메뉴 건너뛰기




Volumn 36, Issue 6, 2007, Pages 589-599

Free energies of binding of R- and S-propranolol to wild-type and F483A mutant cytochrome P450 2D6 from molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME P450 2D6; MUTANT PROTEIN; PROPRANOLOL;

EID: 34347390240     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-006-0126-y     Document Type: Article
Times cited : (21)

References (54)
  • 2
    • 0028155689 scopus 로고
    • A new method for predicting binding affinity in computer-aided drug design
    • Aqvist J, Medina C, Samuelsson JE (1994) A new method for predicting binding affinity in computer-aided drug design. Protein Eng 7:385-391
    • (1994) Protein Eng , vol.7 , pp. 385-391
    • Aqvist, J.1    Medina, C.2    Samuelsson, J.E.3
  • 5
    • 0036204756 scopus 로고    scopus 로고
    • Molecular genetics of CYP2D6: Clinical relevance with focus on psychotropic drugs
    • Bertilsson L, Dahl ML, Dalen P, Al-Shurbaji A (2002) Molecular genetics of CYP2D6: clinical relevance with focus on psychotropic drugs. Br J Clin Pharmacol 53:111-122
    • (2002) Br J Clin Pharmacol , vol.53 , pp. 111-122
    • Bertilsson, L.1    Dahl, M.L.2    Dalen, P.3    Al-Shurbaji, A.4
  • 6
    • 0000249851 scopus 로고
    • Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations
    • Beutler TC, Mark AE, van Schaik RC, Gerber PR, Van Gunsteren WF (1994) Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chem Phys Lett 222:529-539
    • (1994) Chem Phys Lett , vol.222 , pp. 529-539
    • Beutler, T.C.1    Mark, A.E.2    Van Schaik, R.C.3    Gerber, P.R.4    Van Gunsteren, W.F.5
  • 7
    • 0024578173 scopus 로고
    • Free energy via molecular simulation: Applications to chemical and biomolecular systems
    • Beveridge DL, DiCapua FM (1989) Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu Rev Biophys Biophys Chem 18:431-492
    • (1989) Annu Rev Biophys Biophys Chem , vol.18 , pp. 431-492
    • Beveridge, D.L.1    Dicapua, F.M.2
  • 10
    • 0029137434 scopus 로고
    • Computer-assisted, structure-based prediction of substrates for cytochrome P450(Cam)
    • DeVoss JJ, Demontellano PRO (1995) Computer-assisted, structure-based prediction of substrates for cytochrome P450(Cam). J Am Chem Soc 117:4185-4186
    • (1995) J Am Chem Soc , vol.117 , pp. 4185-4186
    • Devoss, J.J.1    Demontellano, P.R.O.2
  • 11
    • 0030749297 scopus 로고    scopus 로고
    • Substrate docking algorithms and prediction of the substrate specificity of cytochrome P450(cam) and its L244A mutant
    • DeVoss JJ, Sibbesen O, Zhang ZP, deMontellano PRO (1997) Substrate docking algorithms and prediction of the substrate specificity of cytochrome P450(cam) and its L244A mutant. J Am Chem Soc 119:5489-5498
    • (1997) J Am Chem Soc , vol.119 , pp. 5489-5498
    • Devoss, J.J.1    Sibbesen, O.2    Zhang, Z.P.3    Demontellano, P.R.O.4
  • 13
    • 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, Vermeulen NP (2005a) 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
  • 14
    • 17444411955 scopus 로고    scopus 로고
    • Cytochrome p450 in silico: An integrative modeling approach
    • de Graaf C, Vermeulen NP, Feenstra KA (2005b) Cytochrome p450 in silico: an integrative modeling approach. J Med Chem 48:2725-2755
    • (2005) J Med Chem , vol.48 , pp. 2725-2755
    • De Graaf, C.1    Vermeulen, N.P.2    Feenstra, K.A.3
  • 15
    • 33646107162 scopus 로고    scopus 로고
    • Catalytic site prediction of and virtual screening accuracy of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking
    • de Graaf C, Oostenbrink C, Keizers PHJ, van der Wijst T, Jongejan A, Vermeulen NP (2006) Catalytic site prediction of and virtual screening accuracy of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking. J Med Chem 49:2417-2430
    • (2006) J Med Chem , vol.49 , pp. 2417-2430
    • De Graaf, C.1    Oostenbrink, C.2    Keizers, P.H.J.3    Van Der Wijst, T.4    Jongejan, A.5    Vermeulen, N.P.6
  • 18
    • 2542520761 scopus 로고    scopus 로고
    • Theoretical study of the ligand-CYP2B4 complexes: Effect of structure on binding free energies and heme spin state
    • Harris DL, Park JY, Gruenke L, Waskell L (2004) Theoretical study of the ligand-CYP2B4 complexes: effect of structure on binding free energies and heme spin state. Proteins 55:895-914
    • (2004) Proteins , vol.55 , pp. 895-914
    • Harris, D.L.1    Park, J.Y.2    Gruenke, L.3    Waskell, L.4
  • 19
    • 0029160249 scopus 로고
    • Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: A molecular dynamics study
    • Helms V, Wade RC (1995) Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study. Biophys J 69:810-824
    • (1995) Biophys J , vol.69 , pp. 810-824
    • Helms, V.1    Wade, R.C.2
  • 20
    • 0742321734 scopus 로고    scopus 로고
    • Human drug metabolising cytochrome P450 enzymes: Properties and polymorphisms
    • Ingelman-Sundberg M (2004) Human drug metabolising cytochrome P450 enzymes: properties and polymorphisms. Naunyn Schmiedebergs Arch Pharmacol 369:89-104
    • (2004) Naunyn Schmiedebergs Arch Pharmacol , vol.369 , pp. 89-104
    • Ingelman-Sundberg, M.1
  • 21
    • 4243754128 scopus 로고    scopus 로고
    • Non equilibrium equality for free energy differences
    • Jarzinsky C (1997) Non equilibrium equality for free energy differences. Phys Rev Lett 87:2690-2693
    • (1997) Phys Rev Lett , vol.87 , pp. 2690-2693
    • Jarzinsky, C.1
  • 22
    • 0017794351 scopus 로고
    • Measurement of substrate and inhibitor binding to microsomal cytochrome P-450 by optical-difference spectroscopy
    • Jefcoate CR (1978) Measurement of substrate and inhibitor binding to microsomal cytochrome P-450 by optical-difference spectroscopy. Methods Enzymol 52:258-279
    • (1978) Methods Enzymol , vol.52 , pp. 258-279
    • Jefcoate, C.R.1
  • 23
    • 0001385119 scopus 로고
    • The binding and regioselectivity of reaction of (R)-nicotine and (S)-nicotine with cytochrome-P-450cam-parallel experimental and theoretical-studies
    • Jones JP, Trager WF, Carlson TJ (1993) The binding and regioselectivity of reaction of (R)-nicotine and (S)-nicotine with cytochrome-P-450cam-parallel experimental and theoretical-studies. J Am Chem Soc 115:381-387
    • (1993) J Am Chem Soc , vol.115 , pp. 381-387
    • Jones, J.P.1    Trager, W.F.2    Carlson, T.J.3
  • 24
    • 7444225179 scopus 로고    scopus 로고
    • Influence of phenylalanine 120 on cytochrome P450 2D6 catalytic selectivity and regiospecificity: Crucial role in 7-methoxy-4-(aminomethyl)- coumarin metabolism
    • Keizers PH, Lussenburg BM, de Graaf C, Mentink LM, Vermeulen NP, Commandeur JN (2004) Influence of phenylalanine 120 on cytochrome P450 2D6 catalytic selectivity and regiospecificity: crucial role in 7-methoxy-4- (aminomethyl)-coumarin metabolism. Biochem Pharmacol 68:2263-2271
    • (2004) Biochem Pharmacol , vol.68 , pp. 2263-2271
    • Keizers, P.H.1    Lussenburg, B.M.2    De Graaf, C.3    Mentink, L.M.4    Vermeulen, N.P.5    Commandeur, J.N.6
  • 25
    • 24944529052 scopus 로고    scopus 로고
    • Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towards 3,4-methylenedioxy-it N-alkylamphetamines: In silico predictions and experimental validation
    • Keizers PH, de Graaf C, de Kanter FJ, Oostenbrink C, Feenstra KA, Commandeur JN, Vermeulen NP (2005a) Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towards 3,4-methylenedioxy-it N-alkylamphetamines: in silico predictions and experimental validation. J Med Chem 48:6117-6127
    • (2005) J Med Chem , vol.48 , pp. 6117-6127
    • Keizers, P.H.1    De Graaf, C.2    De Kanter, F.J.3    Oostenbrink, C.4    Feenstra, K.A.5    Commandeur, J.N.6    Vermeulen, N.P.7
  • 28
    • 0034791141 scopus 로고    scopus 로고
    • A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism
    • Keseru GM (2001) A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism. J Comput Aided Mol Des 15:649-657
    • (2001) J Comput Aided Mol des , vol.15 , pp. 649-657
    • Keseru, G.M.1
  • 29
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • Kirkwood JG (1935) Statistical mechanics of fluid mixtures. J Chem Phys 3:300-313
    • (1935) J Chem Phys , vol.3 , pp. 300-313
    • Kirkwood, J.G.1
  • 31
    • 37649030391 scopus 로고    scopus 로고
    • Variational formula for the free energy based on incomplete sampling in a molecular simulation
    • Lu N, Adhikari J, Kofke DA (2003) Variational formula for the free energy based on incomplete sampling in a molecular simulation. Phys Rev E Stat Nonlinear Soft Matter Phys 68:026122
    • (2003) Phys Rev e Stat Nonlinear Soft Matter Phys , vol.68 , pp. 026122
    • Lu, N.1    Adhikari, J.2    Kofke, D.A.3
  • 33
    • 0000318631 scopus 로고
    • Calculation of relative free energy via indirect pathways
    • Mark AE, Van Gunsteren WF, Berendsen HJC (1991) Calculation of relative free energy via indirect pathways. J Chem Phys 94:3808-3816
    • (1991) J Chem Phys , vol.94 , pp. 3808-3816
    • Mark, A.E.1    Van Gunsteren, W.F.2    Berendsen, H.J.C.3
  • 34
    • 33645386831 scopus 로고    scopus 로고
    • Calculating zeros: Non-equilibrium free energy calculations
    • Oostenbrink C, Van Gunsteren WF (2006) Calculating zeros: Non-equilibrium free energy calculations. Chem Phys 323:102-108
    • (2006) Chem Phys , vol.323 , pp. 102-108
    • Oostenbrink, C.1    Van Gunsteren, W.F.2
  • 35
    • 33645436636 scopus 로고    scopus 로고
    • CYPalleles: A web page for nomenclature of human cytochrome P450 alleles
    • Oscarson M, Ingelman-Sundberg M (2002) CYPalleles: a web page for nomenclature of human cytochrome P450 alleles. Drug Metab Pharmacokinet 17:491-495
    • (2002) Drug Metab Pharmacokinet , vol.17 , pp. 491-495
    • Oscarson, M.1    Ingelman-Sundberg, M.2
  • 36
    • 0037423276 scopus 로고    scopus 로고
    • Residues glutamate 216 and aspartate 301 are key determinants of substrate specificity and product regioselectivity in cytochrome P450 2D6
    • Paine MJ, McLaughlin LA, Flanagan JU, Kemp CA, Sutcliffe MJ, Roberts GC, Wolf CR (2003) Residues glutamate 216 and aspartate 301 are key determinants of substrate specificity and product regioselectivity in cytochrome P450 2D6. J Biol Chem 278:4021-4027
    • (2003) J Biol Chem , vol.278 , pp. 4021-4027
    • Paine, M.J.1    McLaughlin, L.A.2    Flanagan, J.U.3    Kemp, C.A.4    Sutcliffe, M.J.5    Roberts, G.C.6    Wolf, C.R.7
  • 37
    • 0029975720 scopus 로고    scopus 로고
    • Binding free energy calculations for P450cam-substrate complexes
    • Paulsen MD, Ornstein RL (1996) Binding free energy calculations for P450cam-substrate complexes. Protein Eng 9:567-571
    • (1996) Protein Eng , vol.9 , pp. 567-571
    • Paulsen, M.D.1    Ornstein, R.L.2
  • 39
    • 33646940952 scopus 로고
    • Numerical integration of cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert J-P, Cicotti G, Berendsen HJC (1977) Numerical integration of 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    Cicotti, G.2    Berendsen, H.J.C.3
  • 40
    • 0034281087 scopus 로고    scopus 로고
    • Drug-metabolizing enzymes: Mechanisms and functions
    • Sheweita SA (2000) Drug-metabolizing enzymes: mechanisms and functions. Curr Drug Metab 1:107-132
    • (2000) Curr Drug Metab , vol.1 , pp. 107-132
    • Sheweita, S.A.1
  • 41
    • 0036805854 scopus 로고    scopus 로고
    • Molecular modeling of cytochrome P450 1A1: Enzyme-substrate interactions and substrate binding affinities
    • Szklarz GD, Paulsen MD (2002) Molecular modeling of cytochrome P450 1A1: enzyme-substrate interactions and substrate binding affinities. J Biomol Struct Dyn 20:155-162
    • (2002) J Biomol Struct Dyn , vol.20 , pp. 155-162
    • Szklarz, G.D.1    Paulsen, M.D.2
  • 42
    • 0021582448 scopus 로고
    • Ligand-receptor interaction
    • Tembe BL, McCammon JA (1984) Ligand-receptor interaction. Comput Chem 8:281-283
    • (1984) Comput Chem , vol.8 , pp. 281-283
    • Tembe, B.L.1    McCammon, J.A.2
  • 43
    • 4544369164 scopus 로고
    • A generalized reaction force field method for molecular dynamics simulations
    • Tironi IG, Sperb R, Smith PE, Van Gunsteren WF (1995) A generalized reaction force 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
  • 46
    • 0037672866 scopus 로고    scopus 로고
    • Structure of a substrate complex of mammalian cytochrome P450 2C5 at 2.3 a resolution: Evidence for multiple substrate binding modes
    • Wester MR, Johnson EF, Marques-Soares C, Dansette PM, Mansuy D, Stout CD (2003a) Structure of a substrate complex of mammalian cytochrome P450 2C5 at 2.3 A resolution: evidence for multiple substrate binding modes. Biochemistry 42:6370-6379
    • (2003) Biochemistry , vol.42 , pp. 6370-6379
    • Wester, M.R.1    Johnson, E.F.2    Marques-Soares, C.3    Dansette, P.M.4    Mansuy, D.5    Stout, C.D.6
  • 47
    • 0042573727 scopus 로고    scopus 로고
    • Structure of mammalian cytochrome P450 2C5 complexed with diclofenac at 2.1 a resolution: Evidence for an induced fit model of substrate binding
    • Wester MR, Johnson EF, Marques-Soares C, Dijols S, Dansette PM, Mansuy D, Stout CD (2003b) Structure of mammalian cytochrome P450 2C5 complexed with diclofenac at 2.1 A resolution: evidence for an induced fit model of substrate binding. Biochemistry 42:9335-9345
    • (2003) Biochemistry , vol.42 , pp. 9335-9345
    • Wester, M.R.1    Johnson, E.F.2    Marques-Soares, C.3    Dijols, S.4    Dansette, P.M.5    Mansuy, D.6    Stout, C.D.7
  • 48
    • 0033970047 scopus 로고    scopus 로고
    • Mammalian microsomal cytochrome P450 monooxygenase: Structural adaptations for membrane binding and functional diversity
    • Williams PA, Cosme J, Sridhar V, Johnson EF, McRee DE (2000) Mammalian microsomal cytochrome P450 monooxygenase: structural adaptations for membrane binding and functional diversity. Mol Cell 5:121-31
    • (2000) Mol Cell , vol.5 , pp. 121-131
    • Williams, P.A.1    Cosme, J.2    Sridhar, V.3    Johnson, E.F.4    McRee, D.E.5
  • 49
    • 0032934961 scopus 로고    scopus 로고
    • Genetic polymorphisms of human N-acetyltransferase, cytochrome P450, glutathione-it S-transferase, and epoxide hydrolase enzymes: Relevance to xenobiotic metabolism and toxicity
    • Wormhoudt LW, Commandeur JN, Vermeulen NP (1999) Genetic polymorphisms of human N-acetyltransferase, cytochrome P450, glutathione-it S-transferase, and epoxide hydrolase enzymes: relevance to xenobiotic metabolism and toxicity. Crit Rev Toxicol 29:59-124
    • (1999) Crit Rev Toxicol , vol.29 , pp. 59-124
    • Wormhoudt, L.W.1    Commandeur, J.N.2    Vermeulen, N.P.3
  • 50
  • 53
    • 33646243546 scopus 로고    scopus 로고
    • Computational study of ground-state chiral induction in small peptides: Comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations
    • Zhou Y, Oostenbrink C, Jongejan A, Van Gunsteren WF, Hagen WR, De Leeuw SW, Jongejan JA (2006) Computational study of ground-state chiral induction in small peptides: comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations. J Comput Chem 27:857-867
    • (2006) J Comput Chem , vol.27 , pp. 857-867
    • Zhou, Y.1    Oostenbrink, C.2    Jongejan, A.3    Van Gunsteren, W.F.4    Hagen, W.R.5    De Leeuw, S.W.6    Jongejan, J.A.7
  • 54
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method. I. Nonpolar gases
    • Zwanzig RW (1954) High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys 22:1420-1426
    • (1954) J Chem Phys , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.