메뉴 건너뛰기




Volumn 38, Issue 8, 2010, Pages 1347-1354

Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA NAPHTHOFLAVONE; APRINDINE; BEPRIDIL; CYTOCHROME P450 1A2; ELLIPTICINE; FURAFYLLINE; LIDOCAINE; MEXILETINE; PHENACETIN; PROPAFENONE; PROPRANOLOL; QUINIDINE; RILUZOLE; TACRINE;

EID: 77954889093     PISSN: 00909556     EISSN: 1521009X     Source Type: Journal    
DOI: 10.1124/dmd.110.032946     Document Type: Article
Times cited : (32)

References (43)
  • 2
    • 3042549928 scopus 로고    scopus 로고
    • Binding affinity prediction with different force fields: Examination of the linear interaction energy method
    • Almlöf M, Brandsdal BO, and Aqvist J (2004) Binding affinity prediction with different force fields: examination of the linear interaction energy method. J Comput Chem 25:1242-1254.
    • (2004) J Comput Chem , vol.25 , pp. 1242-1254
    • Almlöf, M.1    Brandsdal, B.O.2    Aqvist, J.3
  • 3
    • 0036280661 scopus 로고    scopus 로고
    • Ligand binding affinities from MD simulations
    • Aqvist J, Luzhkov VB, and Brandsdal BO (2002) Ligand binding affinities from MD simulations. Acc Chem Res 35:358-365.
    • (2002) Acc Chem Res , vol.35 , pp. 358-365
    • Aqvist, J.1    Luzhkov, V.B.2    Brandsdal, B.O.3
  • 4
    • 0028155689 scopus 로고
    • A new method for predicting binding affinity in computer-aided drug design
    • Aqvist J, Medina C, and Samuelsson JE (1994) A new method for predicting binding affinity in computer-aided drug design. Protein Eng 7:385-391. (Pubitemid 24063137)
    • (1994) Protein Engineering , vol.7 , Issue.3 , pp. 385-391
    • Aqvist, J.1    Medina, C.2    Samuelsson, J.-E.3
  • 5
    • 33748636018 scopus 로고    scopus 로고
    • Introduction to in vitro estimation of metabolic stability and drug interactions of new chemical entities in drug discovery and development
    • Baranczewski P, Stańczak A, Sundberg K, Svensson R, Wallin A, Jansson J, Garberg P, and Postlind H (2006) Introduction to in vitro estimation of metabolic stability and drug interactions of new chemical entities in drug discovery and development. Pharmacol Rep 58:453-472. (Pubitemid 44383272)
    • (2006) Pharmacological Reports , vol.58 , Issue.4 , pp. 453-472
    • Baranczewski, P.1    Stanczak, A.2    Sundberg, K.3    Svensson, R.4    Wallin, A.5    Jansson, J.6    Garberg, P.7    Postlind, H.8
  • 8
    • 0024578173 scopus 로고
    • Free energy via molecular simulation: Applications to chemical and biomolecular systems
    • Beveridge DL and DiCapua FM (1989) Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu Rev Biophys Biophys Chem 18:431-491
    • (1989) Annu Rev Biophys Biophys Chem , vol.18 , pp. 431-491
    • Beveridge, D.L.1    DiCapua, F.M.2
  • 10
    • 0043027104 scopus 로고    scopus 로고
    • In vitro drug interactions of cytochrome P450: An evaluation of fluorogenic to conventional substrates
    • Cohen LH, Remley MJ, Raunig D, and Vaz AD (2003) In vitro drug interactions of cytochrome P450: an evaluation of fluorogenic to conventional substrates. Drug Metab Dispos 31:1005-1015.
    • (2003) Drug Metab Dispos , vol.31 , pp. 1005-1015
    • Cohen, L.H.1    Remley, M.J.2    Raunig, D.3    Vaz, A.D.4
  • 12
    • 17144368025 scopus 로고    scopus 로고
    • Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking
    • de Graaf C, Pospisil P, Pos W, Folkers G, and Vermeulen NP (2005) Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking. J Med Chem 48:2308-2318.
    • (2005) J Med Chem , vol.48 , pp. 2308-2318
    • De Graaf, C.1    Pospisil, P.2    Pos, W.3    Folkers, G.4    Vermeulen, N.P.5
  • 13
    • 10644249977 scopus 로고    scopus 로고
    • In silico methods for predicting ligand binding determinants of cytochromes P450
    • de Groot MJ, Kirton SB, and Sutcliffe MJ (2004) In silico methods for predicting ligand binding determinants of cytochromes P450. Curr Top Med Chem 4:1803-1824.
    • (2004) Curr Top Med Chem , vol.4 , pp. 1803-1824
    • De Groot, M.J.1    Kirton, S.B.2    Sutcliffe, M.J.3
  • 14
    • 0035336557 scopus 로고    scopus 로고
    • New drug development in the United States from 1963 to 1999
    • Dimasi JA (2001) New drug development in the United States from 1963 to 1999. Clin Pharmacol Ther 69:286-296.
    • (2001) Clin Pharmacol Ther , vol.69 , pp. 286-296
    • Dimasi, J.A.1
  • 15
    • 0034962557 scopus 로고    scopus 로고
    • Pharmacophore and three-dimensional quantitative structure activity relationship methods for modeling cytochrome p450 active sites
    • Ekins S, de Groot MJ, and Jones JP (2001) Pharmacophore and three-dimensional quantitative structure activity relationship methods for modeling cytochrome P450 active sites. Drug Metab Dispos 29:936-944. (Pubitemid 32605906)
    • (2001) Drug Metabolism and Disposition , vol.29 , Issue.7 , pp. 936-944
    • Ekins, S.1    De Groot, M.J.2    Jones, J.P.3
  • 17
  • 18
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford PJ (1985) A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem 28:849-857.
    • (1985) J Med Chem , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 19
    • 33748796911 scopus 로고    scopus 로고
    • A malleable catalyst dominates the metabolism of drugs
    • Guengerich FP (2006) A malleable catalyst dominates the metabolism of drugs. Proc Natl Acad Sci USA 103:13565-13566.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 13565-13566
    • Guengerich, F.P.1
  • 20
    • 0037571112 scopus 로고    scopus 로고
    • Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
    • Halgren TA (1996) Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J Comput Chem 17:490-519.
    • (1996) J Comput Chem , vol.17 , pp. 490-519
    • Halgren, T.A.1
  • 22
    • 2942614915 scopus 로고    scopus 로고
    • In silico predictive metabolism: A structural/electronic filter method
    • Harris DL (2004) In silico predictive metabolism: a structural/electronic filter method. Curr Opin Drug Discov Devel 7:43-48.
    • (2004) Curr Opin Drug Discov Devel , vol.7 , pp. 43-48
    • Harris, D.L.1
  • 23
    • 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
    • Hritz J, de Ruiter A, and Oostenbrink C (2008) Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking. J Med Chem 51:7469-7477.
    • (2008) J Med Chem , vol.51 , pp. 7469-7477
    • Hritz, J.1    De Ruiter, A.2    Oostenbrink, C.3
  • 24
    • 55249116250 scopus 로고    scopus 로고
    • Coffee intake and CYP1A2*1F genotype predict breast volume in young women: Implications for breast cancer
    • Jernström H, Henningson M, Johansson U, and Olsson H (2008) Coffee intake and CYP1A2*1F genotype predict breast volume in young women: implications for breast cancer. Br J Cancer 99:1534-1538.
    • (2008) Br J Cancer , vol.99 , pp. 1534-1538
    • Jernström, H.1    Henningson, M.2    Johansson, U.3    Olsson, H.4
  • 25
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones G, Willett P, Glen RC, Leach AR, and Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748.
    • (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
  • 27
    • 0037377894 scopus 로고    scopus 로고
    • Characterization of substrate binding to cytochrome P450 1A1 using molecular modeling and kinetic analysis: Case of residue 382
    • Liu J, Ericksen SS, Besspiata D, Fisher CW, and Szklarz GD (2003) Characterization of substrate binding to cytochrome P450 1A1 using molecular modeling and kinetic analysis: case of residue 382. Drug Metab Dispos 31:412-420.
    • (2003) Drug Metab Dispos , vol.31 , pp. 412-420
    • Liu, J.1    Ericksen, S.S.2    Besspiata, D.3    Fisher, C.W.4    Szklarz, G.D.5
  • 29
    • 73249132581 scopus 로고    scopus 로고
    • The cytochrome P450 homepage
    • Nelson DR (2009) The cytochrome P450 homepage. Hum Genomics 4:59-65.
    • (2009) Hum Genomics , vol.4 , pp. 59-65
    • Nelson, D.R.1
  • 30
    • 0029975720 scopus 로고    scopus 로고
    • Binding free energy calculations for P450cam-substrate complexes
    • Paulsen MD and Ornstein RL (1996) Binding free energy calculations for P450cam-substrate complexes. Protein Eng 9:567-571. (Pubitemid 26241633)
    • (1996) Protein Engineering , vol.9 , Issue.7 , pp. 567-571
    • Paulsen, M.D.1    Ornstein, R.L.2
  • 31
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert JP, Ciccotti G, and Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327-341.
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 32
  • 33
    • 34347235844 scopus 로고    scopus 로고
    • Adaptations for the oxidation of polycyclic aromatic hydrocarbons exhibited by the structure of human P450 1A2
    • Sansen S, Yano JK, Reynald RL, Schoch GA, Griffin KJ, Stout CD, and Johnson EF (2007) Adaptations for the oxidation of polycyclic aromatic hydrocarbons exhibited by the structure of human P450 1A2. J Biol Chem 282:14348-14355.
    • (2007) J Biol Chem , vol.282 , pp. 14348-14355
    • Sansen, S.1    Yano, J.K.2    Reynald, R.L.3    Schoch, G.A.4    Griffin, K.J.5    Stout, C.D.6    Johnson, E.F.7
  • 34
    • 75749127293 scopus 로고    scopus 로고
    • Role of water in molecular docking simulations of cytochrome P450 2D6
    • Santos R, Hritz J, and Oostenbrink C (2010) Role of water in molecular docking simulations of cytochrome P450 2D6. J Chem Inf Model 50:146-154.
    • (2010) J Chem Inf Model , vol.50 , pp. 146-154
    • Santos, R.1    Hritz, J.2    Oostenbrink, C.3
  • 35
    • 0035070553 scopus 로고    scopus 로고
    • Cytochrome P4501A2 (CYP1A2) activity and lung cancer risk: A preliminary study among Chinese women in Singapore
    • Seow A, Zhao B, Lee EJ, Poh WT, Teh M, Eng P, Wang YT, Tan WC, and Lee HP (2001) Cytochrome P4501A2 (CYP1A2) activity and lung cancer risk: a preliminary study among Chinese women in Singapore. Carcinogenesis 22:673-677.
    • (2001) Carcinogenesis , vol.22 , pp. 673-677
    • Seow, A.1    Zhao, B.2    Lee, E.J.3    Poh, W.T.4    Teh, M.5    Eng, P.6    Wang, Y.T.7    Tan, W.C.8    Lee, H.P.9
  • 36
    • 0030924503 scopus 로고    scopus 로고
    • Properties of cytochrome P450 isoenzymes and their substrates part 1: Active site characteristics
    • Smith DA, Ackland MJ, and Jones BC (1997) Properties of cytochrome P450 isoenzymes and their substrates part 1: active site characteristics. Drug Discov Today 2:406-414.
    • (1997) Drug Discov Today , vol.2 , pp. 406-414
    • Smith, D.A.1    Ackland, M.J.2    Jones, B.C.3
  • 37
    • 45949107967 scopus 로고    scopus 로고
    • Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450
    • Stjernschantz E, Vermeulen NP, and Oostenbrink C (2008) Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450. Exp Opin Drug Metab Toxicol 4:513-527.
    • (2008) Exp Opin Drug Metab Toxicol , vol.4 , pp. 513-527
    • Stjernschantz, E.1    Vermeulen, N.P.2    Oostenbrink, C.3
  • 38
    • 34547679825 scopus 로고    scopus 로고
    • Ligand-based models for the isoform specificity of cytochrome P450 3A4, 2D6, and 2C9 substrates
    • Terfloth L, Bienfait B, and Gasteiger J (2007) Ligand-based models for the isoform specificity of cytochrome P450 3A4, 2D6, and 2C9 substrates. J Chem Inf Model 47:1688-1701.
    • (2007) J Chem Inf Model , vol.47 , pp. 1688-1701
    • Terfloth, L.1    Bienfait, B.2    Gasteiger, J.3
  • 39
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular dynamics simulations
    • Tironi IG, Sperb R, Smith PE, and van Gunsteren WF (1995) A generalized reaction field method for molecular dynamics simulations. J Chem Phys 102:5451-5459.
    • (1995) J Chem Phys , vol.102 , pp. 5451-5459
    • Tironi, I.G.1    Sperb, R.2    Smith, P.E.3    Van Gunsteren, W.F.4
  • 40
    • 0037364162 scopus 로고    scopus 로고
    • ADMET in silico modelling: Towards prediction paradise?
    • van de Waterbeemd H and Gifford E (2003) ADMET in silico modelling: towards prediction paradise? Nat Rev Drug Discov 2:192-204.
    • (2003) Nat Rev Drug Discov , vol.2 , pp. 192-204
    • Van De Waterbeemd, H.1    Gifford, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.