메뉴 건너뛰기




Volumn 24, Issue 5, 2010, Pages 399-408

Site of metabolism prediction on cytochrome P450 2C9: A knowledge-based docking approach

Author keywords

CYP 2C9; Docking; Expert system; Prediction; Site of metabolism

Indexed keywords

BIOMOLECULES; CRYSTAL STRUCTURE; EXPERT SYSTEMS; FORECASTING; METABOLISM; PHYSIOLOGY; SITE SELECTION;

EID: 77953322016     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-010-9347-3     Document Type: Article
Times cited : (41)

References (44)
  • 1
    • 0037364162 scopus 로고    scopus 로고
    • ADMET in silico modelling: Towards prediction paradise?
    • DOI 10.1038/nrd1032
    • H van de Waterbeemd E Gifford 2003 ADMET in silico modelling: towards prediction paradise? Nat Rev Drug Discov 2 192 204 10.1038/nrd1032 (Pubitemid 37361664)
    • (2003) Nature Reviews Drug Discovery , vol.2 , Issue.3 , pp. 192-204
    • Van De Waterbeemd, H.1    Gifford, E.2
  • 2
    • 35949002128 scopus 로고    scopus 로고
    • CYP2C9 structure-metabolism relationships: Substrates, inhibitors, and metabolites
    • DOI 10.1021/jm070745g
    • MM Ahlström M Ridderström I Zamora 2007 CYP2C9 structure-metabolism relationships: substrates, inhibitors, and metabolites J Med Chem 50 5382 5391 10.1021/jm070745g (Pubitemid 350064000)
    • (2007) Journal of Medicinal Chemistry , vol.50 , Issue.22 , pp. 5382-5391
    • Ahlstrom, M.M.1    Ridderstrom, M.2    Zamora, I.3
  • 3
    • 60549095002 scopus 로고    scopus 로고
    • Metabolic soft spot identification and compound optimization in early discovery phases using MetaSite and LC-MS/MS validation
    • 10.1021/jm8008663 1:CAS:528:DC%2BD1cXhsFChsLfJ
    • M Trunzer B Faller A Zimmerlin 2009 Metabolic soft spot identification and compound optimization in early discovery phases using MetaSite and LC-MS/MS validation J Med Chem 52 329 335 10.1021/jm8008663 1:CAS:528:DC%2BD1cXhsFChsLfJ
    • (2009) J Med Chem , vol.52 , pp. 329-335
    • Trunzer, M.1    Faller, B.2    Zimmerlin, A.3
  • 6
    • 0042265520 scopus 로고    scopus 로고
    • Crystal structure of human cytochrome P450 2C9 with bound warfarin
    • DOI 10.1038/nature01862
    • PA Williams J Cosme A Ward HC Angove D Matak Vinković H Jhoti 2003 Crystal structure of human cytochrome P450 2C9 with bound warfarin Nature 424 464 468 10.1038/nature01862 1:CAS:528:DC%2BD3sXls1aqtrk%3D (Pubitemid 36917499)
    • (2003) Nature , vol.424 , Issue.6947 , pp. 464-468
    • Williams, P.A.1    Cosme, J.2    Ward, A.3    Angove, H.C.4    Vinkovic, D.M.5    Jhoti, H.6
  • 7
    • 59649103035 scopus 로고    scopus 로고
    • Safety testing of metabolites: Expectations and outcomes
    • 10.1016/j.cbi.2008.09.013 1:CAS:528:DC%2BD1MXitFShtrg%3D
    • KS Pang 2009 Safety testing of metabolites: expectations and outcomes Chem Biol Interact 179 45 59 10.1016/j.cbi.2008.09.013 1:CAS:528: DC%2BD1MXitFShtrg%3D
    • (2009) Chem Biol Interact , vol.179 , pp. 45-59
    • Pang, K.S.1
  • 9
    • 0031841377 scopus 로고    scopus 로고
    • Cytochrome P4502C9: An enzyme of major importance in human drug metabolism
    • DOI 10.1046/j.1365-2125.1998.00721.x
    • JO Miners DJ Birkett 1998 Cytochrome P4502C9: an enzyme of major importance in human drug metabolism Br J Clin Pharmacol 45 525 538 10.1046/j.1365-2125.1998.00721.x 1:CAS:528:DyaK1cXktFaitro%3D (Pubitemid 28270907)
    • (1998) British Journal of Clinical Pharmacology , vol.45 , Issue.6 , pp. 525-538
    • Miners, J.O.1    Birkett, D.J.2
  • 10
    • 39749093726 scopus 로고    scopus 로고
    • Prediction of metabolism by cytochrome P450 2C9: Alignment and docking studies of a validated database of substrates
    • DOI 10.1021/jm7009793
    • MJ Sykes RA McKinnon JO Miners 2008 Prediction of metabolism by cytochrome P450 2C9: alignment and docking studies of a validated database of substrates J Med Chem 51 780 791 10.1021/jm7009793 1:CAS:528: DC%2BD1cXhsVWiurk%3D (Pubitemid 351304687)
    • (2008) Journal of Medicinal Chemistry , vol.51 , Issue.4 , pp. 780-791
    • Sykes, M.J.1    McKinnon, R.A.2    Miners, J.O.3
  • 11
    • 4143143372 scopus 로고    scopus 로고
    • The structure of human cytochrome P450 2C9 complexed with flurbiprofen at 2.0-A resolution
    • DOI 10.1074/jbc.M405427200
    • MR Wester JK Yano GA Schoch C Yang KJ Griffin CD Stout EF Johnson 2004 The structure of human cytochrome P450 2C9 complexed with flurbiprofen at 2.0-A resolution J Biol Chem 279 35630 35637 10.1074/jbc.M405427200 1:CAS:528:DC%2BD2cXmsl2hsLs%3D (Pubitemid 39100565)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.34 , pp. 35630-35637
    • Wester, M.R.1    Yano, J.K.2    Schoch, G.A.3    Yang, C.4    Griffin, K.J.5    Stout, C.D.6    Johnson, E.F.7
  • 12
    • 35748959344 scopus 로고    scopus 로고
    • Effective virtual screening protocol for CYP2C9 ligands using a screening site constructed from flurbiprofen and S-warfarin pockets
    • DOI 10.1007/s10822-007-9137-8
    • T Polgár DK Menyhárd GM Keseru 2007 Effective virtual screening protocol for CYP2C9 ligands using a screening site constructed from flurbiprofen and S-warfarin pockets J Comput Aided Mol Des 9 539 548 10.1007/s10822-007-9137-8 (Pubitemid 350048153)
    • (2007) Journal of Computer-Aided Molecular Design , vol.21 , Issue.9 , pp. 539-548
    • Polgar, T.1    Menyhard, D.K.2    Keseru, G.M.3
  • 13
    • 33846380189 scopus 로고    scopus 로고
    • What common structural features and variations of mammalian P450 s are known to date?
    • 1:CAS:528:DC%2BD2sXpvVyqtQ%3D%3D
    • M Otyepka J Skopalík E Anzenbacherová P Anzenbacher 2007 What common structural features and variations of mammalian P450 s are known to date? Biochim Biophys Acta 1770 376 389 1:CAS:528:DC%2BD2sXpvVyqtQ%3D%3D
    • (2007) Biochim Biophys Acta , vol.1770 , pp. 376-389
    • Otyepka, M.1    Skopalík, J.2    Anzenbacherová, E.3    Anzenbacher, P.4
  • 14
    • 47049125463 scopus 로고    scopus 로고
    • In silico description of differential enantioselectivity in methoxychlor O-demethylation by CYP2C enzymes
    • Z Bikádi E Hazai 2008 In silico description of differential enantioselectivity in methoxychlor O-demethylation by CYP2C enzymes Biochim Biophys Acta 1780 1070 1079
    • (2008) Biochim Biophys Acta , vol.1780 , pp. 1070-1079
    • Bikádi, Z.1    Hazai, E.2
  • 15
    • 0034721138 scopus 로고    scopus 로고
    • A refined 3-dimensional QSAR of cytochrome P450 2C9: Computational predictions of drug interactions
    • DOI 10.1021/jm000048n
    • S Rao R Aoyama M Schrag WF Trager A Rettie JP Jones 2000 A refined 3-dimensional QSAR of cytochrome P450 2C9: computational predictions of drug interactions J Med Chem 43 2789 2796 10.1021/jm000048n 1:CAS:528: DC%2BD3cXksVaqu7s%3D (Pubitemid 30599636)
    • (2000) Journal of Medicinal Chemistry , vol.43 , Issue.15 , pp. 2789-2796
    • Rao, S.1    Aoyama, R.2    Schrag, M.3    Trager, W.F.4    Rettie, A.5    Jones, J.P.6
  • 16
    • 0035065393 scopus 로고    scopus 로고
    • Competitive CYP2C9 inhibitors: Enzyme inhibition studies, protein homology modeling, and three-dimensional quantitative structure-activity relationship analysis
    • 1:CAS:528:DC%2BD3MXisVSqsLw%3D
    • L Afzelius I Zamora M Ridderström TB Andersson A Karlén CM Masimirembwa 2001 Competitive CYP2C9 inhibitors: enzyme inhibition studies, protein homology modeling, and three-dimensional quantitative structure-activity relationship analysis Mol Pharmacol 59 909 919 1:CAS:528:DC%2BD3MXisVSqsLw%3D
    • (2001) Mol Pharmacol , vol.59 , pp. 909-919
    • Afzelius, L.1    Zamora, I.2    Ridderström, M.3    Andersson, T.B.4    Karlén, A.5    Masimirembwa, C.M.6
  • 17
    • 0037046521 scopus 로고    scopus 로고
    • Development of a combined protein and pharmacophore model for cytochrome P450 2C9
    • DOI 10.1021/jm0110791
    • MJ de Groot AA Alex BC Jones 2002 Development of a combined protein and pharmacophore model for cytochrome P450 2C9 J Med Chem 45 1983 1993 10.1021/jm0110791 (Pubitemid 34477712)
    • (2002) Journal of Medicinal Chemistry , vol.45 , Issue.10 , pp. 1983-1993
    • De Groot, M.J.1    Alex, A.A.2    Jones, B.C.3
  • 18
    • 0038440502 scopus 로고    scopus 로고
    • Predicting drug metabolism: A site of metabolism prediction tool applied to the cytochrome P450 2C9
    • DOI 10.1021/jm021104i
    • I Zamora L Afzelius G Cruciani 2003 Predicting drug metabolism: a site of metabolism prediction tool applied to the cytochrome P450 2C9 J Med Chem 46 2313 2324 10.1021/jm021104i 1:CAS:528:DC%2BD3sXjs12ksLw%3D (Pubitemid 36637916)
    • (2003) Journal of Medicinal Chemistry , vol.46 , Issue.12 , pp. 2313-2324
    • Zamora, I.1    Afzelius, L.2    Cruciani, G.3
  • 19
    • 0036589487 scopus 로고    scopus 로고
    • New methods in predictive metabolism
    • DOI 10.1023/A:1020881520931
    • S Boyer I Zamora 2002 New methods in predictive metabolism J Comput Aided Mol Des 5-6 403 413 10.1023/A:1020881520931 (Pubitemid 35422628)
    • (2002) Journal of Computer-Aided Molecular Design , vol.16 , Issue.5-6 , pp. 403-413
    • Boyer, S.1    Zamora, I.2
  • 20
    • 34447515639 scopus 로고    scopus 로고
    • Empirical regioselectivity models for human cytochromes P450 3A4, 2D6, and 2C9
    • DOI 10.1021/jm0613471
    • RP Sheridan KR Korzekwa RA Torres MJ Walker 2007 Empirical regioselectivity models for human cytochromes P450 3A4, 2D6, and 2C9 J Med Chem 50 3173 3184 10.1021/jm0613471 1:CAS:528:DC%2BD2sXmsFGnsr0%3D (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
  • 21
    • 58149099402 scopus 로고    scopus 로고
    • Cytochrome P450 2C9 type II binding studies on quinoline-4-carboxamide analogues
    • 10.1021/jm8011257 1:CAS:528:DC%2BD1cXhtl2jsbnO
    • CC Peng JL Cape T Rushmore GJ Crouch JP Jones 2008 Cytochrome P450 2C9 type II binding studies on quinoline-4-carboxamide analogues J Med Chem 51 8000 8011 10.1021/jm8011257 1:CAS:528:DC%2BD1cXhtl2jsbnO
    • (2008) J Med Chem , vol.51 , pp. 8000-8011
    • Peng, C.C.1    Cape, J.L.2    Rushmore, T.3    Crouch, G.J.4    Jones, J.P.5
  • 22
  • 23
    • 77953323877 scopus 로고    scopus 로고
    • ROCS Openeye Scientific Software: Sante Fe, NM, 2006
    • ROCS Openeye Scientific Software: Sante Fe, NM, 2006
  • 24
    • 77953325588 scopus 로고    scopus 로고
    • FRED Openeye Scientific Software: Sante Fe, NM, 2005
    • FRED Openeye Scientific Software: Sante Fe, NM, 2005
  • 27
    • 0032530250 scopus 로고    scopus 로고
    • A close family resemblance: The importance of structure in understanding cytochromes P450
    • 10.1016/S0969-2126(98)00109-9 1:CAS:528:DyaK1cXmsVKjt78%3D
    • JA Peterson SE Graham 1998 A close family resemblance: the importance of structure in understanding cytochromes P450 Structure 6 1079 1085 10.1016/S0969-2126(98)00109-9 1:CAS:528:DyaK1cXmsVKjt78%3D
    • (1998) Structure , vol.6 , pp. 1079-1085
    • Peterson, J.A.1    Graham, S.E.2
  • 28
    • 0022919721 scopus 로고
    • Crystal structure of substrate-free Pseudomonas putida cytochrome P-450
    • DOI 10.1021/bi00366a049
    • TL Poulos BC Finzel AJ Howard 1986 Crystal structure of substrate-free Pseudomonas putida cytochrome P-450 Biochemistry 25 5314 5322 10.1021/bi00366a049 1:CAS:528:DyaL28Xlt12ls78%3D (Pubitemid 17016546)
    • (1986) Biochemistry , vol.25 , Issue.18 , pp. 5314-5322
    • Poulos, T.L.1    Finzel, B.C.2    Howard, A.J.3
  • 29
    • 0022273620 scopus 로고
    • The 2.6-A crystal structure of Pseudomonas putida cytochrome P-450
    • 1:CAS:528:DyaL2MXmtV2rtr8%3D
    • TL Poulos BC Finzel IC Gunsalus GC Wagner J Kraut 1985 The 2.6-A crystal structure of Pseudomonas putida cytochrome P-450 J Biol Chem 260 16122 16130 1:CAS:528:DyaL2MXmtV2rtr8%3D
    • (1985) J Biol Chem , vol.260 , pp. 16122-16130
    • Poulos, T.L.1    Finzel, B.C.2    Gunsalus, I.C.3    Wagner, G.C.4    Kraut, J.5
  • 30
    • 0028813639 scopus 로고
    • Crystal structure of cytochrome P-450 complexe with its catalytic product, 5-Exo-Hydroxycamphor
    • 10.1021/ja00128a019 1:CAS:528:DyaK2MXmsFahs7w%3D
    • H Li S Narasimhulu LM Havran JD Winkler TL Poulos 1995 Crystal structure of cytochrome P-450 complexe with its catalytic product, 5-Exo-Hydroxycamphor J Am Chem Soc 117 6297 6299 10.1021/ja00128a019 1:CAS:528:DyaK2MXmsFahs7w%3D
    • (1995) J Am Chem Soc , vol.117 , pp. 6297-6299
    • Li, H.1    Narasimhulu, S.2    Havran, L.M.3    Winkler, J.D.4    Poulos, T.L.5
  • 31
    • 0024974060 scopus 로고
    • Crystal structure of the carbon monoxide-substrate-cytochrome P-450CAM ternary complex
    • 10.1021/bi00445a013 1:CAS:528:DyaL1MXlt12ksLo%3D
    • R Raag TL Poulos 1989 Crystal structure of the carbon monoxide-substrate-cytochrome P-450CAM ternary complex Biochemistry 28 7586 7592 10.1021/bi00445a013 1:CAS:528:DyaL1MXlt12ksLo%3D
    • (1989) Biochemistry , vol.28 , pp. 7586-7592
    • Raag, R.1    Poulos, T.L.2
  • 32
    • 77953321925 scopus 로고    scopus 로고
    • CompuDrug International, Inc (2003) 115 Morgan Drive, Sedona, AZ 86351, USA
    • CompuDrug International, Inc (2003) 115 Morgan Drive, Sedona, AZ 86351, USA
  • 33
    • 77951989079 scopus 로고    scopus 로고
    • Schrödinger, LLC, New York
    • Glide, version 5.0 (2008) Schrödinger, LLC, New York
    • (2008) Glide, Version 5.0
  • 34
    • 77953323709 scopus 로고    scopus 로고
    • National Center for Biotechnology Information
    • National Center for Biotechnology Information http://www.ncbi.nlm.nih. gov/sites/entrez Accessed 2009 February
  • 35
    • 77953324699 scopus 로고    scopus 로고
    • ChemAxon
    • ChemAxon http://www.chemaxon.com Accessed 2009 February
  • 36
    • 77953324562 scopus 로고    scopus 로고
    • CompuDrug
    • CompuDrug http://www.compudrug.com Accessed 2009 February
  • 37
    • 0033485933 scopus 로고    scopus 로고
    • Structural forms of phenprocoumon and warfarin that are metabolized at the active site of CYP2C9
    • 10.1006/abbi.1999.1468 1:CAS:528:DyaK1MXnt1Orsro%3D
    • M He KR Korzekwa JP Jones AE Rettie WF Trager 1999 Structural forms of phenprocoumon and warfarin that are metabolized at the active site of CYP2C9 Arch Biochem Biophys 372 16 28 10.1006/abbi.1999.1468 1:CAS:528: DyaK1MXnt1Orsro%3D
    • (1999) Arch Biochem Biophys , vol.372 , pp. 16-28
    • He, M.1    Korzekwa, K.R.2    Jones, J.P.3    Rettie, A.E.4    Trager, W.F.5
  • 38
    • 77953323157 scopus 로고    scopus 로고
    • Schrödinger, LLC, New York
    • LigPrep, version 2.3 (2009) Schrödinger, LLC, New York
    • (2009) LigPrep, Version 2.3
  • 40
    • 65249117481 scopus 로고    scopus 로고
    • Validation of molecular docking programs for virtual screening against Dihydropteroate synthase
    • 10.1021/ci800293n 1:CAS:528:DC%2BD1MXhtVChtbg%3D
    • KE Hevener W Zhao DM Ball K Babaoglu J Qi SW White RE Lee 2009 Validation of molecular docking programs for virtual screening against Dihydropteroate synthase J Chem Inf Model 49 444 460 10.1021/ci800293n 1:CAS:528: DC%2BD1MXhtVChtbg%3D
    • (2009) J Chem Inf Model , vol.49 , pp. 444-460
    • Hevener, K.E.1    Zhao, W.2    Ball, D.M.3    Babaoglu, K.4    Qi, J.5    White, S.W.6    Lee, R.E.7
  • 41
    • 1642540577 scopus 로고    scopus 로고
    • Evaluation of docking performance: Comparative data on docking algorithms
    • DOI 10.1021/jm0302997
    • M Kontoyianni LM McClellan GS Sokol 2004 Evaluation of docking performance: comparative data on docking algorithms J Med Chem 47 558 565 10.1021/jm0302997 1:CAS:528:DC%2BD2cXjt1Gk (Pubitemid 38129714)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.3 , pp. 558-565
    • Kontoyianni, M.1    McClellan, L.M.2    Sokol, G.S.3
  • 42
    • 0033578349 scopus 로고    scopus 로고
    • Deuterium magic angle spinning studies of substrates bound to cytochrome P450
    • DOI 10.1021/bi990463l
    • H Lee PR Ortiz de Montellano AE McDermott 1999 Deuterium magic angle spinning studies of substrates bound to cytochrome P450 Biochemistry 38 10808 10813 10.1021/bi990463l 1:CAS:528:DyaK1MXksFGiurc%3D (Pubitemid 29404413)
    • (1999) Biochemistry , vol.38 , Issue.33 , pp. 10808-10813
    • Lee, H.1    Ortiz De Montellano, P.R.2    McDermott, A.E.3
  • 43
    • 77953321350 scopus 로고    scopus 로고
    • UNITY, Tripos Inc. 1699 South Hanley Road St. Louis, MO 63144-2319 USA
    • UNITY, Tripos Inc. 1699 South Hanley Road St. Louis, MO 63144-2319 USA
  • 44
    • 33646764551 scopus 로고    scopus 로고
    • Comparison of methods for the prediction of the metabolic sites for CYP3A4-mediated metabolic reactions
    • D Zhou L Afzelius SW Grimm TB Andersson RJ Zauhar I Zamora 2006 Comparison of methods for the prediction of the metabolic sites for CYP3A4-mediated metabolic reactions Drug Metab Dispos 6 976 983
    • (2006) Drug Metab Dispos , vol.6 , pp. 976-983
    • Zhou, D.1    Afzelius, L.2    Grimm, S.W.3    Andersson, T.B.4    Zauhar, R.J.5    Zamora, I.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.