메뉴 건너뛰기




Volumn 54, Issue 17, 2011, Pages 6098-6105

Structure-based site of metabolism prediction for cytochrome P450 2D6

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME P450 2D6; HEME; IRON;

EID: 80052380142     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm2006468     Document Type: Article
Times cited : (47)

References (48)
  • 1
    • 38949204984 scopus 로고    scopus 로고
    • Cytochromes P450: A structure-based summary of biotransformations using representative substrates
    • DOI 10.1080/03602530701836662, PII 790484200
    • Brown, C. M.; Reisfeld, B.; Mayeno, A. N. Cytochromes p450: a structure-based summary of biotransformations using representative substrates Drug Metab. Rev. 2008, 40, 1-100 (Pubitemid 351220646)
    • (2008) Drug Metabolism Reviews , vol.40 , Issue.1 , pp. 1-100
    • Brown, C.M.1    Reisfeld, B.2    Mayeno, A.N.3
  • 2
    • 77950842489 scopus 로고    scopus 로고
    • Update information on drug metabolism systems - 2009, part II. Summary of information on the effects of diseases and environmental factors on human cytochrome P450 (CYP) enzymes and transporters
    • Rendic, S.; Guengerich, F. P. Update information on drug metabolism systems - 2009, part II. Summary of information on the effects of diseases and environmental factors on human cytochrome P450 (CYP) enzymes and transporters Curr. Drug Metab. 2010, 11, 4-84
    • (2010) Curr. Drug Metab. , vol.11 , pp. 4-84
    • Rendic, S.1    Guengerich, F.P.2
  • 4
    • 75749116800 scopus 로고    scopus 로고
    • Genetic polymorphism in cytochrome P450 2D6 (CYP2D6): Population distribution of CYP2D6 activity
    • Neafsey, P.; Ginsberg, G.; Hattis, D.; Sonawane, B. Genetic polymorphism in cytochrome P450 2D6 (CYP2D6): population distribution of CYP2D6 activity J. Toxicol. Environ. Health, Part B 2009, 12, 334-361
    • (2009) J. Toxicol. Environ. Health, Part B , vol.12 , pp. 334-361
    • Neafsey, P.1    Ginsberg, G.2    Hattis, D.3    Sonawane, B.4
  • 6
    • 33746382906 scopus 로고    scopus 로고
    • Introduction to early in vitro identification of metabolites of new chemical entities in drug discovery and development
    • Baranczewski, P.; Stanczak, A.; Kautiainen, A.; Sandin, P.; Edlund, P. Introduction to early in vitro identification of metabolites of new chemical entities in drug discovery and development Pharmacol. Rep. 2006, 58, 341-352 (Pubitemid 44111069)
    • (2006) Pharmacological Reports , vol.58 , Issue.3 , pp. 341-352
    • Baranczewski, P.1    Stanczak, A.2    Kautiainen, A.3    Sandin, P.4    Edlund, P.-O.5
  • 7
    • 36549010477 scopus 로고    scopus 로고
    • Unfinished business: target-based drug discovery
    • DOI 10.1016/j.drudis.2007.10.017, PII S1359644607004576
    • Brown, D. Unfinished business: target-based drug discovery Drug Discovery Today 2007, 12, 1007-1012 (Pubitemid 350180564)
    • (2007) Drug Discovery Today , vol.12 , Issue.23-24 , pp. 1007-1012
    • Brown, D.1
  • 8
    • 67749104100 scopus 로고    scopus 로고
    • Metabolites in safety testing: Metabolite identification strategies in discovery and development
    • Nedderman, A. N. R. Metabolites in safety testing: metabolite identification strategies in discovery and development Biopharm. Drug Dispos. 2009, 30, 153-162
    • (2009) Biopharm. Drug Dispos. , vol.30 , pp. 153-162
    • Nedderman, A.N.R.1
  • 9
    • 45949107967 scopus 로고    scopus 로고
    • Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450
    • DOI 10.1517/17425255.4.5.513
    • Stjernschantz, E.; Vermeulen, N. P. E.; Oostenbrink, C. Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450 Expert Opin. Drug Metab. Toxicol. 2008, 4, 513-527 (Pubitemid 351890736)
    • (2008) Expert Opinion on Drug Metabolism and Toxicology , vol.4 , Issue.5 , pp. 513-527
    • Stjernschantz, E.1    Vermeulen, N.P.E.2    Oostenbrink, C.3
  • 10
    • 0037431382 scopus 로고    scopus 로고
    • A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules
    • DOI 10.1021/jm020400s
    • Singh, S. B.; Shen, L. Q.; Walker, M. J.; Sheridan, R. P. A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules J. Med. Chem. 2003, 46, 1330-1336 (Pubitemid 36512698)
    • (2003) Journal of Medicinal Chemistry , vol.46 , Issue.8 , pp. 1330-1336
    • Singh, S.B.1    Shen, L.Q.2    Walker, M.J.3    Sheridan, R.P.4
  • 11
    • 34447515639 scopus 로고    scopus 로고
    • Empirical regioselectivity models for human cytochromes P450 3A4, 2D6, and 2C9
    • DOI 10.1021/jm0613471
    • Sheridan, R. P.; Korzekwa, K. R.; Torres, R. A.; Walker, M. J. Empirical regioselectivity models for human cytochromes p450 3A4, 2D6, and 2C9 J. Med. Chem. 2007, 50, 3173-3184 (Pubitemid 47065966)
    • (2007) Journal of Medicinal Chemistry , vol.50 , Issue.14 , pp. 3173-3184
    • Sheridan, R.P.1    Korzekwa, K.R.2    Torres, R.A.3    Walker, M.J.4
  • 12
    • 65549103878 scopus 로고    scopus 로고
    • Site of metabolism prediction for six biotransformations mediated by cytochromes P450
    • Zheng, M. Y.; Luo, X. M.; Shen, Q. C.; Wang, Y.; Du, Y.; Zhu, W. L.; Jiang, H. L. Site of metabolism prediction for six biotransformations mediated by cytochromes P450 Bioinformatics 2009, 25, 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
  • 13
  • 14
    • 77953932263 scopus 로고    scopus 로고
    • SMARTCyp: A 2D method for prediction of cytochrome P450-mediated drug metabolism
    • Rydberg, P.; Gloriam, D. E.; Zaretzki, J.; Breneman, C.; Olsen, L. SMARTCyp: a 2D method for prediction of cytochrome P450-mediated drug metabolism ACS Med. Chem. Lett. 2010, 1, 96-100
    • (2010) ACS Med. Chem. Lett. , vol.1 , pp. 96-100
    • Rydberg, P.1    Gloriam, D.E.2    Zaretzki, J.3    Breneman, C.4    Olsen, L.5
  • 16
    • 33646107162 scopus 로고    scopus 로고
    • Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking
    • de Graaf, C.; Oostenbrink, C.; Keizers, P. H. J.; van der Wijst, T.; Jongejan, A.; Vermeulen, N. P. E. Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking J. Med. Chem. 2006, 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.E.6
  • 17
    • 0028909989 scopus 로고
    • Stereoselective hydroxylation of norcamphor by cytochrome P450cam. Experimental verification of molecular dynamics simulations
    • Loida, P. J.; Sligar, S. G.; Paulsen, M. D.; Arnold, G. E.; Ornstein, R. L. Stereoselective hydroxylation of norcamphor by cytochrome P450cam. Experimental verification of molecular dynamics simulations J. Biol. Chem. 1995, 270, 5326-5330
    • (1995) J. Biol. Chem. , vol.270 , pp. 5326-5330
    • Loida, P.J.1    Sligar, S.G.2    Paulsen, M.D.3    Arnold, G.E.4    Ornstein, R.L.5
  • 18
    • 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.; Oostenbrink, C. Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking J. Med. Chem. 2008, 51, 7469-7477
    • (2008) J. Med. Chem. , vol.51 , pp. 7469-7477
    • Hritz, J.1    De Ruiter, A.2    Oostenbrink, C.3
  • 20
    • 0033529017 scopus 로고    scopus 로고
    • Novel approach to predicting P450-mediated drug metabolism: Development of a combined protein and pharmacophore model for CYP2D6
    • DOI 10.1021/jm981118h
    • de Groot, M. J.; Ackland, M. J.; Horne, V. A.; Alex, A. A.; Jones, B. C. Novel approach to predicting P450-mediated drug metabolism: development of a combined protein and pharmacophore model for CYP2D6 J. Med. Chem. 1999, 42, 1515-1524 (Pubitemid 29226723)
    • (1999) Journal of Medicinal Chemistry , vol.42 , Issue.9 , pp. 1515-1524
    • De Groot, M.J.1    Ackland, M.J.2    Horne, V.A.3    Alex, A.A.4    Jones, B.C.5
  • 21
    • 35748982413 scopus 로고    scopus 로고
    • Geometry-Based Sampling of Conformational Transitions in Proteins
    • DOI 10.1016/j.str.2007.09.017, PII S0969212607003681
    • Seeliger, D.; Haas, J.; de Groot, B. L. Geometry-based sampling of conformational transitions in proteins Structure 2007, 15, 1482-1492 (Pubitemid 350051928)
    • (2007) Structure , vol.15 , Issue.11 , pp. 1482-1492
    • Seeliger, D.1    Haas, J.2    De Groot, B.L.3
  • 22
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • DOI 10.1002/elps.1150181505
    • Guex, N.; Peitsch, M. C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling Electrophoresis 1997, 18, 2714-2723 (Pubitemid 28059943)
    • (1997) Electrophoresis , vol.18 , Issue.15 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 23
  • 25
  • 28
    • 0029827090 scopus 로고    scopus 로고
    • Oxidative metabolism of flunarizine and cinnarizine by microsomes from B-lymphoblastoid cell lines expressing human cytochrome P450 enzymes
    • Kariya, S.; Isozaki, S.; Uchino, K.; Suzuki, T.; Narimatsu, S. Oxidative metabolism of flunarizine and cinnarizine by microsomes from B-lymphoblastoid cell lines expressing human cytochrome P450 enzymes Biol. Pharm. Bull. 1996, 19, 1511-1514 (Pubitemid 26403264)
    • (1996) Biological and Pharmaceutical Bulletin , vol.19 , Issue.11 , pp. 1511-1514
    • Kariya, S.1    Isozaki, S.2    Uchino, K.3    Suzuki, T.4    Narimatsu, S.5
  • 32
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • Fawcett, T. An introduction to ROC analysis Pattern Recognit. Lett. 2006, 27, 861-874
    • (2006) Pattern Recognit. Lett. , vol.27 , pp. 861-874
    • Fawcett, T.1
  • 33
    • 4644275807 scopus 로고    scopus 로고
    • Mechanism of oxidation reactions catalyzed by cytochrome P450 enzymes
    • Meunier, B.; de Visser, S. P.; Shaik, S. Mechanism of oxidation reactions catalyzed by cytochrome P450 enzymes Chem. Rev. 2004, 104, 3947-3980
    • (2004) Chem. Rev. , vol.104 , pp. 3947-3980
    • Meunier, B.1    De Visser, S.P.2    Shaik, S.3
  • 34
    • 0015866154 scopus 로고
    • Environment and exposure to solvent of protein atoms. Lysozyme and insulin
    • Shrake, A.; Rupley, J. A. Environment and exposure to solvent of protein atoms. Lysozyme and insulin J. Mol. Biol. 1973, 79, 351-371
    • (1973) J. Mol. Biol. , vol.79 , pp. 351-371
    • Shrake, A.1    Rupley, J.A.2
  • 35
    • 70049114950 scopus 로고    scopus 로고
    • Detection of functional modes in protein dynamics
    • e1000480
    • Hub, J. S.; de Groot, B. L. Detection of functional modes in protein dynamics PLoS Comput. Biol. 2009, 5 e1000480
    • (2009) PLoS Comput. Biol. , vol.5
    • Hub, J.S.1    De Groot, B.L.2
  • 37
    • 0037423276 scopus 로고    scopus 로고
    • Residues glutamate 216 and aspartate 301 are key determinants of substrate specificity and product regioselectivity in cytochrome P450 2D6
    • DOI 10.1074/jbc.M209519200
    • Paine, M. J. I.; McLaughlin, L. A.; Flanagan, J. U.; Kemp, C. A.; Sutcliffe, M. J.; Roberts, G. C. K.; Wolf, C. R. Residues glutamate 216 and aspartate 301 are key determinants of substrate specificity and product regioselectivity in cytochrome P450 2D6 J. Biol. Chem. 2003, 278, 4021-4027 (Pubitemid 36801135)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.6 , pp. 4021-4027
    • Paine, M.J.I.1    McLaughlin, L.A.2    Flanagan, J.U.3    Kemp, C.A.4    Sutcliffe, M.J.5    Roberts, G.C.K.6    Wolf, C.R.7
  • 38
    • 54349105906 scopus 로고    scopus 로고
    • Molecular basis of CYP2D6-mediated N-dealkylation: Balance between metabolic clearance routes and enzyme inhibition
    • Bonn, B.; Masimirembwa, C. M.; Aristei, Y.; Zamora, I. Molecular basis of CYP2D6-mediated N-dealkylation: balance between metabolic clearance routes and enzyme inhibition Drug Metab. Dispos. 2008, 36, 2199-2210
    • (2008) Drug Metab. Dispos. , vol.36 , pp. 2199-2210
    • Bonn, B.1    Masimirembwa, C.M.2    Aristei, Y.3    Zamora, I.4
  • 39
    • 0034973773 scopus 로고    scopus 로고
    • Common and uncommon cytochrome P450 reactions related to metabolism and chemical toxicity
    • Guengerich, F. P. Common and uncommon cytochrome P450 reactions related to metabolism and chemical toxicity Chem. Res. Toxicol. 2001, 14, 611-650 (Pubitemid 32565712)
    • (2001) Chemical Research in Toxicology , vol.14 , Issue.6 , pp. 611-650
    • Guengerich, F.P.1
  • 40
    • 34249819058 scopus 로고    scopus 로고
    • Variations on a (t)heme - Novel mechanisms, redox partners and catalytic functions in the cytochrome P450 superfamily
    • DOI 10.1039/b604190f
    • Munro, A. W.; Girvan, H. M.; McLean, K. J. Variations on a (t)heme - novel mechanisms, redox partners and catalytic functions in the cytochrome P450 superfamily Nat. Prod. Rep. 2007, 24, 585-609 (Pubitemid 46848711)
    • (2007) Natural Product Reports , vol.24 , Issue.3 , pp. 585-609
    • Munro, A.W.1    Girvan, H.M.2    McLean, K.J.3
  • 41
    • 25144520939 scopus 로고    scopus 로고
    • Electronic structure of compound I in human isoforms of cytochrome P450 from QM/MM modeling
    • DOI 10.1021/ja0520924
    • Bathelt, C. M.; Zurek, J.; Mulholland, A. J.; Harvey, J. N. Electronic structure of compound I in human isoforms of cytochrome P450 from QM/MM modeling J. Am. Chem. Soc. 2005, 127, 12900-12908 (Pubitemid 41339174)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.37 , pp. 12900-12908
    • Bathelt, C.M.1    Zurek, J.2    Mulholland, A.J.3    Harvey, J.N.4
  • 43
    • 75749127293 scopus 로고    scopus 로고
    • Role of water in molecular docking simulations of cytochrome P450 2D6
    • Santos, R.; Hritz, J.; Oostenbrink, C. Role of water in molecular docking simulations of cytochrome P450 2D6 J. Chem. Inf. Model. 2010, 50, 146-154
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 146-154
    • Santos, R.1    Hritz, J.2    Oostenbrink, C.3
  • 45
    • 58149333699 scopus 로고    scopus 로고
    • What induces pocket openings on protein surface patches involved in protein-protein interactions?
    • Eyrisch, S.; Helms, V. What induces pocket openings on protein surface patches involved in protein-protein interactions? J. Comput.-Aided Mol. Des. 2009, 23, 73-86
    • (2009) J. Comput.-Aided Mol. Des. , vol.23 , pp. 73-86
    • Eyrisch, S.1    Helms, V.2
  • 46
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • PII S0009261499011239
    • Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 1999, 314, 141-151 (Pubitemid 129556751)
    • (1999) Chemical Physics Letters , vol.314 , Issue.1-2 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 47
    • 78651367226 scopus 로고    scopus 로고
    • Improved replica exchange method for native-state protein sampling
    • Moors, S. L. C.; Michielssens, S.; Ceulemans, A. Improved replica exchange method for native-state protein sampling J. Chem. Theory Comput. 2011, 7, 231-237
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 231-237
    • Moors, S.L.C.1    Michielssens, S.2    Ceulemans, A.3
  • 48
    • 33846000313 scopus 로고    scopus 로고
    • Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
    • Huang, S. Y.; Zou, X. Q. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking Proteins 2007, 66, 399-421
    • (2007) Proteins , vol.66 , pp. 399-421
    • Huang, S.Y.1    Zou, X.Q.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.