CoMFA/CoMSIA/HQSAR and Docking study of the binding mode of selective cyclooxygenase (COX-2) inhibitors

QSAR and Combinatorial Science

Volumn 23, Issue 1, 2004, Pages 36-55

  Chen, Haifeng ^a,b   Li, Qiang ^b   Yao, Xiaojun ^a   Fan, BoTao ^a   Yuan, Shengang ^b   Panaye, A ^a   Doucet, J P ^a  

^a UNIVERSITÉ PARIS DIDEROT   (France)

^b SHANGHAI INSTITUTE OF ORGANIC CHEMISTRY   (China)

Author keywords

3D QSAR; Cyclooxygenase (COX 2) Inhibitors; Docking; HQSAR

Indexed keywords

BINDING ENERGY; COMPUTATIONAL CHEMISTRY; HYDROPHOBICITY; MOLECULAR GRAPHICS;

3D-QSAR; ANTI-INFLAMMATORIES; BINDING MODES; CYCLOOXYGENASE (COX-2) INHIBITOR; CYCLOOXYGENASES; DOCKING; DOCKING STUDIES; HQSAR; INTERACTION MECHANISMS; INTERMOLECULAR INTERACTIONS;

HYDROGEN BONDS;

ARGININE; CYCLOOXYGENASE 2; CYCLOOXYGENASE 2 INHIBITOR; CYCLOOXYGENASE 2 RECEPTOR; HISTIDINE; IMIDAZOLE DERIVATIVE; LEUCINE; OXAZOLE DERIVATIVE; PHENYLALANINE; PYRAZOLE DERIVATIVE; UNCLASSIFIED DRUG;

ANTIINFLAMMATORY ACTIVITY; ARTICLE; BINDING AFFINITY; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; DRUG CONFORMATION; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR DOCKING; MOLECULAR INTERACTION; MOLECULAR MECHANICS; MOLECULAR MODEL; MOLECULAR RECOGNITION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; QUANTITATIVE STRUCTURE ACTIVITY RELATION; VALIDATION PROCESS;

EID: 8544243478     PISSN: 1611020X     EISSN: None     Source Type: Journal    
DOI: 10.1002/qsar.200330844     Document Type: Article

References (34)

1. J. Y. Fu, J. L. Masferrer, K. Seibert, A. Raz, P. Needleman, The Induction and Suppression of Prostaglandin H2 Synthase (Cyclooxygenase) in Human Monocytes, J. Biol. Chem. 1990, 265, 16737-16740.
2. F. Julémont, L. Xavier, C. Michaux, J. Damas, C. Charlier, F. Durant, B. Pirotte, J. M. Dogné, Spectral and Crystallographic Study of Pyridinic Analogues of Nimesulide: Determination of the Active Form of Methanesulfonamides as COX-2 SelectiveInhibitors, J. Med. Chem. 2002, 45, 5182-5185
3. K. Subbaramaiah, D. Zakim, B. B. Weksler, A. J. Dannenberg, Inhibition of Cyclooxygenase: A Novel Approach to Cancer Prevention, Proc. Soc. Exp. Biol. Med. 1997, 216, 201-210.
4. G. M. Pasinetti, Cyclooxygenase and Inflammation in Alzheimer's Disease: Experimental Approaches and Clinical Intervention, J. Neurosci. Res. 1998, 54, 1-6.
5. A. Christie, Bulletin of the World Health Organization, 2002, 1, 80-81.
6. H. Hashimoto, K. Imamura, J. Haruta, K. Wakitani, 4-(4-Cycloalkyl/aryl- oxazol-5-yl) benzenesulfonamides as Selective Cyclooxygenase-2 Inhibitors: Enhancement of the Selectivity by Introduction of a Fluorine Atom and Identification of a Potent, Highly Selective, and Orally Active COX-2 Inhibitor JTE-522, J. Med. Chem. 2002, 4545, 1511-1517.
7. R. G. Kurumbail, A. M. Stevens, J. K. Gierse, J. J. McDonald, R. A. Stegeman, J. Y. Pak, D. Gildehaus, J. M. Miyashiro, T. D. Penning, K. Seibert, P. C. Isakson, W. C. Stallings, Structural Basis for Selective Inhibition of Cyclooxygenase-2 by Antiinflammatory Agents, NatureNature 1996, 384, 644-648.
8. Y. Leblanc, W. C. Black, C. C. Chan, S. Charleson, D. Delorme, D. Denis, J. Y. Gauthier, E. L. Grimm, R. Gardon, D. Guay, P. Hamel, S. Kargman, C. K. Lau, J. Mancini, M. Quellet, D. Percival, P. Roy, K. Skorey, P. Tagari, P. Vickers, E. Wong, L. Xu, P. Prasit, Synthesis and Biological Evaluation of Both Enantionmers of L-761,000 as Inhibitors of Cyclooxygenase-1 and 2, Biorg. Med. Chem. Lett. 1996, 6, 731-736.
9. K. M. Woods, R. W. McCroskey, M. R. Michaelides, (Abbott) Patent WO9839330, 1997.
10. T. Klein, R. M. Nusing, J. Pfeilschifter, V. Ullrich, Selective Inhibition of Cyclooxygenase 2, Biochem. Pharmacol. 1994, 48, 1605-1610.
11. P. Chavatte, S. Yous, C. Maro, N. Baurin, D. Lesieur, Three-Dimensional Quantitative Structure-Activity Relationships of Cyclo-oxygenase-2 (COX-2) Inhibitors: A Comparative Molecular Field Analysis, J. Med. Chem. 2001, 44, 3223-3230.
12. G. R. Desiraju, B. Gopalakrishnan, R. K. R. Jetti, A. Nagaraju, D. Raveendra, J. R. P. Sarma, M. E. Sobhia, R. Thilagavathi, Computer-Aided Design of Selective COX-2 Inhibitors: Comparative Molecular Field Analysis, Comparative Molecular Similarity Indices Analysis, and Docking Studies of Some 1,2-Diarylimidazole Derivatives, J. Med. Chem. 2002, 45, 4847-4857.
13. H. Liu, X. Q. Huang, J. H. Shen, X. M. Luo, M. H. Li, B. Xiong, G. Chen, J. K. Shen, Y. M. Yang, H. L. Jiang, K. X. Chen, Inhibitory Mode of 1,5-Diarylpyrazole Derivatives against Cyclooxygenase-2 and Cyclooxygenase-1: Molecular Docking and 3D QSAR Analyses, J. Med. Chem. 2002, 45, 4816-4827.
14. R. Soliva, C. Almansa, S. G. Kalko, F. J. Luque, M. Orozco, Theoretical Studies on the Inhibition Mechanism of Cyclooxygenase-2. Is There a Unique Recognition Site? J. Med. Chem. 2003, 46, 1372-1382.
15. R. Garg, A. Kurup, S. B. Mekapati, C. Hansch, Cyclooxygenase (COX) Inhibitors: A Comparative QSAR Study, Chem. Rev. 2003, 103, 703-732.
16. J. J. Talley, S. R. Bertenshaw, D. L. Brown, J. S. Carter, M. J. Graneto, C. M. Koboldt, J. L. Masferrer, B. H. Norman, D. J. Jr. Rogier, B. S. Zweifel, K. Seibert, 4,5-Diaryloxazole inhibitors of cyclooxygenase-2 (COX-2), Med. Res. Rev. 1999, 79, 199-208.
17. T. D. Penning, J. J. Talley, S. R. Bertenshaw, J. S. Carter, P. W. Collins, S. Docter, M. J. Graneto, L. F. Lee, J. W. Malecha, J. M. Miyashiro, R. S. Rogers, D. J. Rogier, S. S. Yu, G. D. Anderson, E. G. Burton, J. N. Cogburn, S. A. Gregory, C. M. Koboldt, W. E. Perkins, K. Seibert, A. W. Veenhuizen, Y. Y. Zhang, P. C. Isakson, Synthesis and Biological Evaluation of the 1,5-Diarylpyrazole Class of Cyclooxygenase-2 Inhibitors: Identification of 4-[5-(4-Methylphenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]benzenesulfonamide (SC-58635, Celecoxib), J. Med. Chem. 1997, 40, 1347-1365.
18. I. K. Khanna, R. M. Weier, Y. Yu, P. W. Collins, J. M. Miyashiro, C. M. Koboldt, A. W. Veenhuizen, J. L. Currie, K. Seibert, P C. Isakson, 1,2-Diarylpyrroles as Potent and Selective Inhibitors of Cyclooxygenase-2, J. Med. Chem. 1997, 40, 1619-1633.
19. I. K. Khanna, R. M. Weier, Y. Yu, X. D. Xu, F. J. Koszyk, P. W. Collins, C. M. Koboldt, A. W. Veenhuizen, W. E. Perkins, J. J. Casler, J. L. Masferrer, Y. Y. Zhang, S. A. Gregory, K. Seibert, P. C. Isakson, 1,2-Diarylimidazoles as Potent, Cyclooxygenase-2 Selective, and Orally Active Anti-inflammatory Agents, J. Med. Chem. 1997, 40, 1634-1647.
20. I. K. Khanna, Y. Yu, R. M. Huff, R. M. Weier, X. Xu, F. J. Koszyk, P. W. Collins, J. N. Cogburn, P. C. Isakson, C. M. Koboldt, J. L. Masferrer, W. E. Perkins, K. Seibert, A. W. Veenhuizen, J. Yuan, D. C. Yang, Y. Y. Zhang, Selective Cyclooxygenase-2 Inhibitors: Heteroaryl Modified 1,2-Diarylimidazoles Are Potent, Orally Active Antiinflammatory Agents, J. Med. Chem. 2000, 43, 3168-3185.
21. Gaussian 98 (Revision A.1) +, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P. M. W. Gill, B. G. Johnson, W. Chen, M. W. Wong, J. L. Andres, M. Head-Gordon, E. S. Replogle and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 1998.
22. M. Clark III, R. D. Cramer, N. Van Opdenbosh, The Tripos Force Field, J. Comput. Chem. 1989, 10, 982-1012.
23. SYBYL[Computer Program]. Version 6.9, St. Louis(MO): Tripos Associates Inc(2003).
24. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. J. Profeta, P. Weiner, A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins, J. Am. Chem. Soc. 1984, 106, 765-784.
25. G. M. Morris, D. S. Goodsell, R. S. Halliday, R. Huey, W. E. Hart, R. K. Belew, A. J. Olson, Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function, J. Comput. Chem. 1998, 19, 1639-1662.
26. G. M. Morris, D. S. Goodsell, R. Huey, A. J. Olson, Distributed Automated Docking of Flexible Ligands to Proteins: Parallel Applications of AutoDock 2.4, J. Comput.-Aided Mol. Des. 1996, 10, 293-304.
27. 2-guided Region Selection for Comparative Molecular Field Analysis (CoMFA): A Simple Method to Achieve Consistent Results, J. Med. Chem. 1995, 38, 1060-1066.
28. L. Stahle, S. Wold, Multivariate Data Analysis and Experimental Design in Biomedical Research, in Progress in Medicinal Chemistry, G. P. Ellis, G. B. West, (Eds.), Elsevier. 1988, pp. 292-338.
29. G. Klebe, U. Abraham, Comparative Molecular Similarity Index Analysis (CoMSIA) to Study Hydrogen Bonding Properties and to Score Combinatorial Libraries, J. Comput.-Aided Mol. Des. 1999, 13, 1-10.
30. M. Böhm, J. Stürzebecher, G. Klebe, 3D QSAR Analyses using CoMFA and CoMSIA to Elucidate Selectivity Differences of Inhibitors Binding to Trypsin, Thrombin and Factor Xa, J. Med. Chem. 1999, 42, 458-477.
31. R. X. Wang, Y. Gao, L. Liu, L. H. Lai, All-Orientation Search and All-Placement Search in Comparative Molecular Field Analysis, J. Mol. Model. 1998, 4, 276-283.
32. T. W. Heritage, D. R. Lowis, Molecular Hologram QSAR, in A. L. Parrill, M. R. Reddy (Eds.), Rational Drug Design. Novel Methodology and Practical Applications, American Chemical Society, Washington, DC, 1999, pp. 212-225.
33. M. A. Avery, M. Alvim-Gaston, C R. Rodrigues, E. J. Barreiro, F. E. Cohen, Y. A. Sabnis, J. R. Woolfrey, Structure-Activity Relationships of the Antimalarial Agent Artemisinin. 6. The Development of Predictive In Vitro Potency Models Using CoMFA and QSAR Methodologies, J. Med. Chem. 2002, 45, 292-303.
34. D. T. Stanton, P. C. Jurs, Development and use of charged partial surface area descriptors in computer-assisted quantitative structure-property relationship studies, Anal. Chem. 1990, 62, 2323-2329.