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Volumn 15, Issue 1, 2009, Pages 41-51

Receptor independent and receptor dependent CoMSA modeling with IVE-PLS: Application to CBG benchmark steroids and reductase activators

Author keywords

CoMSA; IVE PLS; Molecular surface analysis; Receptor dependent 3D QSAR; Reductase activators; Sulforaphane

Indexed keywords

ENZYME ACTIVATOR; OXIDOREDUCTASE; QUINONE DERIVATIVE; STEROID; SULFORAPHANE; TRANSCORTIN;

EID: 56949094880     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-008-0373-1     Document Type: Article
Times cited : (11)

References (44)
  • 3
    • 0029995624 scopus 로고    scopus 로고
    • VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands
    • doi: 10.1021/ja9539002
    • Head RD, Smythe ML, Oprea TI, Waller CL, Green SM, Marshall GR (1996) VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands. J Am Chem Soc 118:3959-3969. doi: 10.1021/ ja9539002
    • (1996) J Am Chem Soc , vol.118 , pp. 3959-3969
    • Head, R.D.1    Smythe, M.L.2    Oprea, T.I.3    Waller, C.L.4    Green, S.M.5    Marshall, G.R.6
  • 4
    • 0030700312 scopus 로고    scopus 로고
    • Construction of 3D-QSAR Models Using the 4D-QSAR Analysis Formalism
    • doi: 10.1021/ja9718937
    • Hopfinger AJ, Wang S, Tokarski JS, Jin B, Albuquerque M, Madhav PJ et al (1997) Construction of 3D-QSAR Models Using the 4D-QSAR Analysis Formalism. J Am Chem Soc 119:10509-10524. doi: 10.1021/ja9718937
    • (1997) J Am Chem Soc , vol.119 , pp. 10509-10524
    • Hopfinger, A.J.1    Wang, S.2    Tokarski, J.S.3    Jin, B.4    Albuquerque, M.5    Madhav, P.J.6
  • 5
    • 0034676316 scopus 로고    scopus 로고
    • Multiple-conformation and protonation-state representation in 4D-QSAR: The neurokinin-1 receptor system
    • doi: 10.1021/jm000986n
    • Vedani A, Briem H, Dobler M, Dollinger H, McMasters DR (2000) Multiple-conformation and protonation-state representation in 4D-QSAR: the neurokinin-1 receptor system. J Med Chem 43:4416-4427. doi: 10.1021/ jm000986n
    • (2000) J Med Chem , vol.43 , pp. 4416-4427
    • Vedani, A.1    Briem, H.2    Dobler, M.3    Dollinger, H.4    McMasters, D.R.5
  • 6
    • 20144371130 scopus 로고    scopus 로고
    • Combining protein modeling and 6D-QSAR. Simulating the binding of structurally diverse ligands to the estrogen receptor
    • doi: 10.1021/jm050185q
    • Vedani A, Dobler M, Lill MA (2005) Combining protein modeling and 6D-QSAR. Simulating the binding of structurally diverse ligands to the estrogen receptor. J Med Chem 48:3700-3703. doi: 10.1021/jm050185q
    • (2005) J Med Chem , vol.48 , pp. 3700-3703
    • Vedani, A.1    Dobler, M.2    Lill, M.A.3
  • 7
    • 33750346405 scopus 로고    scopus 로고
    • Combining 4D pharmacophore generation and multidimensional QSAR: Modeling ligand binding to the bradykinin B2 receptor
    • doi: 10.1021/ci6001944
    • Lill MA, Vedani A (2006) Combining 4D pharmacophore generation and multidimensional QSAR: Modeling ligand binding to the bradykinin B2 receptor. J Chem Inf Model 46:2135-2145. doi: 10.1021/ci6001944
    • (2006) J Chem Inf Model , vol.46 , pp. 2135-2145
    • Lill, M.A.1    Vedani, A.2
  • 9
    • 38949179532 scopus 로고    scopus 로고
    • Natural and synthetic quinones and their reduction by the quinone reductase enzyme NQO1: From synthetic organic chemistry to compounds with anticancer potential
    • doi: 10.1039/b715270a
    • Colucci MA, Moody CJ, Couch GD (2008) Natural and synthetic quinones and their reduction by the quinone reductase enzyme NQO1: From synthetic organic chemistry to compounds with anticancer potential. Org Biomol Chem 6:637-656. doi: 10.1039/b715270a
    • (2008) Org Biomol Chem , vol.6 , pp. 637-656
    • Colucci, M.A.1    Moody, C.J.2    Couch, G.D.3
  • 10
    • 33750694243 scopus 로고    scopus 로고
    • In silico identification and biochemical characterization of novel inhibitors of NQO1
    • doi: 10.1016/j.bmcl.2006.09.015
    • Nolan KA, Timson DJ, Stratford IJ, Bryce RA (2006) In silico identification and biochemical characterization of novel inhibitors of NQO1. Bioorg Med Chem Lett 16:6246-6254. doi: 10.1016/j.bmcl.2006.09.015
    • (2006) Bioorg Med Chem Lett , vol.16 , pp. 6246-6254
    • Nolan, K.A.1    Timson, D.J.2    Stratford, I.J.3    Bryce, R.A.4
  • 11
    • 0028127980 scopus 로고
    • Design and synthesis of bifunctional isotiocyanate analogs of sulforaphane. Corelation between structure and potency as inducers of anticarcinogenic detoxication enzymes
    • doi: 10.1021/jm00027a021
    • Posner GH, Cheon-Gyu C, Green JV, Zhang Y, Talalay P (1994) Design and synthesis of bifunctional isotiocyanate analogs of sulforaphane. Corelation between structure and potency as inducers of anticarcinogenic detoxication enzymes. J Med Chem 37:170-176. doi: 10.1021/jm00027a021
    • (1994) J Med Chem , vol.37 , pp. 170-176
    • Posner, G.H.1    Cheon-Gyu, C.2    Green, J.V.3    Zhang, Y.4    Talalay, P.5
  • 12
    • 4644318491 scopus 로고    scopus 로고
    • Sulforaphane mediated induction of a phase 2 detoxifying enzyme NAD(P)H quinone reductase and apoptosis in human lymphoblastoid cells
    • Misiewicz I, Skupińska K, Kowalska E, Lubiński J, Kasprzycka-Guttman T (2004) Sulforaphane mediated induction of a phase 2 detoxifying enzyme NAD(P)H quinone reductase and apoptosis in human lymphoblastoid cells. Acta Biochim Pol 51:711-721
    • (2004) Acta Biochim Pol , vol.51 , pp. 711-721
    • Misiewicz, I.1    Skupińska, K.2    Kowalska, E.3    Lubiński, J.4    Kasprzycka-Guttman, T.5
  • 13
    • 34047191454 scopus 로고    scopus 로고
    • Differential response of human healthy lymphoblastoid and CCRF-SB leukemia cells to sulphoraphane and its two analogues: 2-oxohexyl isothiocyanate and alyssin
    • Misiewicz I, Skupińska K, Kasprzycka-Guttman T (2007) Differential response of human healthy lymphoblastoid and CCRF-SB leukemia cells to sulphoraphane and its two analogues: 2-oxohexyl isothiocyanate and alyssin. Pharmacol Rep 59:80-87
    • (2007) Pharmacol Rep , vol.59 , pp. 80-87
    • Misiewicz, I.1    Skupińska, K.2    Kasprzycka-Guttman, T.3
  • 15
    • 34147128555 scopus 로고    scopus 로고
    • In-Silico docking of HIV-1 integrase inhibitors reveals a novel drug type acting on an enzyme/DNA reaction intermediate
    • doi: 10.1186/1742-4690-4-21
    • Savarino A (2007) In-Silico docking of HIV-1 integrase inhibitors reveals a novel drug type acting on an enzyme/DNA reaction intermediate. Retrovirology 4:21. doi: 10.1186/1742-4690-4-21
    • (2007) Retrovirology , vol.4 , pp. 21
    • Savarino, A.1
  • 16
    • 4043144227 scopus 로고    scopus 로고
    • The grid formalism for the comparative molecular surface analysis: Application to the CoMFA benchmark steroids, azo dyes and HEPT derivatives
    • doi: 10.1021/ci049960l
    • Polanski J, Gieleciak R, Magdziarz T (2004) The grid formalism for the comparative molecular surface analysis: Application to the CoMFA benchmark steroids, azo dyes and HEPT derivatives. J Chem Inf Comput Sci 44:1423-1435. doi: 10.1021/ci049960l
    • (2004) J Chem Inf Comput Sci , vol.44 , pp. 1423-1435
    • Polanski, J.1    Gieleciak, R.2    Magdziarz, T.3
  • 17
    • 0542380422 scopus 로고    scopus 로고
    • The CoMFA steroids as a benchmark dataset for development of 3D QSAR methods
    • doi: 10.1023/A:1017050508855
    • Coats E (1998) The CoMFA steroids as a benchmark dataset for development of 3D QSAR methods. Perspect Drug Discov Des 12/13(14):199-213. doi: 10.1023/A:1017050508855
    • (1998) Perspect Drug Discov Des , vol.12-13 , Issue.14 , pp. 199-213
    • Coats, E.1
  • 19
    • 0036522888 scopus 로고    scopus 로고
    • The comparative molecular surface analysis (CoMSA) - A nongrid 3D QSAR method by a coupled neural network and PLS system: Predicting pKa values of benzoic and alkanoic acids
    • doi: 10.1021/ci010031t
    • Polanski J, Gieleciak R, Bak A (2002) The comparative molecular surface analysis (CoMSA) - a nongrid 3D QSAR method by a coupled neural network and PLS system: Predicting pKa values of benzoic and alkanoic acids. J Chem Inf Comput Sci 42:184-191. doi: 10.1021/ci010031t
    • (2002) J Chem Inf Comput Sci , vol.42 , pp. 184-191
    • Polanski, J.1    Gieleciak, R.2    Bak, A.3
  • 20
    • 0037362091 scopus 로고    scopus 로고
    • The comparative molecular surface analysis (CoMSA) with modified uninformative variable elimination-PLS (UVE-PLS) method: Application to the steroids binding the aromatase enzym
    • doi: 10.1021/ci020038q
    • Polanski J, Gieleciak R (2003) The comparative molecular surface analysis (CoMSA) with modified uninformative variable elimination-PLS (UVE-PLS) method: Application to the steroids binding the aromatase enzym. J Chem Inf Comput Sci 43:656-666. doi: 10.1021/ci020038q
    • (2003) J Chem Inf Comput Sci , vol.43 , pp. 656-666
    • Polanski, J.1    Gieleciak, R.2
  • 21
    • 0348209083 scopus 로고    scopus 로고
    • Comparative molecular surface analysis (CoMSA) for modeling dye-fiber affinities of the azo and antraquinone dyes
    • doi: 10.1021/ci0340761
    • Polanski J, Gieleciak R, Wyszomirski M (2003) Comparative molecular surface analysis (CoMSA) for modeling dye-fiber affinities of the azo and antraquinone dyes. J Chem Inf Comput Sci 43:1754-1762. doi: 10.1021/ ci0340761
    • (2003) J Chem Inf Comput Sci , vol.43 , pp. 1754-1762
    • Polanski, J.1    Gieleciak, R.2    Wyszomirski, M.3
  • 22
    • 0347087255 scopus 로고    scopus 로고
    • Comparative molecular surface analysis: A novel tool for drug design and molecular diversity studies
    • doi: 10.1023/B:MODI.0000006536.02970.f0
    • Polanski J, Gieleciak R (2003) Comparative molecular surface analysis: A novel tool for drug design and molecular diversity studies. Mol Divers 7:45-59. doi: 10.1023/B:MODI.0000006536.02970.f0
    • (2003) Mol Divers , vol.7 , pp. 45-59
    • Polanski, J.1    Gieleciak, R.2
  • 23
    • 9444252849 scopus 로고    scopus 로고
    • Probability issues in molecular design: Predictive and modeling ability in 3D-QSAR schemes
    • doi: 10.2174/1386207043328292
    • Polanski J, Gieleciak R, Bak A (2004) Probability issues in molecular design: Predictive and modeling ability in 3D-QSAR schemes. Comb Chem High Throughput Screen 7:793-807. doi: 10.2174/1386207043328292
    • (2004) Comb Chem High Throughput Screen , vol.7 , pp. 793-807
    • Polanski, J.1    Gieleciak, R.2    Bak, A.3
  • 24
    • 0033623964 scopus 로고    scopus 로고
    • The comparative molecular surface analysis (CoMSA): A novel tool for molecular design
    • doi: 10.1016/S0097-8485(00)00064-4
    • Polanski J, Walczak B (2000) The comparative molecular surface analysis (CoMSA): A novel tool for molecular design. Comput Chem 24:615-625. doi: 10.1016/S0097-8485(00)00064-4
    • (2000) Comput Chem , vol.24 , pp. 615-625
    • Polanski, J.1    Walczak, B.2
  • 25
    • 34247208582 scopus 로고    scopus 로고
    • Modeling robust QSAR. 2. Iterative variable elimination schemes for CoMSA: Application for modeling benzoic Acid pKa values
    • doi: 10.1021/ci600295z
    • Gieleciak R, Polanski J (2007) Modeling robust QSAR. 2. Iterative variable elimination schemes for CoMSA: Application for modeling benzoic Acid pKa values. J Chem Inf Model 47:547-556. doi: 10.1021/ci600295z
    • (2007) J Chem Inf Model , vol.47 , pp. 547-556
    • Gieleciak, R.1    Polanski, J.2
  • 26
    • 0028203252 scopus 로고
    • Anticarcinogenic activities of sulforaphane and structurally related synthetic norbonyl isothiocyanates
    • doi: 10.1073/pnas.91.8.3147
    • Zhang Y, Kensler TW, Posner GH, Talalay P (1994) Anticarcinogenic activities of sulforaphane and structurally related synthetic norbonyl isothiocyanates. Proc Natl Acad Sci USA 91:3147-3150. doi: 10.1073/ pnas.91.8.3147
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 3147-3150
    • Zhang, Y.1    Kensler, T.W.2    Posner, G.H.3    Talalay, P.4
  • 27
    • 0034724218 scopus 로고    scopus 로고
    • Structures of recombinant human and mouse NAD(P)H: Quinone oxidoreductases: Species comparison and structural changes with substrate binding and release
    • doi: 10.1073/pnas.050585797
    • Faig M, Bianchet MA, Talalay P, Chen S, Winski S, Ross D et al (2000) Structures of recombinant human and mouse NAD(P)H:qUinone oxidoreductases: Species comparison and structural changes with substrate binding and release. Proc Natl Acad Sci USA 97:3177-3182. doi: 10.1073/pnas.050585797
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 3177-3182
    • Faig, M.1    Bianchet, M.A.2    Talalay, P.3    Chen, S.4    Winski, S.5    Ross, D.6
  • 29
    • 41549129876 scopus 로고    scopus 로고
    • Toward robust QSPR models: Synergistic utilization of robust regression and variable elimination
    • doi: 10.1002/jcc.20831
    • Grohmann R, Schindler T (2008) Toward robust QSPR models: Synergistic utilization of robust regression and variable elimination. J Comput Chem 29:847-860. doi: 10.1002/jcc.20831
    • (2008) J Comput Chem , vol.29 , pp. 847-860
    • Grohmann, R.1    Schindler, T.2
  • 32
    • 56949083688 scopus 로고    scopus 로고
    • CORINA Generation of 3D coordinates Accessed 17 Jun
    • CORINA Generation of 3D coordinates http://www.mol-net.com/software/ corina/ Accessed 17 Jun 2008
    • (2008)
  • 33
    • 0000381930 scopus 로고    scopus 로고
    • Prediction of hydrophobic (Lipophilic) properties of small organic molecules using fragmental methods: An analysis of ALOGP and CLOGP methods
    • doi: 10.1021/jp980230o
    • Ghose A, Viswanadhan V, Wendoloski J (1998) Prediction of hydrophobic (Lipophilic) properties of small organic molecules using fragmental methods: An analysis of ALOGP and CLOGP methods. J Phys Chem A 102:3762A-3772A. doi: 10.1021/jp980230o
    • (1998) J Phys Chem A , vol.102
    • Ghose, A.1    Viswanadhan, V.2    Wendoloski, J.3
  • 34
    • 0022649317 scopus 로고
    • A new approach to structureactivity relations: The "Molecular Lipophilicity Potential"
    • Audry E, Dubost JP, Colleter JC, Dallet P (1986) A new approach to structureactivity relations: The "Molecular Lipophilicity Potential". J Med Chem 21:71-72
    • (1986) J Med Chem , vol.21 , pp. 71-72
    • Audry, E.1    Dubost, J.P.2    Colleter, J.C.3    Dallet, P.4
  • 35
    • 0346841737 scopus 로고    scopus 로고
    • Copyright (C) 2000-2005 by Esa Alhoniemi, Johan Himberg, Juha Parhankangas and Juha Vesanto Accessed 17 Jan 2008
    • Alhoniemi E, Himberg J, Parhankangas J, Vesanto J (2005) SOM Toolbox, Copyright (C) 2000-2005 by Esa Alhoniemi, Johan Himberg, Juha Parhankangas and Juha Vesanto http://www.cis.hut.fi/projects/somtoolbox/ Accessed 17 Jan 2008
    • (2005) SOM Toolbox
    • Alhoniemi, E.1    Himberg, J.2    Parhankangas, J.3    Vesanto, J.4
  • 36
    • 31044431624 scopus 로고    scopus 로고
    • 3D QSAR study of hypolipidemic asarones by comparative molecular surface analysis
    • doi: 10.1016/j.bmc.2005.10.014
    • Magdziarz T, Lozowicka B, Gieleciak R, Bak A, Polanski J, Chilmonczyk Z (2006) 3D QSAR study of hypolipidemic asarones by comparative molecular surface analysis. Bioorg Med Chem 14:1630-1643. doi: 10.1016/ j.bmc.2005.10.014
    • (2006) Bioorg Med Chem , vol.14 , pp. 1630-1643
    • Magdziarz, T.1    Lozowicka, B.2    Gieleciak, R.3    Bak, A.4    Polanski, J.5    Chilmonczyk, Z.6
  • 37
    • 26944432634 scopus 로고    scopus 로고
    • Modeling robust QSAR. 1. Coding molecules in 3D-QSAR - From a point to surface sectors and molecular volumes
    • doi: 10.1021/ci0501488
    • Gieleciak R, Magdziarz T, Bak A, Polanski J (2005) Modeling robust QSAR. 1. Coding molecules in 3D-QSAR - from a point to surface sectors and molecular volumes. J Chem Inf Model 45:1447-1455. doi: 10.1021/ci0501488
    • (2005) J Chem Inf Model , vol.45 , pp. 1447-1455
    • Gieleciak, R.1    Magdziarz, T.2    Bak, A.3    Polanski, J.4
  • 38
    • 0019833012 scopus 로고
    • Steroid-protein interactions. Human corticosteroid binding globulin: Some physicochemical properties and binding specificity
    • doi: 10.1021/bi00524a047
    • Mickelson KE, Forsthoefel J, Westphal U (1981) Steroid-protein interactions. Human corticosteroid binding globulin: Some physicochemical properties and binding specificity. Biochemistry 20:6211-6218. doi: 10.1021/bi00524a047
    • (1981) Biochemistry , vol.20 , pp. 6211-6218
    • Mickelson, K.E.1    Forsthoefel, J.2    Westphal, U.3
  • 40
    • 0021733924 scopus 로고
    • Multivariate structure-activity relationships between data from a battery of biological tests and an ensemble of structure descriptors: The PLS method
    • doi: 10.1002/qsar.19840030402
    • Dunn WJ III, Wold S, Edlund U, Hellberg S, Gasteiger J (1984) Multivariate structure-activity relationships between data from a battery of biological tests and an ensemble of structure descriptors: the PLS method. Quant Struct Act Relat 3:131-137. doi: 10.1002/ qsar.19840030402
    • (1984) Quant Struct Act Relat , vol.3 , pp. 131-137
    • Dunn III, W.J.1    Wold, S.2    Edlund, U.3    Hellberg, S.4    Gasteiger, J.5
  • 41
    • 0028851251 scopus 로고
    • Autocorrelation of molecular surface properties for modeling corticosteroid binding globulin and cytosolic ah receptor activity by neural networks
    • doi: 10.1021/ja00134a023
    • Wagener M, Sadowski J, Gasteiger J (1995) Autocorrelation of molecular surface properties for modeling corticosteroid binding globulin and cytosolic ah receptor activity by neural networks. J Am Chem Soc 117:7769-7775. doi: 10.1021/ja00134a023
    • (1995) J Am Chem Soc , vol.117 , pp. 7769-7775
    • Wagener, M.1    Sadowski, J.2    Gasteiger, J.3
  • 43
    • 0033602217 scopus 로고    scopus 로고
    • Self-organizing molecular field analysis: A tool for structure-activity studies
    • doi: 10.1021/jm9810607
    • Robinson DD, Winn PJ, Lyne PD, Richards WG (1999) Self-organizing molecular field analysis: A tool for structure-activity studies. J Med Chem 42:573-583. doi: 10.1021/jm9810607
    • (1999) J Med Chem , vol.42 , pp. 573-583
    • Robinson, D.D.1    Winn, P.J.2    Lyne, P.D.3    Richards, W.G.4
  • 44
    • 37349097759 scopus 로고    scopus 로고
    • y-Randomization and its variants in QSPR/QSAR
    • doi: 10.1021/ci700157b
    • Rucker C, Rucker G, Meringer M (2007) y-Randomization and its variants in QSPR/QSAR. J Chem Inf Model 47:2345-2357. doi: 10.1021/ci700157b
    • (2007) J Chem Inf Model , vol.47 , pp. 2345-2357
    • Rucker, C.1    Rucker, G.2    Meringer, M.3


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