Binding affinities and geometries of various metal ligands in peptide deformylase inhibitors

Biophysical Chemistry

Volumn 101-102, Issue , 2002, Pages 239-247

  Madison, Vincent ^a   Duca, J ^a   Bennett, F ^a   Bohanon, S ^a   Cooper, A ^a   Chu, M ^a   Desai, J ^a   Girijavallabhan, V ^a   Hare, R ^a   Hruza, A ^a   Hendrata, S ^a   Huang, Y ^a   Kravec, C ^a   Malcolm, B ^a   McCormick, J ^a   Miesel, L ^a   Ramanathan, L ^a   Reichert, P ^a   Saksena, A ^a   Wang, J ^a   Weber, P C ^a   Zhu, H ^a   Fischmann, T ^a   more..

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

Actinonin; Antibiotics; Crystallographic structures; Matlystatin; Peptide deformylase; Protonation states; QM MM

Indexed keywords

ACTINONIN; ANTIINFECTIVE AGENT; GLUTAMIC ACID; LIGAND; MATLYSTATIN; METAL; PEPTIDE DEFORMYLASE INHIBITOR; UNCLASSIFIED DRUG; AMIDASE; AMINOPEPTIDASE; ENZYME INHIBITOR; PEPTIDE DEFORMYLASE;

AMINO TERMINAL SEQUENCE; ANTIMICROBIAL ACTIVITY; ARTICLE; BACTERIAL GROWTH; BACTERIOSTASIS; BINDING AFFINITY; DRUG IDENTIFICATION; DRUG SYNTHESIS; GEOMETRY; IN VITRO STUDY; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTEIN SYNTHESIS; PROTON TRANSPORT; QUANTUM MECHANICS; REPRODUCIBILITY; SCREENING; CHEMICAL STRUCTURE; CHEMISTRY; DRUG ANTAGONISM; METABOLISM;

AMIDOHYDROLASES; AMINOPEPTIDASES; ENZYME INHIBITORS; LIGANDS; METALS; MODELS, MOLECULAR;

EID: 0037058966     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(02)00179-5     Document Type: Article

References (28)

1. Giglione C., Serero A., Pierre M., Boisson B., Meinnel T. Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms. EMBO J. 19:2000;5916-5929.
2. Yuan Z., Trias J., White R.J. Deformylase as a novel antibacterial target. Drug Discovery Today. 6:2001;954-961.
3. Chan M.K., Gong W., Rajagopalan P.T.R., Hao B., Tsai C.M., Pei D. Crystal structure of Escherichia coli peptide deformylase. Biochemistry. 36:1997;13904-13909.
4. Becker A., Schlichting I., Kabsch W., Groche D., Schultz S., Wagner A.F.V. Iron center, substrate recognition and mechanism of peptide deformylase. Nature Struct. Biol. 5:1998;1053-1058.
5. Ragusa S., Mouchet P., Lazennec C., Dive V., Meinnel T. Substrate recognition and selectivity of peptide deformylase. Similarities and differences with metzincins and thermolysin. J. Mol. Biol. 289:1999;1445-1457.
6. Clements J.M., Beckett R.P., Brown A., et al. Antibiotic activity and characterization of BB-3497, a novel peptide deformylase inhibitor. Antimicrob. Agents Chemother. 45:2001;563-570.
7. Chen D.Z., Patel D.V., Hackbarth C.J., et al. Actinonin, a naturally occurring antibacterial agent, is a potent deformylase inhibitor. Biochemistry. 39:2000;1256-1262.
8. 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. 11:2001;1355-1358.
9. 6-benzo[1,2,6]thiadiazin-3- yl)-N-hydroxy-acetamides as potent and selective peptide deformylase inhibitors. J. Med. Chem. 44:2001;1847-1852.
10. Green B.G., Toney J.H., Kozarich J.W., Grant S.K. Inhibition of bacterial peptide deformylase by biaryl acid analogs. Arch. Biochem. Biophys. 375:2000;355-358.
11. Rajagopalan P.T.R., Datta A., Pei D. Purification, characterization, and inhibition of peptide deformylase from Escherichia coli. Biochemistry. 36:1997;13910-13918.
12. S. Bohanon, A. Hruza, L. Ramanathan et al., Peptide deformylase of Staphylococcus aureus: Kinetic and structural comparison to the E. coli enzyme, The 14th Protein Society Symposium, San Diego, CA, August 5-9, 2000.
13. Wei Y., Pei D. Continuous spectrophotometric assay of peptide deformylase. Anal. Biochem. 250:1997;29-34.
14. Morrison J.F., Walsh C.T. The behavior and significance of slow-binding enzyme inhibitors. Adv. Enzymol. Relat. Areas Mol. Biol. 61:1988;201-301.
15. Becker A., Schlichting I., Kabsch W., Schultz S., Wagner A.F.V. Structure of peptide deformylase and identification of the substrate binding site. J. Biol. Chem. 273:1998;11413-11416.
16. Navaza J. AMoRe: an automatic package for molecular replacement. Acta Cryst. A50:1994;157-163.
17. Bricogne G. The Bayesian statistical viewpoint on structure determination: basic concepts and examples. Meth. Enzymol. 276A:1997;361-423.
18. Murphy R.B., Philipp D.M., Friesner R.A. A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments. J. Comp. Chem. 21:2000;1442-1457.
19. Murphy R.B., Philipp D.M., Friesner R.A. Frozen orbital QM/MM methods for density functional theory. Chem. Phys. Lett. 321:2000;113-120.
20. Hay P.J., Wadt W.R. Ab initio effective core potentials for molecular orbital calculations. Potentials for K to Au including the outermost core orbitals. J. Chem. Phys. 82:1985;299-310.
21. Rovira C., Schulze B., Eichinger M., Evanseck J.D., Parrinello M. Influence of the Heme pocket conformation on the structure and vibrations of the Fe-CO Bond in myoglobin: a QM/MM density functional study. Biophys. J. 81:2001;435-445.
22. Morokuma K., Musaev D.G., Vreven T., Basch H., Torrent M., Khoroshun D.V. Model studies of the structures, reactivities, and reaction mechanisms of metalloenzymes. IBM J. Res. Dev. 45:2001.
23. Babine R.E., Bender S.L. Molecular recognition of protein-ligand complexes: applications to drug design. Chem. Rev. 97:1997;1359-1472.
24. Rajagopalan P.T.R., Grimme S., Pei D. Characterization of cobalt(II)-substituted peptide deformylase: function of the metal ion and the catalytic residue Glu-133. Biochemistry. 39:2000;779-790.
25. Johnson L.L., Pavlovsky A.G., Johnson A.R., et al. A rationalization of the acidic pH dependence for stromelysin-1 (matrix metalloproteinase-3) catalysis and inhibition. J. Biol. Chem. 275:2000;11026-11033.
26. Apfel C.M., Locher H., Evers S., et al. Peptide deformylase as an antibacterial drug target: target validation and resistance development. Antimicrob. Agents Chemother. 45:2001;1058-1064.
27. Margolis P.S., Hackbarth C.J., Young D.C., et al. Peptide deformylase in Staphylococcus aureus: resistance to inhibition is mediated by mutations in the formyltransferase gene. Antimicrob. Agents Chemother. 44:2000;1825-1831.
28. Margolis P., Hackbarth C., Lopez S., et al. Resistance of Streptococcus pneumoniae to deformylase inhibitors is due to mutations in defB. Antimicrob. Agents Chemother. 45:2001;2432-2435.