3D-QSAR and docking study of the binding mode of steroids to progesterone receptor in active site

QSAR and Combinatorial Science

Volumn 22, Issue 6, 2003, Pages 604-613

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

^a UNIVERSITÉ PARIS DIDEROT   (France)

^b SHANGHAI INSTITUTE OF ORGANIC CHEMISTRY   (China)

Author keywords

3D QSAR; Binding activity; Docking; Progesterone Receptor; Steroids

Indexed keywords

BINDING ENERGY; COMPUTATIONAL CHEMISTRY; DOCKING; LIPIDS; MOLECULAR GRAPHICS;

3D-QSAR; ACTIVE SITE; AUTODOCK; BINDING ACTIVITIES; BINDING MODES; DOCKING; DOCKING STUDIES; PROGESTERONE RECEPTOR; QSAR STUDIES; STEROID;

HYDROGEN BONDS;

ALKYL GROUP; AMINO ACID; ARGININE; GLYCINE; HYDROGEN; PROGESTERONE RECEPTOR; STEROID; THIOL GROUP;

AMINO ACID SEQUENCE; ARTICLE; DRUG RECEPTOR BINDING; DRUG STRUCTURE; HYDROGEN BOND; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; RECEPTOR AFFINITY; STRUCTURE ANALYSIS; VALIDATION PROCESS;

EID: 0041968533     PISSN: 1611020X     EISSN: None     Source Type: Journal    
DOI: 10.1002/qsar.200330820     Document Type: Article

References (49)

1. F. Cadepond, A. Ulmann, E. E. Baulieu, RU486 (mifepristone): mechanisms of action and clinical uses. Ann. Rev. Med., 1997, 48, 129-56.
2. R. Peyron, E. Aubeny, V. Targosz, L. Silvestre, M. Renault, F. Elkik, F. Leclerc, A. Ulmann, E. E. Baulieu, Early termination of pregnancy with mifepristone (RU 486) and the orally active prostaglandin misoprostol. New Engl. J. Med., 1993, 328, 1509-13.
3. E. E. Baulieu, RU 486 (mifepristone). A short overview of its mechanisms of action and clinical uses at the end of 1996. Ann. N.Y. Acad. Sci., 1997, 828, 47-58.
4. M. D. Creinin, Medical Abortion Regimens: Historical Context and Overview. Am. J. Obstet. Gynecol., 2000,183, S3-S9.
5. M. L. Swahn, S. Cekan, G. Wang, V. Lujndstron, M. Bygdeman, Pharmacokinetics and Clinical Studies of RU 486 for Fertility Regulation. In: Baulieu E.E., Siegel S., ed. The Antiprogestin Steroid RU 486 and Human Fertility Control. New York, NY: Plenum; 1985, p 249-258.
6. M. Bydgeman, M. L. Swahn, Progesterone Receptor Blockage. Effect on Uterine Contractility and Early Pregnancy. Contraception, 1985, 32, 45-51.
7. O. Heikinheimo, Clinical pharmacokinetics of mifepristone. Clin. Pharmacokinet., 1997, 33, 7-17.
8. E. M. F. El, Y. Liang, R. W. Wrenn, P. V. Schoenlein, Additive effect of mifepristone and tamoxifen on apoptotic pathways in MCF-7 human breast cancer cells. Breast Cancer Res. Treat, 1998, 51, 149-168.
9. S. S. Koide, Mifepristone. Auxiliary therapeutic use in cancer and related disorders. J. Reprod. Med., 1998, 43, 551-560.
10. E. M. F. El, Y. Liang, R. W. Lewis, Induction of apoptosis by mifepristone and tamoxifen in human LNCaP prostate cancer cells in culture. Prostate, 2000, 43, 31-42.
11. S. S. Koide, Mifepristone. Auxiliary therapeutic use in cancer and related disorders. J. Reprod. Med., 1998, 43, 551-560.
12. J. R. Goldberg, M. G. Plescia, G. D. Anastasio, Mifepristone (RU 486): current knowledge and future prospects. Arch. Fam. Med., 1998, 7, 219-22.
13. P. F. Van Look, H. Von Hertzen, Clinical uses of antiprogestogens. Hum. Reprod. Update, 1995, 1, 19-34.
14. G. Teutsch, M. Klich, F. Bouchowx, E. Cerede, D. Philibert, Synthesis of a fluorescent steroid derivative with high affinities for the glucocorticoid and progesterone receptors. Steroids, 1994, 59, 22.
15. C. E. Cook, M. C. Wani, Y. W Lee, P. A. Fail, V. Petrow, Reversal of activity profile in analogs of the antiprogestin RU 486: effect of a 16 alpha-substituent on progestational (agonist) activity. Life Science, 1993, 52, 155.
16. R. D. Cramer III, J. D. Bunce, The DYLOMMS method: initial results from a comparative study of approaches to 3D QSAR. QSAR Drug Des. Toxicol., 1987, 10, 3-12.
17. U. Norinder, 3D-QSAR investigation of the Tripos benchmark steroids and some protein-tyrosine kinase inhibitors of styrene type using the TDQ approach. J. Chemometrics, 1996, 10, 533-545.
18. U. Norinder U, Single and domain mode variables selection in 3D QSAR applications. J. Chemometrics, 1996, 10, 95-105.
19. U. Norinder, 3-D QSAR analysis of steroid/protein interactions: the use of difference maps. J. Comput.-Aided Mol. Des., 1991, 5, 419-426.
20. U. Norinder, Experimental design based 3-D QSAR analysis of steroid-protein interactions: application to human CBG complexes. J. Comput.-Aided Mol. Des., 1990, 4, 381-389.
21. D. A. Loughney, C. F. Schwender, A comparison of progestin and androgen receptor binding using the CoMFA technique. J. Comput.-Aided Mol. Des.,1992, 6, 569-581.
22. 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.
23. G. M. Morris, D. S. Goodsell, R. Heuey, W. E. Hart, S. Halliday, R. Belew, A. J. Olson, Autodock version 3.03. The scripps research Institute, Molecular Graphics Laboratory, Department of Molecular Biology, 1999.
24. G. M. Morris, D. S. Goodsell, R. S. Halliday, R. Heuey, W. E. Hart, R. K. Belew, A. J. Olson, Automated docking using Lamarckian genetic algorithm and empirical binding free energy functiuon. J. Comput. Chem., 1998, 19, 1639-1662.
25. J. Kua, Y. K. Zhang, J. A. McCammon, Studying Enzyme Binding Specificity in Acetylcholinesterase Using a Combined Molecular Dynamics and Multiple Docking Approach. J. Am. Chem. Soc., 2002, 124, 8260-8267.
26. M. Rarey, B. Kramer, T. Lengauer, Docking of hydrophobic ligands with interaction-based matching algorithms. Bioinformatics, 1991, 15, 243-250.
27. D. Hoffmann, B. Kramer, T. Washio, T. Steinmetzer, M. Rarey, A two-stage method for protein-ligand docking. J. Med. Chem., 1999, 42, 4422-4433.
28. E. E. Baulien, Contragestion and Other Clinical Applications of RU486, an Antiprogesterone at the Receptor. Science, 1989, 245, 1351-1357.
29. R. M. A. Knegtel, M. Wagener, Efficacy and Selectivity in Flexible Database Docking. Proteins: Struct. Funct. Genet., 1999, 37, 334-345.
30. S. Farah, Y. Agazie, N. Ohan, J. K. Ngsee, X. Liu, A. Johne, Rho-associated Protein Kinase ROKa Binds Insulin Receptor Substrate-1 and Modulates Insulin Signaling. J. Biol. Chem., 1998, 273, 4740-4746.
31. R. D. Cramer III, D. E. Patterson, J. D. Bunce, Comparative molecular field analysis (CoMFA).1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc., 1988, 110, 5959-5967.
32. M. Clark, R. D. Cramer III, The Probability of Chance Correlation Using Partial Least Squares (PLS). Quant. Struct.-Act. Relat., 1993, 12, 137-145.
33. G. Klebe, U. Abraham, T. Mietzner, Molecular Similarity Indices in a Comparative Analysis (CoMSIA) of Drug Molecules to Correlate and Predict their Biological Activity. J. Med. Chem., 1994, 37, 4130-4146.
34. 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.
35. M. Clark, R. D. Cramer III, O. N. Van Opdenbosch, The Tripos Force Field. J. Comput. Chem., 1989, 10, 982-1012.
36. SYBYL[Computer Program]. Version 6.8, St. Louis(MO): Tripos Associates Inc 2001.
37. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta Jr., P. Weiner,. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc., 1984, 106, 765-784.
38. 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.
39. 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. Design, 1996, 10, 293-304.
40. 2-guided Region Selection for Comparative Molecular Field Analysis (CoMFA): A Simple Method to Achieve Consistent Results. J. Med. Chem., 1995, 38, 1060-1066.
41. 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, p 292-338.
42. G. R. Desiraju, B. Gopalakrishnan, R. K. R Jetti, A. Nagaraju, D. Raveendra, J. A. R. P. Sarma, M. E. Sobhia, R. Thilagavathi, Computer-Aided Design of Selective COX-2 Inhibitors: Comparative Molecular Field Analysis, Comparative Similarity Indices Analysis, and Docking Studies of Some 1,2-Diarylimidazole Derivatives. J. Med. Chem., 2002, 45, 4847-4857.
43. G. Klebe, U. Abraham, Comparative Molecular Similarity Index Analysis (CoMSIA) to Study Hydrogen Bonding Properties and to Score Combinatorial Libraries. J. Comput.-Aided Mol. Design, 1991, 13, 1-10.
44. R. L. Andrew, Molecular Modelling Principles and Applications, Henry Ling LTd Press. 2001, p 695-702.
45. 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.
46. W. S. Zhou, Z. P. Zhuang, The Progress of Steroid Chemistry, Science Press, Beijing. 2002, p 184-187.
47. P. W. Shawn, B. S. Paul, Atomic Structure of Progesterone Complexed with its Receptor. Nature., 1998, 393, 392-396.
48. G. Teutsch, T. Ojasoo, J. P. Raynaud, 11β-substituted Steroids, an Original Pathway to Antihormones. J. Steroid Biochem., 1988, 31, 549-565.
49. M. Böhm, J. Stürzebecher, G. Klebe, Three-Dimensional Quantitative Structure-Activity Relationship Analyses Using Comparative Molecular Field Analysis and Comparative Molecular Similarity Indices Analysis To Elucidate Selectivity Differences of Inhibitors Binding to Trypsin, Thrombin, and Factor Xa. J. Med. Chem., 1999, 42, 458-477.