Ligand coordinate analysis of SC-558 from the active site to the surface of COX-2: A molecular dynamics study

Journal of Chemical Information and Modeling

Volumn 46, Issue 4, 2006, Pages 1784-1794

  Sai Ram, K V V M ^a   Rambabu, G ^b   Sarma, J A R P ^b   Desiraju, G R ^a  

^a UNIVERSITY OF HYDERABAD   (India)

^b GVK BIOSCIENCES PVT LTD   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CARDIOVASCULAR SYSTEM; COMPUTATION THEORY; CONFORMATIONS; CRYSTAL STRUCTURE; HYDRATION; MOLECULAR DYNAMICS; TOXICITY;

GEOMETRY DISCONTINUITIES; LIGAND COORDINATE ANALYSIS; ROOT-MEAN-SQUARE DEVIATION; STRUCTURAL INSTABILITY;

ENZYME INHIBITION;

4 [5 (4 BROMOPHENYL) 3 TRIFLUOROMETHYL 1H PYRAZOL 1 YL]BENZENESULFONAMIDE; CYCLOOXYGENASE 2; LIGAND; PYRAZOLE DERIVATIVE;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; ELECTRICITY; METABOLISM;

BINDING SITES; CYCLOOXYGENASE 2; ELECTROSTATICS; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PYRAZOLES;

EID: 33746904319     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050142i     Document Type: Review

References (40)

1. Simmons, D. L.; Botting, R. M.; Hla, T. Cyclooxygenase Isozymes: The Biology of Prostaglandin Synthesis and Inhibition. Pharm. Rev. 2004, 56, 387-437.
2. Vane, J. R.; Botting, R. Mechanism of Action of Antiinflammatory Drugs. Scand. J. Rheumatol. Suppl. 1996, 102, 9-21.
3. FitzGerald, G. A. Coxibs and Cardiovascular Disease. N. Engl. J. Med. 2004, 351, 1709-1711.
4. Solomon, D. H.; Schneeweiss, S.; Glynn, R. J.; Kiyota, Y.; Levin, R.; Mogun, H.; Avron, J. Relationship between Selective Cyclooxy-genase-2 Inhibitors and Acute Myocardial Infarction in Older Adults. Circulation 2004, 109, 2068-2073.
5. Davies, N. M.; Jamali, F. COX-2 Selective Inhibitors Cardiac Toxicity: Getting to the Heart of the Matter. J. Pharm. Pharm. Sci. 2004, 7, 332-336.
6. Finckh, A.; Aronson, M. D. Cardiovascular Risks of Cyclooxygenase-2 Inhibitors: Where We Stand Now. Ann. Intern. Med. 2005, 142, 212-214.
7. Dogne, J. M.; Supuran, C. T.; Pratico, D. Adverse Cardiovascular Effects of the Coxibs. J. Med. Chem. 2005, 48, 2251-2257.
8. FitzGerald, G. A. COX-2 and Beyond: Approaches to Prostaglandin Inhibition in Human Disease. Nat. Rev. Drug Discovery 2003, 2, 879-902.
9. Black, W. C. Selective Cyclooxygenase-2 Inhibitors. Annu. Rep. Med. Chem. 2004, 39, 125-138.
10. Price, M. L. P.; Jorgensen W. L. Analysis of Binding Affinities for Celecoxib Analogues with Cox-1 and Cox-2 from Combined Docking and Monte Carlo Simulations and Insight into the Cox-2/Cox-1 Selectivity. J. Am. Chem. Soc. 2000, 122, 9455-9466.
11. Solvia, R.; Almansa, C.; Kalko, S. G. Luque, F. J.; Orozco, M. Theoretical Studies on the Inhibition Mechanism of Cyclooxygenase-2. Is There a Unique Recognition Site? J. Med. Chem. 2003, 46, 1372-1382.
12. Llorens, O.; Perez, J. J.; Palomer, A.; Mauleon, D. Structural Basis of the Dynamic Mechanism of Ligand Binding to Cyclooxygenase. Bioorg. Med. Chem. Lett. 1999, 9, 2779-2784.
13. Desiraju, G. R.; Gopalakrishnan, B.; Jetti, R. K. R.; Nagaraju, A.; Raveendra, D.; Sarma, J. A. R. P.; Sobhia, M. E.; Thilagavathi, R. 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.
14. Llorens, O.; Perez, J. J.; Palomer, A.; Mauleon, D. Differential Binding Mode of Diverse Cyclooxygenase Inhibitors. J. Mol. Graphics Modell. 2002, 20, 359-371.
15. Lanzo, C. A.; Sutin, J.; Rowlinson, S.; Talley, J.; Marnett, L. J. Fluorescence Quenching Analysis of the Association and Dissociation of a Diarylheterocycle to Cyclooxygenase-1 and Cyclooxygenase-2: Dynamic Basis of Cyclooxygenase-2 Selectivity. Biochemistry 2000, 39, 6228-6234.
16. Kurumbail, R. G.; Stevens, A. M.; Gierse, J. M.; McDonald, J. J.; Stegeman, R. A.; Pak, J. Y.; Gildehaus, D.; Miyashiro, J. M.; Penning, T. D.; Seibert, K.; Isakson, P. C.; Stellings, W. C. Structural Basis for Selective Inhibition of Cyclooxygenase-2 by Antiinflammatory Agents. Nature 1996, 384, 644-648.
17. Xu, Y.; Shen, J.; Luo, X.; Silman, I.; Sussman, J. L.; Chen, K.; Jiang, H. How Does Huperzine A Enter and Leave the Binding Gorge of Acetylcholinesterase? Steered Molecular Dynamics Simulation. J. Am. Chem. Soc. 2003, 125, 11340-11349.
18. Camacho, C. J.; Vajda, S. Protein Docking along Smooth Association Pathways. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10636-10641.
19. Deka, R. C.; Vetrivel, R. Adsorption Sites and Diffusion Mechanism of Alkylbenzenes in Large Pore Zeolite Catalysts as Predicted by Molecular Modeling Techniques. J. Catal. 1998, 174, 88-97.
20. Steiner, T.; Koellner, G. Coexistence of Both Histidine Tautomers in the Solid State and Stabilization of the Unfavourable Nδ-H Form by Intramolecular Hydrogen Bonding: Crystalline L-His-Gly Hemihydrate. Chem. Commun. 1997, 1207-1208.
21. MOE 2002.03; Chemical Computing Group Inc.: Montreal, Canada.
22. 2; Accelrys Ltd.: Cambridge, U. K.
23. Insight II; Accelrys Ltd.: Cambridge, U. K.
24. At each new position, r, w, L, and U are set as 1,9, -0.1, and 0.1, respectively. This upper and lower interval is a "flat-bottomed" restraint in that the force is zero inside the interval and large outside. At each point, Ad was considered as the new r.
25. Simmons, D. L.; Botting, R. M.; Hla, T. Cyclooxygenase Isozymes: The Biology of Prostaglandin Synthesis and Inhibition. Pharmacol. Rev. 2004, 56, 387-437.
26. Rowlinson, S. W.; Kiefer, J. R.; Prusakiewicz, J. J.; Pawlitz, J. L.; Kozak, K. R.; Kalgutkar, A. S.; Stallings, W. C.; Kurumbail, R. G.; Marnett, L. J. A Novel Mechanism of Cyclooxygenase-2 Inhibition Involving Interactions with Ser-530 and Tyr-385. J. Biol. Chem. 2003, 278, 45763-457639.
27. 2 Synthase: Time-Dependent and Time-Independent Inhibitors Elicit Identical Enzyme Conformations. Biochemistry 2001, 40, 5172-5180.
28. Pouplana, R.; Lozano, J. J.; Perez, C.; Ruiz, J. Structure-Based QSAR Study on Differential Inhibition of Human Prostaglandin Endoperoxide H Synthase-2 (COX-2) by Nonsteroidal Antiinflammatory Drugs. J. Comput.-Aided Mol. Des. 2002, 16, 683-701.
29. Jeffrey, G. A. In An Introduction to Hydrogen Bonding; Oxford University Press: New York, 1997.
30. Dunitz, J. D.; Taylor, R. Organic Fluorine Hardly Ever Accepts Hydrogen Bonds. Chem.-Eur. J. 1997, 3, 89-98.
31. Thalladi, V. R.; Weiss, H. C.; Blaser, D.; Boese, R.; Nangia, A.; Desiraju, G. R. C-H⋯F Interactions in the Crystal Structures of Some Fluorobenzenes. J. Am. Chem. Soc. 1998, 120, 8702-8710.
32. Hof, F.; Diederich, F. Medicinal Chemistry in Academia: Molecular Recognition with Biological Receptors. Chem. Commun. 2004, 477-480.
33. Kui, S. C. F.; Zhu, N.; Chan, M. C. W. Observation of Intramolecular C-H⋯F-C Contacts in Nonmetallocene Polyolefin Catalysts: Model for Weak Attractive Interactions between Polymer Chain and Noninnocent Ligand. Angew. Chem., Int. Ed. 2003, 42, 1628-1632.
34. Sarma, J. A. R. P.; Dunitz, J. D. Structures of Three Crystalline Phases of p-(Trimethylammonio)benzenesulfonate and Their Interconversions. Acta Crystallogr., Sect. B 1990, 46, 784-794.
35. Jeffrey, G. A. In Comprehensive Supramolecular Chemistry; MacNicol, D. D., Toda, F., Bishop, R., Ed.; Pergamon: Oxford, U. K., 1996; Vol. 6, pp 757-788.
36. Dunitz, J. D. Win Some, Lose Some: Enthalpy-Entropy Compensation in Weak Intermolecular Interactions. Chem. Biol. 1995, 2, 709-712.
37. Williams, D. H.; Stephens, E.; Zhou, M. How Can Enzymes Be So Efficient? Chem. Commun. 2003, 1973-1976.
38. Drug Database and Clinical Candidate Database; GVK Biosciences Pvt. Ltd.: Hyderabad, India, 2005.
39. Benet, L. Z.; Perotti, B. Y. T. In Burger's Medicinal Chemistry and Drug Discovery; Wolff, M. E., Ed.; Wiley: New York, 1995; Vol. 1, Chapters, pp 121-122.
40. Krötz, F.; Schiele, T. M.; Klauss, V.; Sohn, H.-Y. Selective COX-2 Inhibitors and Risk of Myocardial Infarction. J. Vasc. Res. 2005, 42, 312-324.