메뉴 건너뛰기




Volumn 46, Issue 9, 2011, Pages 3953-3963

Potentially increasing the metabolic stability of drug candidates via computational site of metabolism prediction by CYP2C9: The utility of incorporating protein flexibility via an ensemble of structures

Author keywords

Computational chemistry; CYP2C9; Docking; Metabolism; Protein flexibility

Indexed keywords

CYTOCHROME P450 2C9;

EID: 80052949153     PISSN: 02235234     EISSN: 17683254     Source Type: Journal    
DOI: 10.1016/j.ejmech.2011.05.067     Document Type: Article
Times cited : (26)

References (55)
  • 2
    • 27644596457 scopus 로고    scopus 로고
    • Predicting in vivo drug interactions from in vitro drug discovery data
    • L.C. Wienkers, and T.G. Heath Predicting in vivo drug interactions from in vitro drug discovery data Nat. Rev. Drug Discov. 4 2005 825 833
    • (2005) Nat. Rev. Drug Discov. , vol.4 , pp. 825-833
    • Wienkers, L.C.1    Heath, T.G.2
  • 4
    • 17444411955 scopus 로고    scopus 로고
    • Cytochrome p450 in silico: An integrative modeling approach
    • G.C. de, N.P. Vermeulen, and K.A. Feenstra Cytochrome p450 in silico: an integrative modeling approach J. Med. Chem. 48 2005 2725 2755
    • (2005) J. Med. Chem. , vol.48 , pp. 2725-2755
    • De, G.C.1    Vermeulen, N.P.2    Feenstra, K.A.3
  • 5
    • 65549171233 scopus 로고    scopus 로고
    • CypScore: Quantitative prediction of reactivity toward cytochromes P450 based on semiempirical molecular orbital theory
    • M. Hennemann, A. Friedl, M. Lobell, J. Keldenich, A. Hillisch, T. Clark, and A.H. Goller CypScore: quantitative prediction of reactivity toward cytochromes P450 based on semiempirical molecular orbital theory ChemMedChem 4 2009 657 669
    • (2009) ChemMedChem , vol.4 , pp. 657-669
    • Hennemann, M.1    Friedl, A.2    Lobell, M.3    Keldenich, J.4    Hillisch, A.5    Clark, T.6    Goller, A.H.7
  • 6
    • 57349106476 scopus 로고    scopus 로고
    • Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: A combined approach of molecular dynamics and ligand docking
    • J. Hritz, R.A. de, and C. Oostenbrink Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking J. Med. Chem. 51 2008 7469 7477
    • (2008) J. Med. Chem. , vol.51 , pp. 7469-7477
    • Hritz, J.1    De, R.A.2    Oostenbrink, C.3
  • 8
    • 68149168645 scopus 로고    scopus 로고
    • EaMEAD: Activation energy prediction of cytochrome P450 mediated metabolism with effective atomic descriptors
    • D.N. Kim, K.H. Cho, W.S. Oh, C.J. Lee, S.K. Lee, J. Jung, and K.T. No EaMEAD: activation energy prediction of cytochrome P450 mediated metabolism with effective atomic descriptors J. Chem. Inf. Model. 49 2009 1643 1654
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1643-1654
    • Kim, D.N.1    Cho, K.H.2    Oh, W.S.3    Lee, C.J.4    Lee, S.K.5    Jung, J.6    No, K.T.7
  • 9
    • 0025150366 scopus 로고
    • Theoretical-studies on cytochrome-P-450 mediated hydroxylation - A predictive model for hydrogen-atom abstractions
    • K.R. Korzekwa, J.P. Jones, and J.R. Gillette Theoretical-studies on cytochrome-P-450 mediated hydroxylation - A predictive model for hydrogen-atom abstractions J. Am. Chem. Soc. 112 1990 7042 7046
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 7042-7046
    • Korzekwa, K.R.1    Jones, J.P.2    Gillette, J.R.3
  • 10
    • 33750486521 scopus 로고    scopus 로고
    • Prediction of activation energies for hydrogen abstraction by cytochrome p450
    • L. Olsen, P. Rydberg, T.H. Rod, and U. Ryde Prediction of activation energies for hydrogen abstraction by cytochrome p450 J. Med. Chem. 49 2006 6489 6499
    • (2006) J. Med. Chem. , vol.49 , pp. 6489-6499
    • Olsen, L.1    Rydberg, P.2    Rod, T.H.3    Ryde, U.4
  • 11
  • 12
    • 0037431382 scopus 로고    scopus 로고
    • A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules
    • S.B. Singh, L.Q. Shen, M.J. Walker, and R.P. Sheridan A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules J. Med. Chem. 46 2003 1330 1336
    • (2003) J. Med. Chem. , vol.46 , pp. 1330-1336
    • Singh, S.B.1    Shen, L.Q.2    Walker, M.J.3    Sheridan, R.P.4
  • 13
    • 0141611170 scopus 로고    scopus 로고
    • Prediction of drug metabolism: The case of cytochrome P450 2D6
    • N.P.E. Vermeulen Prediction of drug metabolism: the case of cytochrome P450 2D6 Curr. Top. Med. Chem. 3 2003 1227 1239
    • (2003) Curr. Top. Med. Chem. , vol.3 , pp. 1227-1239
    • Vermeulen, N.P.E.1
  • 14
    • 0038440502 scopus 로고    scopus 로고
    • Predicting drug metabolism: A site of metabolism prediction tool applied to the cytochrome P4502C9
    • I. Zamora, L. Afzelius, and G. Cruciani Predicting drug metabolism: a site of metabolism prediction tool applied to the cytochrome P4502C9 J. Med. Chem. 46 2003 2313 2324
    • (2003) J. Med. Chem. , vol.46 , pp. 2313-2324
    • Zamora, I.1    Afzelius, L.2    Cruciani, G.3
  • 15
    • 77953322016 scopus 로고    scopus 로고
    • Site of metabolism prediction on cytochrome P450 2C9: A knowledge-based docking approach
    • A. Tarcsay, R. Kiss, and G.M. Keseru Site of metabolism prediction on cytochrome P450 2C9: a knowledge-based docking approach J. Comput. Aid. Mol. Des. 24 2010 399 408
    • (2010) J. Comput. Aid. Mol. Des. , vol.24 , pp. 399-408
    • Tarcsay, A.1    Kiss, R.2    Keseru, G.M.3
  • 16
    • 39749093726 scopus 로고    scopus 로고
    • Prediction of metabolism by cytochrome P450 2C9: Alignment and docking studies of a validated database of substrates
    • M.J. Sykes, R.A. McKinnon, and J.O. Miners Prediction of metabolism by cytochrome P450 2C9: alignment and docking studies of a validated database of substrates J. Med. Chem. 51 2008 780 791
    • (2008) J. Med. Chem. , vol.51 , pp. 780-791
    • Sykes, M.J.1    McKinnon, R.A.2    Miners, J.O.3
  • 18
    • 53249095707 scopus 로고    scopus 로고
    • Considerations and recent advances in QSAR models for cytochrome P450-mediated drug metabolism prediction
    • H. Li, J. Sun, X. Fan, X. Sui, L. Zhang, Y. Wang, and Z. He Considerations and recent advances in QSAR models for cytochrome P450-mediated drug metabolism prediction J. Comput. Aid. Mol. Des. 22 2008 843 855
    • (2008) J. Comput. Aid. Mol. Des. , vol.22 , pp. 843-855
    • Li, H.1    Sun, J.2    Fan, X.3    Sui, X.4    Zhang, L.5    Wang, Y.6    He, Z.7
  • 20
    • 33745741280 scopus 로고    scopus 로고
    • Computational approaches for predicting CYP-related metabolism properties in the screening of new drugs
    • P. Crivori, and I. Poggesi Computational approaches for predicting CYP-related metabolism properties in the screening of new drugs Eur. J. Med. Chem. 41 2006 795 808
    • (2006) Eur. J. Med. Chem. , vol.41 , pp. 795-808
    • Crivori, P.1    Poggesi, I.2
  • 21
    • 45949107967 scopus 로고    scopus 로고
    • Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450
    • E. Stjernschantz, N.P. Vermeulen, and C. Oostenbrink Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450 Expert Opin. Drug Metab. Toxicol. 4 2008 513 527
    • (2008) Expert Opin. Drug Metab. Toxicol. , vol.4 , pp. 513-527
    • Stjernschantz, E.1    Vermeulen, N.P.2    Oostenbrink, C.3
  • 22
    • 84888464415 scopus 로고    scopus 로고
    • Computational models for cytochrome P450: A predictive electronic model for aromatic oxidation and hydrogen atom abstraction
    • J.P. Jones, M. Mysinger, and K.R. Korzekwa Computational models for cytochrome P450: a predictive electronic model for aromatic oxidation and hydrogen atom abstraction FASEB J. 17 2003 A608
    • (2003) FASEB J. , vol.17 , pp. 608
    • Jones, J.P.1    Mysinger, M.2    Korzekwa, K.R.3
  • 23
    • 58149166592 scopus 로고    scopus 로고
    • Prediction of activation energies for aromatic oxidation by cytochrome P450
    • P. Rydberg, U. Ryde, and L. Olsen Prediction of activation energies for aromatic oxidation by cytochrome P450 J. Phys. Chem. A 112 2008 13058 13065
    • (2008) J. Phys. Chem. A , vol.112 , pp. 13058-13065
    • Rydberg, P.1    Ryde, U.2    Olsen, L.3
  • 24
    • 58149157800 scopus 로고    scopus 로고
    • Sulfoxide, sulfur, and nitrogen oxidation and dealkylation by cytochrome P450
    • P. Rydberg, U. Ryde, and L. Olsen Sulfoxide, sulfur, and nitrogen oxidation and dealkylation by cytochrome P450 J. Chem. Theory Comput. 4 2008 1369 1377
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 1369-1377
    • Rydberg, P.1    Ryde, U.2    Olsen, L.3
  • 25
    • 42149138057 scopus 로고    scopus 로고
    • New combined model for the prediction of regioselectivity in cytochrome P450/3A4 mediated metabolism
    • W.S. Oh, D.N. Kim, J. Jung, K.H. Cho, and K.T. No New combined model for the prediction of regioselectivity in cytochrome P450/3A4 mediated metabolism J. Chem. Inf. Model. 48 2008 591 601
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 591-601
    • Oh, W.S.1    Kim, D.N.2    Jung, J.3    Cho, K.H.4    No, K.T.5
  • 26
    • 70350362083 scopus 로고    scopus 로고
    • Improvement of site of metabolism predictions for CYP3A4 by using discriminant analysis of compound preference of CYP3A4 X-Ray structural conformers and subsequent docking
    • P. Prusis, and L. Afzelius Improvement of site of metabolism predictions for CYP3A4 by using discriminant analysis of compound preference of CYP3A4 X-Ray structural conformers and subsequent docking QSAR Comb. Sci. 28 2009 865 868
    • (2009) QSAR Comb. Sci. , vol.28 , pp. 865-868
    • Prusis, P.1    Afzelius, L.2
  • 27
    • 65549103878 scopus 로고    scopus 로고
    • Site of metabolism prediction for six biotransformations mediated by cytochromes P450
    • M.Y. Zheng, X.M. Luo, Q.C. Shen, Y. Wang, Y. Du, W.L. Zhu, and H.L. Jiang Site of metabolism prediction for six biotransformations mediated by cytochromes P450 Bioinformatics 25 2009 1251 1258
    • (2009) Bioinformatics , vol.25 , pp. 1251-1258
    • Zheng, M.Y.1    Luo, X.M.2    Shen, Q.C.3    Wang, Y.4    Du, Y.5    Zhu, W.L.6    Jiang, H.L.7
  • 28
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • G. Jones, P. Willett, R.C. Glen, A.R. Leach, and R. Taylor Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 267 1997 727 748
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 30
    • 0031013972 scopus 로고    scopus 로고
    • The structure of the cytochrome p450BM-3 haem domain complexed with the fatty acid substrate, palmitoleic acid
    • H. Li, and T.L. Poulos The structure of the cytochrome p450BM-3 haem domain complexed with the fatty acid substrate, palmitoleic acid Nat. Struct. Biol. 4 1997 140 146
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 140-146
    • Li, H.1    Poulos, T.L.2
  • 31
    • 0037145075 scopus 로고    scopus 로고
    • Thermophilic cytochrome P450 (CYP119) from Sulfolobus solfataricus: High resolution structure and functional properties
    • S.Y. Park, K. Yamane, S. Adachi, Y. Shiro, K.E. Weiss, S.A. Maves, and S.G. Sligar Thermophilic cytochrome P450 (CYP119) from Sulfolobus solfataricus: high resolution structure and functional properties J. Inorg. Biochem. 91 2002 491 501
    • (2002) J. Inorg. Biochem. , vol.91 , pp. 491-501
    • Park, S.Y.1    Yamane, K.2    Adachi, S.3    Shiro, Y.4    Weiss, K.E.5    Maves, S.A.6    Sligar, S.G.7
  • 32
    • 0034613190 scopus 로고    scopus 로고
    • Crystal structure of a thermophilic cytochrome P450 from the archaeon Sulfolobus solfataricus
    • J.K. Yano, L.S. Koo, D.J. Schuller, H. Li, P.R. Ortiz de Montellano, and T.L. Poulos Crystal structure of a thermophilic cytochrome P450 from the archaeon Sulfolobus solfataricus J. Biol. Chem. 275 2000 31086 31092
    • (2000) J. Biol. Chem. , vol.275 , pp. 31086-31092
    • Yano, J.K.1    Koo, L.S.2    Schuller, D.J.3    Li, H.4    Ortiz De Montellano, P.R.5    Poulos, T.L.6
  • 33
    • 4644301430 scopus 로고    scopus 로고
    • The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-A resolution
    • J.K. Yano, M.R. Wester, G.A. Schoch, K.J. Griffin, C.D. Stout, and E.F. Johnson The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-A resolution J. Biol. Chem. 279 2004 38091 38094
    • (2004) J. Biol. Chem. , vol.279 , pp. 38091-38094
    • Yano, J.K.1    Wester, M.R.2    Schoch, G.A.3    Griffin, K.J.4    Stout, C.D.5    Johnson, E.F.6
  • 34
    • 33748802003 scopus 로고    scopus 로고
    • Structural basis for ligand promiscuity in cytochrome P450 3A4
    • M. Ekroos, and T. Sjogren Structural basis for ligand promiscuity in cytochrome P450 3A4 Proc. Natl. Acad. Sci. USA. 103 2006 13682 13687
    • (2006) Proc. Natl. Acad. Sci. USA. , vol.103 , pp. 13682-13687
    • Ekroos, M.1    Sjogren, T.2
  • 37
    • 76149120388 scopus 로고    scopus 로고
    • Software news and update AutoDock Vina: Improving the speed and accuracy of docking with a New scoring function, Efficient optimization, and multithreading
    • O. Trott, and A.J. Olson Software news and update AutoDock Vina: improving the speed and accuracy of docking with a New scoring function, Efficient optimization, and multithreading J. Comput. Chem. 31 2010 455 461
    • (2010) J. Comput. Chem. , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 39
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • H. Frauenfelder, S.G. Sligar, and P.G. Wolynes The energy landscapes and motions of proteins Science 254 1991 1598 1603
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 40
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • C.J. Tsai, S. Kumar, B. Ma, and R. Nussinov Folding funnels, binding funnels, and protein function Protein Sci. 8 1999 1181 1190
    • (1999) Protein Sci. , vol.8 , pp. 1181-1190
    • Tsai, C.J.1    Kumar, S.2    Ma, B.3    Nussinov, R.4
  • 41
  • 42
    • 0032729435 scopus 로고    scopus 로고
    • Exploring expression data: Identification and analysis of coexpressed genes
    • L.J. Heyer, S. Kruglyak, and S. Yooseph Exploring expression data: identification and analysis of coexpressed genes Genome Res. 9 1999 1106 1115
    • (1999) Genome Res. , vol.9 , pp. 1106-1115
    • Heyer, L.J.1    Kruglyak, S.2    Yooseph, S.3
  • 43
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • D.E. Koshland Application of a theory of enzyme specificity to protein synthesis Proc. Natl. Acad. Sci. USA. 44 1958 98 104
    • (1958) Proc. Natl. Acad. Sci. USA. , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 44
    • 0037125501 scopus 로고    scopus 로고
    • Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach
    • J. Kua, Y. Zhang, and J.A. McCammon Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach J. Am. Chem. Soc. 124 2002 8260 8267
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 8260-8267
    • Kua, J.1    Zhang, Y.2    McCammon, J.A.3
  • 45
    • 0038460858 scopus 로고    scopus 로고
    • Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
    • S.L. McGovern, and B.K. Shoichet Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes J. Med. Chem. 46 2003 2895 2907
    • (2003) J. Med. Chem. , vol.46 , pp. 2895-2907
    • McGovern, S.L.1    Shoichet, B.K.2
  • 46
    • 0032718788 scopus 로고    scopus 로고
    • The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
    • C.W. Murray, C.A. Baxter, and A.D. Frenkel The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase J. Comput. Aided Mol. Des 13 1999 547 562
    • (1999) J. Comput. Aided Mol. des , vol.13 , pp. 547-562
    • Murray, C.W.1    Baxter, C.A.2    Frenkel, A.D.3
  • 48
  • 49
    • 37249091134 scopus 로고    scopus 로고
    • Computation of octanol-water partition coefficients by guiding an additive model with knowledge
    • T. Cheng, Y. Zhao, X. Li, F. Lin, Y. Xu, X. Zhang, Y. Li, R. Wang, and L. Lai Computation of octanol-water partition coefficients by guiding an additive model with knowledge J. Chem. Inf. Model. 47 2007 2140 2148
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 2140-2148
    • Cheng, T.1    Zhao, Y.2    Li, X.3    Lin, F.4    Xu, Y.5    Zhang, X.6    Li, Y.7    Wang, R.8    Lai, L.9
  • 51
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • J.M. Word, S.C. Lovell, J.S. Richardson, and D.C. Richardson Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation J. Mol. Biol. 285 1999 1735 1747
    • (1999) J. Mol. Biol. , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 52
    • 78651235334 scopus 로고    scopus 로고
    • Computer-aided drug design platform using PyMOL
    • M.A. Lill, and M.L. Danielson Computer-aided drug design platform using PyMOL J. Comput. Aided Mol. Des. 25 2011 13 19
    • (2011) J. Comput. Aided Mol. Des. , vol.25 , pp. 13-19
    • Lill, M.A.1    Danielson, M.L.2
  • 54
    • 0029633186 scopus 로고
    • Amber, A package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules
    • D.A. Pearlman, D.A. Case, J.W. Caldwell, W.S. Ross, T.E. Cheatham, S. Debolt, D. Ferguson, G. Seibel, and P. Kollman Amber, A package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules Comput. Phys. Commun. 91 1995 1 41
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham, T.E.5    Debolt, S.6    Ferguson, D.7    Seibel, G.8    Kollman, P.9
  • 55
    • 0027159949 scopus 로고
    • The molecular surface package
    • M.L. Connolly The molecular surface package J. Mol. Graph. 11 1993 139 141
    • (1993) J. Mol. Graph. , vol.11 , pp. 139-141
    • Connolly, M.L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.