Exploiting enzyme plasticity in virtual screening: High efficiency inhibitors of glutamate racemase

ACS Medicinal Chemistry Letters

Volumn 1, Issue 1, 2010, Pages 9-13

  Whalen, Katie L ^a   Pankow, Katherine L ^a   Blanke, Steven R ^a,b   Spies, M Ashley ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Glutamate racemase; inhibitor; protein dynamics; virtual screening

Indexed keywords

ENZYME INHIBITOR; GLUTAMATE RACEMASE INHIBITOR; RACEMASE; UNCLASSIFIED DRUG;

ARTICLE; BACILLUS ANTHRACIS; BACILLUS SUBTILIS; COMPETITIVE INHIBITION; CRYSTAL STRUCTURE; DRUG EFFICACY; DRUG TARGETING; ENZYME ACTIVITY; ENZYME CONFORMATION; ENZYME INHIBITION; HIGH THROUGHPUT SCREENING; NONHUMAN; PHASE TRANSITION; PRIORITY JOURNAL;

EID: 77956645841     PISSN: None     EISSN: 19485875     Source Type: Journal    
DOI: 10.1021/ml900005b     Document Type: Article

References (26)

1. Gallo, K. A.; Tanner, M. E.; Knowles, J. R. Mechanism of the Reaction Catalyzed by Glutamate Racemase Biochemistry 1993, 32, 3991-7
2. Bugg, T. D.; Walsh, C. T. Intracellular steps of bacterial cell wall peptidoglycan biosynthesis: Enzymology, antibiotics, and antibiotic resistance Nat. Prod. Rep. 1992, 9, 199-215
3. de Dios, A.; Prieto, L.; Martin, J. A.; Rubio, A.; Ezquerra, J.; Tebbe, M.; Lopez de Uralde, B.; Martin, J.; Sanchez, A.; LeTourneau, D. L.; McGee, J. E.; Boylan, C.; Parr, T. R., Jr.; Smith, M. C. 4-Substituted d -Glutamic Acid Analogues: The First Potent Inhibitors of Glutamate Racemase (MurI) Enzyme with Antibacterial Activity J. Med. Chem. 2002, 45, 4559-70
4. Lundqvist, T.; Fisher, S. L.; Kern, G.; Folmer, R. H.; Xue, Y.; Newton, D. T.; Keating, T. A.; Alm, R. A.; de Jonge, B. L. Exploitation of structural and regulatory diversity in glutamate racemases Nature 2007, 447, 817-22
5. Tanner, M. E.; Gallo, K. A.; Knowles, J. R. Isotope Effects and the Identification of Catalytic Residues in the Reaction Catalyzed by Glutamate Racemase Biochemistry 1993, 32, 3998-4006
6. Koo, C. W.; Blanchard, J. S. Chemical Mechanism of Haemophilus influenzae Diaminopimelate Epimerase Biochemistry 1999, 38, 4416-22
7. Pillai, B.; Cherney, M. M.; Diaper, C. M.; Sutherland, A.; Blanchard, J. S.; Vederas, J. C.; James, M. N. Structural insights into stereochemical inversion by diaminopimelate epimerase: an antibacterial drug target Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 8668-73
8. Ruzheinikov, S. N.; Taal, M. A.; Sedelnikova, S. E.; Baker, P. J.; Rice, D. W. Substrate-induced conformational changes in Bacillus subtilis glutamate racemase and their implications for drug discovery Structure 2005, 13, 1707-13
9. Spies, M. A.; Reese, J. G.; Dodd, D.; Pankow, K. L.; Blanke, S. R.; Baudry, J. Determinants of Catalytic Power and Ligand Binding in Glutamate Racemase J. Am. Chem. Soc. 2009, 131, 5274-5284
10. Alvarez, J.; Shoichet, B. Virtual Screening in Drug Discovery; Taylor & Francis: Boca Raton, 2005; p 470.
11. Dodd, D.; Reese, J. G.; Louer, C. R.; Ballard, J. D.; Spies, M. A.; Blanke, S. R. Functional comparison of the two Bacillus anthracis glutamate racemases J. Bacteriol. 2007, 189, 5265-75
12. Shoichet, B. K. Screening in a spirit haunted world Drug Discovery Today 2006, 11, 607-615
13. Feng, B. Y.; Shoichet, B. K. A detergent-based assay for the detection of promiscuous inhibitors Nat. Protoc. 2006, 1, 550-553
14. Oprea, T. I. Property distribution of drug-related chemical databases J. Comput.-Aided Mol. Des. 2000, 14, 251-264
15. Molecular Operating Environment (/MOE/), version 2008.10. Chemical Computing Group, Inc., Montreal, Quebec, Canada, 2005.
16. Bou, A.; Pericas, M. A.; Serratosa, F. Synthetic applications of di-tert-butoxyethyne, II: New syntheses of squaric, semisquaric, and croconic acids Tetrahedron Lett. 1982, 23, 361-364
17. Fatiadi, A. J. Pseudooxocarbons. Synthesis of 1,2,3- Tris(dicyanomethylene)croconate Salts. A New Bond-Delocalized Dianion, Croconate Blue J. Org. Chem. 1980, 45, 1338-1339
18. Warren, G. L.; Andrews, C. W.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A Critical Assessment of Docking Programs and Scoring Functions J. Med. Chem. 2006, 49, 5912-5931
19. Buschiazzo, A.; Goytia, M.; Schaeffer, F.; Degrave, W.; Shepard, W.; Gregoire, C.; Chamond, N.; Cosson, A.; Berneman, A.; Coatnoan, N.; Alzari, P. M.; Minoprio, P. Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase Proc. Natl. Acad. Sci. U.S.A. 2005, 103, 1705-1710
20. Howard, S.; Berdini, V.; Boulstridge, J. A.; Carr, M. G.; Cross, D. M.; Curry, J.; Devine, L. A.; Early, T. R.; Fazal, L.; Gill, A. L.; Heathcote, M.; Maman, S.; Matthews, J. E.; McMenamin, R. L.; Navarro, E. F.; O'Brien, M. A.; O'Reilly, M.; Rees, D. C.; Reule, M.; Tisi, D.; Williams, G.; Vinkovic, M.; Wyatt, P. G. Fragment-Based Discovery of the Pyrazol-4-yl Urea (AT9283), a Multitargeted Kinase Inhibitor with Potent Aurora Kinase Activity J. Med. Chem. 2009, 52, 379-388
21. Murray, C. W.; Rees, D. C. The rise of fragment-based drug discovery Nat. Chem. 2009, 1, 187-192
22. Monod, J.; Wyman, J.; Changeux, J. P. On the Nature of Allosteric Transitions: A Plausible Model J. Mol. Biol. 1965, 12, 88-118
23. Tsai, C. J.; Kumar, S.; Ma, B.; Nussinov, R. Folding funnels, binding funnels, and protein function Protein Sci. 1999, 8, 1181-90
24. Weber, G. Ligand Binding and Internal Equilibria in Proteins Biochemistry 1972, 11, 864-878
25. Lee, G. M.; Craik, C. S. Trapping moving targets with small molecules Science 2009, 324, 213-215
26. Koshland, D. E., Jr.; Nemethy, G.; Filmer, D. Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits Biochemistry 1966, 5, 365-385