D, Pochet S, Marliere P (1994) Genetic characterization of polypeptide deformylase, adistinctive enzyme of eubacterial translation. EMBO J 13: 914-923.
21. Meinnel T (2000) Peptide deformylase of eukaryotic protists: A target for new antiparasitic agents? Parasitol Today 16: 165-168.
22. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, et al. (1998) Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function J Comput Chem 19: 1639-1662.
23. Pei D (2001) Peptide deformylase: a target for novel antibiotics? Emerg Ther Targets 5: 23-40.
24. Perola E, Walters WP Charifson PS (2004) A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 56: 235-249.
25. Ramanathan-Girish S, McColm J, Clements JM, Taupin P, Barrowcliffe S, et al. (2004) Pharmacokinetics in animals and humans of a first-in- class peptide deformylase inhibitor. Antimicrob Agents Chemother 48: 4835-4842.
26. Serero A, Giglione C, Meinnel T (2001) Distinctive features of the two classes of eukaryotic peptide deformylases. J Mol Biol 314: 695-708.
27. Serero A, Giglione C, Sardini A, Martinez Sanz J, Meinnel T (2003) An unusual peptide deformylase features in the human mitochondrial N- terminal methionine excision pathway J Biol Chem 278: 52953-52963.
28. Yuan Z, Trias J, White RJ (2001) Deformylase as a novel antibacterial target. Drug Discovery Today 6: 954-961.