Refining the multiple protein structure pharmacophore method: Consistency across three independent HIV-1 protease models

Journal of Medicinal Chemistry

Volumn 49, Issue 12, 2006, Pages 3478-3484

  Meagher, Kristin L ^a   Lerner, Michael G ^a   Carlson, Heather A ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; PROTEINASE; PROTEINASE INHIBITOR;

ARTICLE; AUTOMATION; BINDING SITE; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG RECEPTOR BINDING; DRUG STRUCTURE; DRUG TARGETING; HUMAN IMMUNODEFICIENCY VIRUS 1; MODEL; PHARMACOPHORE; PROTEIN CONFORMATION; PROTEIN STRUCTURE;

HIV PROTEASE; HIV PROTEASE INHIBITORS; HIV-1; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 33745123314     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm050755m     Document Type: Article

References (27)

1. Lyne, P. D. Structure-Based Virtual Screening: An Overview. Drug Discov. Today 2002, 7, 1047-1055.
2. Jorgensen, W. L. The Many Roles of Computation in Drug Discovery. Science 2004, 303, 1813-1818.
3. Teodoro, M. L.; Kavraki, L. E. Conformational Flexibility Models for the Receptor in Structure Based Drug Design. Curr. Pharm. Des. 2003, 9, 1635-1648.
4. Teague, S. J. Implications of Protein Flexibility for Drug Discovery. Nat. Rev. Drug Discov. 2003, 2, 527-541.
5. Wong, C. F.; McCammon, J. A. Protein Flexibility and Computer-Aided Drug Design. Annu. Rev. Pharmacol. 2003, 43, 31-45.
6. Carlson, H. A. Protein Flexibility and Drug Design: How to Hit a Moving Target. Curr. Opin. Chem. Biol. 2002, 6, 447-452.
7. Carlson, H. A.; Masukawa, K. M.; Rubins, K.; Bushman, F. D.; Jorgensen, W. L.; Lins, R. D.; Briggs, J. M.; McCammon, J. A. Developing a Dynamic Pharmacophore Model for HIV-1 Integrase. J. Med. Chem. 2000, 43, 2100-2114.
8. Carlson, H. A.; Masukawa, K. M.; McCammon, J. A. Method for Including the Dynamic Fluctuations of a Protein in Computer-Aided Drug Design. J. Phys. Chem. A 1999, 103, 10213-10219.
9. Meagher, K. L.; Carlson, H. A. Incorporating Protein Flexibility in Structure-Based Drug Discovery: Using HIV-1 Protease as a Test Case. J. Am. Chem. Soc. 2004, 126, 13276-13281.
10. Mustata, G. I.; Briggs, J. M. A Structure-Based Design Approach for the Identification of Novel Inhibitors: Application to an Alanine Racemase. J. Comput. Aided Mol. Des. 2002, 16, 935-953.
11. Deng, J. X.; Lee, K. W.; Sanchez, T.; Cui, M.; Neamati, N.; Briggs, J. M. Dynamic Receptor-Based Pharmacophore Model Development and Its Application in Designing Novel HIV-1 Integrase Inhibitors. J. Med. Chem. 2005, 48, 1496-1505.
12. Schechner, M.; Sirockin, F.; Stote, R. H.; Dejaegere, A. P. Functionality Maps of the ATP Binding Site of DNA Gyrase B: Generation of a Consensus Model of Ligand Binding. J. Med. Chem. 2004, 47, 4373-4390.
13. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
14. Lerner, M. G.; Carlson, H. A. Unpublished data.
15. Spinelli, S.; Liu, Q. Z.; Alzari, P. M.; Hirel, P. H.; Poljak, R. J. The 3-Dimensional Structure of the Aspartyl Protease from the HIV-1 Isolate BRU. Biochimie 1991, 73, 1391-1396.
16. Wlodawer, A.; Miller, M.; Jaskolski, M.; Sathyanarayana, B. K.; Baldwin, E.; Weber, I. T.; Selk, L. M.; Clawson, L.; Schneider, J.; Kent, S. B. H. Conserved Folding in Retroviral Proteases-Crystal-Structure of a Synthetic HIV-1 Protease. Science 1989, 245, 616-621.
17. Lapatto, R.; Blundell, T.; Hemmings, A.; Overington, J.; Wilderspin, A.; Wood, S.; Merson, J. R.; Whittle, P. J.; Danley, D. E.; Geoghegan, K. F.; Hawrylik, S. J.; Lee, S. E.; Scheid, K. G.; Hobart, P. M. X-ray-Analysis of HIV-1 Proteinase at 2.7 Å Resolution Confirms Structural Homology among Retroviral Enzymes. Nature 1989, 342, 299-302.
18. Meagher, K. L.; Carlson, H. A. Solvation Influences Flap Collapse in HIV-1 Protease. Proteins 2005, 58, 119-125.
19. Case, D. A.; Pearlman, D. A. C., J. W.; Cheatham, T. E., III; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Tsui, V.; Radmer, R. J.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER6; University of California: San Francisco, CA, 1996.
20. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force-Field for the Simulation of Proteins, Nucleic-Acids, and Organic-Molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
21. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79, 926-935.
22. Jorgensen, W. L. BOSS, 4.2; Yale University: New Haven, CT, 2000.
23. Comprehensive Medicinal Chemistry Database; MDL Information Systems, Inc.: San Leandro, CA, 2003.
24. Molecular Operating Environment, 2003.02; Chemical Computing Group Inc.: Montreal, Canada, 2003.
25. Halgren, T. A. Merck Molecular Force Field I. Basis, Form, Scope. Parameterization, and Performance of MMFF94. J. Comput. Chem. 1996, 17, 490-519.
26. DeLano, W. L. The Pymol Molecular Graphics System; DeLano Scientific: San Carlos, CA, 2002.
27. Wlodawer, A.; Gustchina, A. Structural and Biochemical Studies of Retroviral Proteases. Biochim. Blophysica. Acta 2000, 1477, 16-34. 3485-3495