Structural determination of three different series of compounds as Hsp90 inhibitors using 3D-QSAR modeling, molecular docking and molecular dynamics methods

International Journal of Molecular Sciences

Volumn 12, Issue 2, 2011, Pages 946-970

  Liu, Jianling ^a   Wang, Fangfang ^a   Ma, Zhi ^b   Wang, Xia ^b   Wang, Yonghua ^b  

^a NORTHWEST UNIVERSITY   (China)

^b NORTHWEST A F UNIVERSITY   (China)

Author keywords

3D QSAR; CoMFA; CoMSIA; Hsp90; Molecular docking; Molecular dynamics

Indexed keywords

AT 13387; BENZAMIDE TETRAHYDRO 4H CARBAZOL 4 ONE DERIVATIVE; DIHYDROXYPHENYLAMIDE DERIVATIVE; HEAT SHOCK PROTEIN 90 INHIBITOR; UNCLASSIFIED DRUG; (2,4-DIHYDROXY-5-ISOPROPYLPHENYL)-(5-(4-METHYLPIPERAZIN-1-YLMETHYL)-1,3-DIHYDROISOINDOL-2-YL)METHANONE; BENZAMIDE DERIVATIVE; CARBAZOLE DERIVATIVE; HEAT SHOCK PROTEIN 90; ISOINDOLE DERIVATIVE; PROTEIN BINDING;

ARTICLE; CHEMICAL STRUCTURE; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; DRUG STRUCTURE; HYDROGEN BOND; HYDROPHOBICITY; INTERMETHOD COMPARISON; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PREDICTION; QUANTITATIVE STRUCTURE PROPERTY RELATION; STATIC ELECTRICITY; STRUCTURE ANALYSIS; VALIDITY; AMINO ACID SEQUENCE; ANTAGONISTS AND INHIBITORS; BINDING SITE; CHEMISTRY; MOLECULAR GENETICS; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; BENZAMIDES; BINDING SITES; CARBAZOLES; HSP90 HEAT-SHOCK PROTEINS; ISOINDOLES; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 79952275745     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms12020946     Document Type: Article

References (52)

1. Smith, D.F.; Whitesell, L; Katsanis, E. Molecular chaperones: biology and prospects for pharmacological intervention. Pharmacol. Rev. 1998, 50, 493-513.
2. Smith, D.F. Chaperones in signal transduction. In Molecular Chaperones in the Cell; Lund, P., Ed.; Oxford University Press: Oxford, UK, 2001; pp. 165-178.
3. Jolly, C.; Morimoto, R.I. Role of the heat shock response and molecular chaperones in oncogenesis and cell death. J. Natl. Cancer Inst. 2000, 92, 1564-1572.
4. Solit, D.B.; Chiosis, G. Development and application of Hsp90 inhibitors. Drug Discov. Today 2008, 13, 38-43.
5. Neckers, L. Heat shock protein 90: the cancer chaperone. J. Biosci. 2007, 32, 517-530.
6. Pratt, W.B. The hsp90-based chaperone system: involvement in signal transduction from a variety of hormone and growth factor receptors. Proc. Soc. Exp. Biol. Med. 1998, 217, 420-434.
7. Maloney, A.; Workman, P. Hsp90 as a new therapeutic target for cancer therapy: The story unfolds. Expert Opin. Biol. Ther. 2002, 2, 3-24.
8. Conroy, S.E.; Latchman, D.S. Do heat shock proteins have a role in breast cancer? Br. J. Cancer 1996, 74, 717-721.
9. Ferranini, M.; Helta, S.; Zocchi, M.R.; Rugarli, C. Unusual expressionand localization of heat shock proteins in human tumour cells. Int. J. Cancer 1992, 16, 613-619.
10. Kawanishi, K.; Shiozaki, H.; Doki, Y.; Sakita, I.; Inoue, M.; Yano, M.; Tsujinaka, T.; Shamma, A.; Monden, M. Prognostic significance of heat shock proteins 27 and 70 in patients with squamous cell carcinoma of the esophagus. Cancer 1999, 85, 1649-1657.
11. Jameel, A.; Skilton, R.A.; Campbell, T.A.; Chander, S.K.; Coombes, R.C.; Luqmani, Y.A. Clinical and biological significance of Hsp89a in human breast cancer. Int. J. Cancer 1992, 50, 409-415.
12. Lebeau, J.; Le Cholony, C.; Prosperi, M.T.; Goubin, G. Constitutiveoverexpression of 89 kDa heat shock protein gene in the HBL100 mammary cell line converted to a tumorigenic phenotype by the EJ/T24 Harvey-ras oncogene. Oncogene 1991, 6, 1125-1132.
13. Wataba, K.; Saito, T.; Fukunaka, K.; Nishimura, M.; Kudo, R. Overexpression of heat shock proteins in carcinogenic endometrium. Int. J. Cancer 2001, 91, 448-456.
14. Cornford, P.A.; Dodson, A.R.; Parsons, K.F.; Desmond, A.D.; Woolfenden, A.; Fordham, M.; Neoptolemos, J.P.; Ke, Y.; Foster, C.S. Heat shock protein expression independently predicts clinical outcome in prostate cancer. Cancer Res. 2000, 60, 7099-7105.
15. Biamonte, M.A.; Van de Water, R.; Joseph W.A.; Scannevin, R.H.; Perret, D.; Lee, W.C. Heat shock Protein 90: Inhibitors in clinical trials. J. Med. Chem. 2010, 53, 3-17.
16. Porter, J.R.; Fritz, C.C.; Depew, K.M. Discovery and development of Hsp90 inhibitors: A promising pathway for cancer therapy. Curr. Opin. Chem. Biol. 2010, 14, 1-9.
17. Whitesell, L.; Lindquist, S.L. Hsp90 and the chaperoning of cancer. Nat. Rev. Cancer 2005, 5, 761-772.
18. Wandinger, S.K.; Richter, K.; Buchner, J. The Hsp90 chaperone machinery. J. Biol. Chem. 2008, 283, 18473-18477.
19. BeBoer, C.; Dietz, A. The description and antibiotic production of Streptomyces hygroscopicus var, Geldanus. J. Antibiot. 1976, 29, 1182-1188.
20. Supko, J.G.; Hickman, R.L.; Grever, M.R.; Malspeis, L. Preclinical pharmacologic evaluation of geldanamycin as an antitumor agent. Cancer Chemother. Pharmacol. 1997, 36, 305-315.
21. Kelland, L.R.; Sharp, S.Y.; Rogers, P.M.; Myers, T.G.; Workman, P. DT-Diaphorase expression and tumor cell sensitivity to 17-allylamino, 17-demethoxygeldanamycin, an inhibitor of heat shock protein 90. J. Natl. Cancer Inst. 1999, 91, 1940-1949.
22. Chiosis, G.; Huezo, H.; Rosen, N.; Whitesell, E.; Mimnaugh, L.; Neckers, L. 17AAG: Low target binding affinity and potent cell activity-finding an explanation. Mol. Cancan Ther. 2003, 2, 123-129.
23. Chiosis, G. Discovery and development of purine-scaffold Hsp90 inhibitors. Curr. Top. Med. Chem. 2006, 6, 1183-1191.
24. Chiosis, G.; Timaul, M.N.; Lucas, B.; Munster, P.N.; Zheng, F.F.; Sepp-Lorenzino, L.; Rosen, N. A small molecule designed to bind to the adenine nucleotide pocket of Hsp90 causes Her2 degradation and the growth arrest and differentiation of breast cancer cells. Chem. Biol. 2001, 8, 289-299.
25. Radanyi, C.; Le Bras, G.; Marsaud, V.; Peyrat, J.F.; Messaoudi, S.; Catelli, M.G.; Brion, J.D.; Alami, M.; Renoir, J.M. Antiproliferative and apoptotic activities of tosylcyclonovobiocic acids as potent heat shock protein 90 inhibitors in human cancer cells. Cancer Lett. 2009, 274, 88-94.
26. Dymock, B.; Barril, X.; Beswick, M.; Collier, A.; Davies, N.; Drysdale, M.; Fink, A.; Fromont, C.; Hubbard, E.R.; Massey, A.; Surgenor, A.; Wright, L. Adenine derived inhibitors of the molecular chaperone HSP90-SAR explained through multiple X-ray structures. Bioorg. Med. Chem. Lett. 2004, 14, 325-328.
27. Sanam, R.; Tajne, S.; Gundla, R.; Vadivelan, S.; Machiraju, P.K.; Dayam, R.; Narasu, L.; Jagarlapudi, S.; Neamati, N. Combined pharmacophore and structure-guided studies to identify diverse HSP90 inhibitors. J. Mol. Graph. Model. 2010, 28, 472-477.
28. Jadhav, V.D.; Duerfeldt, A.S.; Blagg, B.S.J. Design, synthesis, and biological activity of bicyclic radester analogues. Bioorg. Med. Chem. Lett. 2009, 19, 6845-6850.
29. Chen, C.Y.; Chen, C.Y.C. Insights into designing the dual-targeted HER2/HSP90 inhibitors. J. Mol. Graph. Model. 2010, 29, 21-31.
30. Liu, H.C.; Lyu, P.C.; Leong, M.K.; Tsai, K.C.; Hsiue, G.H. 3D-QSAR studies on PU3 analogues by comparative molecular field analysis. Bioorg. Med. Chem. Lett. 2004, 14, 731-734.
31. Roy, K.K.; Singh, S.; Saxena, A.K. Integration-mediated prediction enrichment of quantitative model for Hsp90 inhibitors as anti-cancer agents: 3D-QSAR study. Mol. Divers. 2010, doi:10.1007/s11030-010-9269-y.
32. Barta, T.E.; Veal, J.M.; Rice, J.W.; Partridge, J.M.; Fadden, R.P.; Ma, W.; Jenks, M.; Geng, L.F.; Hanson, G.J.; Huang, K.H.; et al. Discovery of benzamide tetrahydro-4H-carbazol-4-ones as novel small molecule inhibitors of Hsp90. Bioorg. Med. Chem. Lett. 2008, 18, 3517-3521.
33. Woodhead, A.J.; Angove, H.; Carr, M.G.; Chessari, G.; Congreve, M.; Coyle, J.E.; Cosme, J.; Graham, B.; Day, P.J.; Downham, R.; et al. Discovery of (2,4-Dihydroxy-5-isopropylphenyl) [5-(4-methylpiperazin-1-ylmethyl)-1,3-dihydroisoindol-2-yl] methanone (AT13387), a novel inhibitor of the molecular chaperone Hsp90 by fragment based drug design. J. Med. Chem. 2010, 53, 5956-5969.
34. Kung, P.P.; Funk, L.; Meng, J.; Collins, M.; Zhou, J.Z.X.; Johnson, M.C.; Ekker, A.; Wang, J.; Mehta, P.; Yin, M.J.; et al. Dihydroxylphenyl amides as inhibitors of the Hsp90 molecular chaperone. Bioorg. Med. Chem. Lett. 2008, 18, 6273-6278.
35. Cramer, R.D., III; Bunce, J.D.; Patterson, D.E. Cross validation, bootstrapping, and partial least squares compared with multiple regression in conventional QSAR studies. Quant. Struct. Act. Relat. 1988, 7, 18-25.
36. Klebe, G.; Abraham, U.; Mietzner, T. Molecular similarity in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J. Med. Chem. 1994, 37, 4130-4146.
37. Martin, Y.C. 3D-QSAR: Current state, scope, and limitations. Perspect. Drug Disc. Des. 1998, 12, 3-23.
38. Matthew, C.; Cramer, R.D., III; Van Opdenbosch, N. Validation of the general purpose tripos 5.2 force field. J. Comput. Chem. 1989, 10, 982-1012.
39. Zaheer-ul, H.; Uddin, R.; Yuan, H.; Petukhov, P.A.; Choudhary, M.I.; Madura, J.D. Receptor-based modeling and 3D-QSAR for a quantitative production of the Butyrylcholinesterase inhibitors based on genetic algorithm. J. Chem. Inf. Model. 2008, 48, 1092-1103.
40. Wold, S.; Ruhe, A.; Wold, H.; Dunn, W.J., III. The collinearity problemin linear regression. The partial least squares (PLS) approach to generalized inverses SIAM. J. Sci. Stat. Comput. 1984, 5, 735-743.
41. Kirkpatrick, P. Virtual screening: Gliding to success. Nat. Rev. Drug Discov. 2004, 3, 299.
42. Homepage of RCSB Protein Data Bank. Available online: http://www.pdb.org (accessed on 27 January 2011)
43. Welch, W.; Ruppert, J.; Jain, A.N. Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites. Chem. Biol. 1996, 3, 449-462.
44. Lindahl, E.; Hess, B.; Van der Spoel, D. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model. 2001, 7, 306-317.
45. Van der Spoel, D.; Van Buuren, A.R.; Tieleman, D.P.; Berendsen, H.J. Molecular dynamics simulations of peptides from BPTI: A closer look at amide-aromatic interactions. J. Biomol. NMR 1996, 8, 229-238.
46. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089-10092.
47. Berendsen, H.J.C.; Grigerra, J.R.; Straatsma, T.P.J. The missing term in effective pair potential. Phys. Chem. 1987, 91, 6269-6271.
48. Hess, B.; Bekker, H.; Berendsen, H.J.C. Fraaije JGEM Lincs: A linear constraint solver for molecular simulations. J. Comput. Chem. 1997, 18, 1463-1472.
49. Wang, G.X.; Li, Y.; Liu, X.L.; Wang. Y.H. Understanding the aquatic toxicity of pesticide: Structure-activity relationship and molecular descriptors to distinguish the ratings of toxicity. QSAR Comb. Sci. 2009, 28, 1418-1431.
50. Bringmann, G.; Rummey, C.J. 3D-QSAR Investigations on antimalarial naphthylisoquinoline alkaloids, by Comparative Molecular Similarity Indices Analysis (CoMSIA), based on different alignment approaches. J. Chem. Inf. Comput. Sci. 2003, 43, 304-316.
51. Bohm, M.; Strzebecher, J.; Klebe, G. 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.
52. Du, J.; Qin, J.; Liu, H.X.; Yao, X.J. 3D-QSAR and molecular docking studies of selective agonists for the thyroidhormone receptor ß. J. Mol. Graph. Model. 2008, 27, 95-104.