Integration-mediated prediction enrichment of Quantitative model for Hsp90 inhibitors as anti-cancer agents: 3D-QSAR study

Molecular Diversity

Volumn 15, Issue 2, 2011, Pages 477-489

  Roy, Kuldeep K ^a   Singh, Supriya ^a   Saxena, Anil K ^a  

^a CENTRAL DRUG RESEARCH INSTITUTE   (India)

Author keywords

Cancer; Catalyst; Hsp90; Integration; Pharmacophore; QSAR

Indexed keywords

ANTINEOPLASTIC AGENT; CHAPERONE; HEAT SHOCK PROTEIN 90; HEAT SHOCK PROTEIN 90 INHIBITOR; LIGAND;

ALGORITHM; ARTICLE; BINDING AFFINITY; CATALYSIS; DRUG DESIGN; HYDROGEN BOND; MOLECULAR DOCKING; PHARMACOPHORE; PREDICTION; PRIORITY JOURNAL; QUALITY CONTROL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; CHEMICAL STRUCTURE; CHEMISTRY; DRUG ANTAGONISM; ENZYME ACTIVE SITE; METABOLISM; MOLECULAR DYNAMICS; PHYSIOLOGY; PROTEIN BINDING; REPRODUCIBILITY;

ALGORITHMS; ANTINEOPLASTIC AGENTS; CATALYSIS; CATALYTIC DOMAIN; DRUG DESIGN; HSP90 HEAT-SHOCK PROTEINS; LIGANDS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REPRODUCIBILITY OF RESULTS;

EID: 80051556999     PISSN: 13811991     EISSN: 1573501X     Source Type: Journal    
DOI: 10.1007/s11030-010-9269-y     Document Type: Article

References (36)

1. Pearl LH (2005) Hsp90 and Cdc37-a chaperone cancer conspiracy. Curr Opin Genet DeV 15:55-61. doi:10.1016/j.gde.2004.12. 011 (Pubitemid 40127632)
2. Powers MV, Workman P (2007) Inhibitors of the heat shock response: biology and pharmacology. FEBS Lett 581:3758-3769. doi:10.1016/j.febslet.2007. 05.040 (Pubitemid 47081010)
3. Soldano K L, Jivan A, Nicchitta CV, Gewirth DT (2003) Structure of the N-terminal domain of GRP94: basis for ligand specificity and regulation. J Biol Chem 278:48330-48338. doi:10.1074/jbc. M308661200 (Pubitemid 37523288)
4. Miriam S, Giulio R. (2009) Structure-based and in-silico design of Hsp90 inhibitors. ChemMedChem 4:1399-1409. doi:10.1002/cmdc.200900256
5. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Delivery Rev 23:3-25. doi:10.1016/S0169-409X (96) 00423-1 (Pubitemid 27046991)
6. Xue L, Stahura FL, Bajorath J (2004) Similarity search profiling reveals effects of fingerprint scaling in virtual screening. J Chem Inf Comput Sci 44:2032-2039. doi:10.1021/ci0400819
7. Srinivasan J, Castellino A, Bradley EK, Eksterowicz JE, Grootenhuis PDJ, Putta S, Stanton RV (2002) Evaluation of a novel shape-based computational filter for lead evolution application to thrombin inhibitors. J Med Chem 45:2494-2500. doi:10.1021/jm010494q (Pubitemid 34595218)
8. Prathipati P, Pandey G, Saxena AK (2005) CoMFA and docking studies on glycogen phosphorylase a inhibitors as antidiabetic Agents. J Chem Inf Model 45:136-145. doi:10.1021/ci049762u (Pubitemid 40736966)
9. Sun H (2008) Pharmacophore-based virtual screening. Curr Med Chem 15:1018-1024. doi:10.2174/092986708784049630 (Pubitemid 351736404)
10. Leach AR, Shoichet BK, Peishoff CE (2006) Prediction of protein-ligand interactions. docking and scoring: successes and gaps. J Med Chem 49:5851-5855. doi:10.1021/jm060999m (Pubitemid 44484931)
11. Nicolotti O, Miscioscia TF, Carotti A, Leonetti F, Carotti A (2008) An integrated approach to ligand-and structure-based drug design: development and application to a series of serine protease inhibitors. J Chem Inf Model 48:1211-1226. doi:10.1021/ci800015s
12. Knox AJS, Price T, Pawlak M, Golfis G, Flood CT, Fayne D, Williams DC, Meegan MJ, Lloyd DJ (2009) Integration of ligand and structure-based virtual screening for the identification of the first dual targeting agent for heat shock protein 90 (Hsp90) and tubulin. J Med Chem 52:2177-2180. doi:10.1021/jm801569z
13. Sugunadevi S, Sundarapandian T, Shalini J, Yong JK, Keun WL (2010) 3D QSAR pharmacophore based virtual screening and molecular docking for identification of potential HSP90 inhibitors. Eu J Med Chem 45:2132-2140. doi:10.1016/j.ejmech.2010.01.016
14. Accelrys Inc (2002) Catalyst, version 4.7. Accelrys, Inc., San Diego, CA
15. Venkatachalam CM, Jiang X, Oldfield T, Waldman M (2003) LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J Mol Graph Model 21:289-307. doi:10.1016/S1093-3263 (02) 00164-X (Pubitemid 35441326)
16. Accelrys Software Inc (2001) Discovery studio software, version 2.0. Accelrys Software Inc., San Diego, CA (2001)
17. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748. doi:10.1006/jmbi.1996.0897 (Pubitemid 27170693)
18. Schrödinger LLC (2008) Glide, version 5.0. Schrödinger, LLC, New York, NY
19. Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem 49:6177-6196. doi:10.1021/jm051256o (Pubitemid 44595196)
20. Schrödinger LLC (2005) Schrödinger software, version 8.0. Schrödinger LLC, New York, NY
21. Todeschini R, Consonni V (2001) Dragon software (version 1.11). Milano Chemometrics and QSAR Research group, Talete, Milano, Italy
22. Llauger L, He H, Kim J, Aguirre J, Rosen N, Peters U, Davies P, Chiosis G (2005) Evaluation of 8-arylsulfanyl, 8-arylsulfoxyl, and 8-arylsulfonyl adenine derivatives as inhibitors of the heat shock protein 90. J Med Chem 48:2892-2905. doi:10.1021/jm049012b (Pubitemid 40548103)
23. Li H, Sutter J, Hoffman R (1999) HypoGen: an automated system for generating 3D predictive pharmacophore models. In: Guner OF (ed) Pharmacophore perception, development, and use in drug design. International University Line, La Jolla, CA
24. Kurogi Y, Güner OF (2001) Pharmacophore modeling and threedimensional database searching for drug design using catalyst. Curr Med Chem 8:1035-1055. doi:10.2174/0929867013372481 (Pubitemid 32633658)
25. Sprague PW (1995) Automated chemical hypothesis generation and database searching with Catalyst. In: Müller K (ed) Perspectives in drug discovery and design. ESCOM Science Publishers BV, Leiden, Netherlands
26. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CharmM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217. doi:10.1002/jcc.540040211
27. Sutter J, Güner OF, Hoffman R, Li H, Waldman M (1999) Effect of variable weight and tolerances on predictive model generation. In: Güner OF (ed) Pharmacophore perception, development, and use in drug design. International University Line, La Jolla, CA
28. Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP (1997) Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des 11:425-445. doi:10.1023/A:1007996124545 (Pubitemid 127505895)
29. Krammer A, Kirchhoff PD, Jiang X, Venkatachalam CM, Waldman M (2005) LigScore: a novel scoring function for predicting binding affinities. J Mol Graph Model 23:395-407. doi:10.1016/j. jmgm.2004.11.007 (Pubitemid 40386869)
30. Böhm HJ (1998) Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J Comput Aided Mol Des 12:309-323. doi:10.1023/A:1007999920146
31. Muegge I, Martin YC (1999) A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem 42:791-804. doi:10.1021/jm980536j (Pubitemid 29136170)
32. Muegge I (2006) PMF scoring revisited. J Med Chem 49:5895-5902. doi:10.1021/jm050038s (Pubitemid 44484936)
33. Cheng T, Li X, Li Y, Liu Z, Wang R (2009) Comparative assessment of scoring functions on a diverse test set. J Chem Inf Model 49:1079-1093. doi:10.1021/ci9000053
34. Jain AN (1996) Scoring non-covalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. J Comput Aided Mol Des 10:427-440. doi:10.1007/BF00124474 (Pubitemid 126712439)
35. Wright L, Barril X, Dymock B, Sheridan L, Surgenor A, Beswick M, Drysdale M, Collier A, Massey A, Davies N, Fink A, Fromont C, Aherne W, Boxall K, Sharp S, Workman P, Hubbard RE (2004) Structure-activity relationships in purine-based inhibitor binding to Hsp90 isoforms. Chem Biol 11:775-785. doi:10. 1016/j.chembiol.2004.03.033 (Pubitemid 38836894)
36. Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK (2007) BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucl Acids Res 35:D198-D201. doi:10. 1093/nar/gkl999 (Pubitemid 46056198)