Pharmacophore mapping of selective binding affinity of estrogen modulators through classical and space modeling approaches: Exploration of bridged-cyclic compounds with diarylethylene linkage

Journal of Chemical Information and Modeling

Volumn 47, Issue 2, 2007, Pages 475-487

  Mukherjee, Subhendu ^a   Nagar, Shuchi ^a   Mullick, Sanchita ^a   Mukherjee, Arup ^a   Saha, Achintya ^a  

^a UNIVERSITY OF CALCUTTA   (India)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUNDS; BINDING SITES; CATALYSTS; DRUG PRODUCTS; HYDROGEN BONDS; HYDROPHOBICITY; PHARMACOKINETICS; STEREOCHEMISTRY;

ARYL RING SYSTEMS; BINDING AFFINITY; CYCLIC COMPOUNDS; ESTROGEN; PHARMACOPHORE MAPPING;

HORMONES;

CROSS LINKING REAGENT; DRUG; ESTROGEN; ETHYLENE; ETHYLENE DERIVATIVE;

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; CYCLIZATION; METABOLISM; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

COMPUTATIONAL BIOLOGY; CROSS-LINKING REAGENTS; CYCLIZATION; ESTROGENS; ETHYLENES; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PHARMACEUTICAL PREPARATIONS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 34247209071     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci600419s     Document Type: Article

References (48)

1. Yaffe, K.; Sawaya, G.; Lieberburg, I.; Grady, D. Estrogen Therapy in Postmenopausal Women: Effects on Cognitive Function and Dementia. JAMA 1998, 279, 688-695.
2. Writing Group for the Women's Health Initiative Investigators. Risks and Benefits of Estrogen Plus Progestin in Healthy Postmenopausal Women. JAMA 2002, 288, 321-333.
3. Kuiper, G. G.; Enmark, E.; Pelto-Huikko, M.; Nilsson, S.; Gustafsson, J. A. Cloning of a Novel Receptor Expressed in Rat Prostate and Ovary. Proc. Natl. Acad. Sci. 1996, 93, 5925-5930.
4. Levenson, A. S.; Jordan, V. C. Selective Oestrogen Receptor Modulation: Molecular Pharmacology for the Millennium. Eur. J. Cancer 1999, 35, 1628-1639.
5. Kuiper, G. G.; Carlsson, B.; Grandien, K.; Enmark, E.; Haggblad, J.; Nilsson, S.; Gustafsson, J. A. Comparison of the Ligand Binding Specificity and Transcript Tissue Distribution of Estrogen Receptors α and β. Endocrinology 1997, 138, 863-870.
6. Barkhem, T.; Carlsson, B.; Nilsson, Y.; Enmark, E.; Gustafsson, J.; Nilsson. S. Differential Response of Estrogen Receptor a and Estrogen Receptor β to Partial Estrogen Agonists/Antagonists. Mol. Pharmacol. 1998, 54, 105-112.
7. Pike, A. C. W.; Brzozowski, A. M.; Hubbard, R. E.; Bonn, T.; Thorsell, A.; Engstrom, O.; Ljunggren, J.; Gustafsson, J.; Carlquist, M. Structure of the Ligand-binding Domain of Oestrogen Receptor beta in the Presence of a Partial Agonist and a Full Antagonist. EMBO J. 1999, 18, 4608-4618.
8. Renaud, J.; Bischoff, S. F.; Buhl, T.; Floersheim, P.; Fournier, B.; Halleux, C.; Kallen, J.; Keller, H.; Schlaeppi, J. M.; Stark, W. Estrogen Receptor Modulators: Identification and Structure-Activity Relationships of Potent ERα-Selective Tetrahydroisoquinoline Ligands. J. Med. Chem. 2003, 46, 2945-2957.
9. Goldstein, S. R.; Siddhanti, S.; Ciaccia, A. V.; Plouffe, L., Jr. A Pharmacological Review of Selective Oestrogen Receptor Modulators. Hum. Reprod. Update 2000, 6, 212-224.
10. Burger, H. G. Selective Oestrogen Receptor Modulators. Horm. Res. 2000, 53, 25-29.
11. Henke, B. R.; Consler, T. G.; Go, N.; Hale, R. L.; Hohman, D. R.; Jones, S. A.; Lu, A. T.; Moore, L. B.; Moore, J. T.; Orband-Miller, L. A.; Robinett, R. G.; Shearin, J.; Spearing, P. K.; Stewart, E. L.; Turnbull, P. S.; Weaver, S. L.; Williams, S. P.; Wisely, G. B.; Lambert, M. H. A New Series of Estrogen Receptor Modulators that Display Selectivity for Estrogen Receptor β. J. Med. Chem. 2002, 45, 5492-5505.
12. Grese, T. A.; Dodge, J. A. Selective Estrogen Receptor Modulators (SERMs). Curr. Pharm. Des. 1998, 4, 71-92.
13. Lin, X.; Huebner, V. Non-steroidal Ligands for Steroid Hormone Receptors. Curr. Opin. Drug Discovery Dev. 2000, 3, 383-398.
14. McDonnell, D. P. The Molecular Pharmacology of SERMs. Trends Endocrinol. Metab. 1999, 10, 301-311.
15. Jordan, V. C. Antiestrogens and Selective Estrogen Receptor Modulators as Multifunctional Medicines. 2. Clinical Considerations and New Agents. J. Med. Chem. 2003, 46, 1081-1111.
16. Mukherjee, S.; Mukherjee, A.; Saha, A. Predicting Pharmacophore Signals for Post-Coital Antifertility Activity of 1-Trifluoromethyl-1, 2, 2-Triphenylethylene Derivatives: A Statistical Approximation Using E-state Index. Bioorg. Med. Chem. Lett. 2004, 14, 897-900.
17. Mukherjee, S.; Mukherjee, A.; Saha, A. Exploring Pharmacophore Signals for Uterotrophic Activity of Bromotriphenylethylene Derivatives. Internet Electron. J. Mol. Des. 2005, 4, 270-278.
18. Mukherjee, S.; Mukherjee, A.; Saha A. QSAR Studies with E-state Index: Predicting Pharmacophore Signals for Estrogen Receptor Binding Affinity of Triphenylacrylonitriles. Biol. Pharm. Bull. 2005, 28, 154-157.
19. Suzuki, T.; Ide, K.; Ishida, M.; Shapiro, S. Classification of Environmental Estrogens by Phyisicochemical Principal Component Analysis and Hierarchical Cluster Analysis. J. Chem. Inf. Comput. Sci. 2001, 41, 718-726.
20. Famini, G. R.; Wilson, L. Y. Using Theoritical Descriptors in Linear Solvation Energy Relationships. Theor. Comput. Chem. 1994, 1, 213-241.
21. Fink, B. E.; Mortensen, D. S.; Stauffer, S. R.; Aron, Z. D.; Katzenellenbogen, J. A. Novel Structural Templates for Estrogen Receptor Ligands and Prospects for Combinatorial Synthesis of Estrogens. Chem. Biol. 1999, 6, 205-219.
22. da Cunha, E. F. F.; Martins, R. C. A.; Albuquerque, M. G.; de Alencastro, R. B. LIV-3D-QSAR Model for Estrogen Receptor Ligands. J. Mol. Model. 2004, 10, 297-304.
23. Fang, H.; Tong, W.: Shi, L. M.; Blair, R.; Perkins, R.; Branham, W.; Hass, B. S.; Xie, Q.; Dial, S. L.; Moland, C. L.; Sheehan, D. M. Structure-Activity Relationship for a Large Diverse Set of Natural, Synthetic and Environmental Estrogens. Chem. Res. Toxicol. 2001, 14, 280-294.
24. Mukherjee, S.; Saha, A.; Roy, K. QSAR of Estrogen Receptor Modulators Exploring Selectivity Requirements for ER (alpha) versus ER (beta) Binding of Tetrahydroquinoline Derivatives Using E-state and Physicochemical Parameters. Bioorg. Med. Chem. Lett. 2005, 15, 957-961.
25. Schmidt, J. M.; Mercure, J.; Tremblay, G. B.; Page, M.; Feher, M.; Dunn-Dufault, R.; Peter, M. G.; Redden, P. R. De Novo Design, Synthesis and Evaluation of a Non-Steroidal Diphenylnapthyl Propylene Ligand for the Estrogen Receptor. Bioorg. Med. Chem. 2003, 11, 1389-1396.
26. Kristam, R.; Gillet, V. J.; Lewis, R. A.; Thorner, D. Comparison of Conformational Analysis Techniques to Generate Pharmacophore Hypotheses Using Catalyst. J. Chem. Inf. Model. 2005, 45, 461-476.
27. Guner, O. F. In Pharmacophore Perception, Development, and Use in Drug Design; International University Line: California, 2000.
28. Mortensen, D. S.; Rodriguez, A. L.; Carlson, K. E.; Sun, J.; Katzenellenbogen, B. S.; Katzenellenbogen, J. A. Synthesis and Biological Evaluation of a Novel Series of Furans: Ligands Selective for Estrogen Receptor α. J. Med. Chem. 2001, 44, 3838-3848.
29. Henke, B. R.; Consler, T. G.; Go, N.; Hale, R. L.; Hohman, D. R.; Jones, S. A.; Lu, A. T.; Moore, L. B.; Moore, J. T.; Orband-Miller, L. A.; Robinett, R. G.; Shearin, J.; Spearing, P. K.; Stewart, E. L.; Turnbull, P. S.; Weaver, S. L.; Williams, S. P.; Wisely, G. B.; Lambert, M. H. A New Series of Estrogen Receptor Modulators that Display Selectivity for Estrogen Receptor β. J. Med. Chem. 2002, 45, 5492-5505.
30. Zong-Ru, G.; Xiang, Y.; Zhi-Bin, X. Molecular Simulation of Interactions between Estrogen Receptor and Selective Estrogen Receptor Modulators. Acta Pharmacol. Sin. 2002, 23, 208-212.
31. Schuster, D.; Laggner, C.; Steindl, T. M.; Palusczak, A.; Hartmann, R. W.; Langer, T. Pharmacophore Modeling and in Silico Screening for New P450 19 (Aromatase) Inhibitors. J. Chem. Inf. Model. 2006, 46, 1301-1311.
32. Lopez-Rodrýguez, M. L.; Benhamu, B.; de la Fuente, T.; Sanz, A.; Pardo, L.; Campillo, M. A Three-Dimensional Pharmacophore Model for 5-Hydroxytryptamine6 (5-HT6) Receptor Antagonists. J. Med. Chem. 2005, 48, 4216-4219.
33. Taha, M. O.; Qandil, A. M.; Zaki, D. D.; AIDamen, M. A. Ligand-based Assessment of Factor Xa Binding Site Flexibility via Elaborate Pharmacophore Exploration and Genetic Algorithm based QSAR Modeling. Eur. J. Med. Chem. 2005, 40, 701-727.
34. Catalyst, version 4.11; Accelrys Inc.: San Diego, CA, 2005.
35. Barnum, D.; Greene, J.; Smellie, A.; Sprague, P. Identification of Common Functional Configurations Among Molecules. J. Chem. Inf. Comput. Sci. 1996, 36, 563-571.
36. Jones, G.; Willett, P.; Glen, R. C. A Genetic Algorithm for Flexible Molecular Overlay and Pharmacophore Elucidation. J. Comput.-Aided Mol. Des. 1995, 9, 532-549.
37. Martin, Y. C.; Bures, M. G.; Danaher, E. A.; DeLazzer, J.; Lico, I.; Pavlik, P. A. A Fast New Approach to Pharmacophore Mapping and its Application to Dopaminergic and Benzodiazepine Agonists. J. Comput.-Aided Mol. Des. 1993, 7, 83-102.
38. Zhou, H. B.; Comninos, J. S.; Stossi, F.; Katzenellenbogen, B. S.; Katzenellenbogen, J. A. Synthesis and Evaluation of Estrogen Receptor Ligands with Bridged Oxabicyclic Cores Containing a Diarylethylene Motif: Estrogen Antagonists of Unusual Structure. J. Med. Chem. 2005, 48, 7261-7274.
39. Muthyala, R. S.; Sheng, S.; Carlson, K. E.; Katzenellenbogen, B. S.; Katzenellenbogen, J. A. Bridged Bicyclic Cores Containing a 1,1-Diarylethylene Motif are High-Affinity Subtype-Selective Ligands for the Estrogen Receptor. J. Med. Chem. 2003, 46, 589-1602.
40. CS Chem3D Pro and CS MOPAC Pro, version 5.0; Cambridge Soft, Corporation: Cambridge, U.S.A.
41. Kier, L. B.; Hall, L. H. An Electrotopological-state Index for Atoms in Molecules. Pharm. Res. 1990, 7, 801-807.
42. ETSA-CS, Cyber-Mate; Srirampur, Hooghly, W. Bengal, India.
43. TSAR 3D, version 3.3; Oxford Molecular Limited: Accelrys.
44. Statistica, version 5.0; StatSoft Inc.: Tulsa, U.S.A.
45. Wold, S.; Eriksson, L. Chemometric Methods in Molecular Design. In Chemometric Methods; de Waterbeemd, H. V., Ed.; VCH Verlags-gesellschaft mbh: Weinheim, 1995; Vol. 2, Chapter 5, p 312.
46. Barnum, D.; Greene, J.; Smellie, A.; Sprague, P. Identification of Common Functional Configurations Among Molecules. J. Chem. Inf. Comput. Sci. 1996, 36, 563-571.
47. Snedecor, G. W.; Cochran, W. G. In Statistical Methods, 6th ed.; Iowa State University Press: Iowa, 1967.
48. Jordan, V. C.; Mittal, S.; Gosdon, B.; Koch, R.; Lieberman, M. E. Structure-activity Relationships of Estrogens. Environ. Health Perspect. 1985, 67, 97-110.