SEARCH

SEARCH BY CITATION

References

  • 1
    Lajiness M.S., Vieth M., Erickson J. (2004) Molecular properties that influence oral drug-like behavior. Curr Opin Drug Discov Devel;7:470477.
  • 2
    Pratt W.B., Taylor P. (1990) Principles of Drug Action: the Basis of Pharmacology. Churchill Livingstone, New York, NY, USA.
  • 3
    Ortiz de Montellano P.R. (2005) Cytochrome P450: Structure, Mechanism, and Biochemistry, 3rd edn. Kluwer Academic/Plenum Publishers, New York, NY, USA.
  • 4
    Van De Waterbeemd H., Gifford E. (2003) ADMET in silico modelling: towards prediction paradise? Nat Rev Drug Discov;2:192204.
  • 5
    De Groot M.J. (2006) Designing better drugs: predicting cytochrome P450 metabolism. Drug Discov Today;11:601606.
  • 6
    Fratev F., Benfenati E. (2008) A combination of 3D-QSAR, docking, local-binding energy (LBE) and GRID study of the species differences in the carcinogenicity of benzene derivatives chemicals. J Mol Graph Model;27:147160.
  • 7
    Leach A.R. (2001) Molecular Modelling: principles and Applications, 2 edn. Pearson Prentice Hall, London, UK.
  • 8
    Kola I., Landis J. (2004) Can the pharmaceutical industry reduce attrition rates? Nat Rev Drug Discov;3:711715.
  • 9
    Schnecke V., Bostrom J. (2006) Computational chemistry-driven decision making in lead generation. Drug Discov Today;11:4350.
  • 10
    Bhogal N., Grindon C., Combes R., Balls M. (2005) Toxicity testing: creating a revolution based on new technologies. Trends Biotechnol;23:299307.
  • 11
    Baillie T.A. (2008) Metabolism and toxicity of drugs. Two decades of progress in industrial drug metabolism. Chem Res Toxicol;21:129137.
  • 12
    Stevens J.L. (2006) Future of toxicology–mechanisms of toxicity and drug safety: where do we go from here? Chem Res Toxicol;19:13931401.
  • 13
    Smith D.A., Obach R.S. (2005) Seeing through the mist: abundance versus percentage. Commentary on metabolites in safety testing. Drug Metab Dispos;33:14091417.
  • 14
    Dykens J.A., Will Y. (2007) The significance of mitochondrial toxicity testing in drug development. Drug Discov Today;12:777785.
  • 15
    Baillie T.A. (2006) Future of toxicology-metabolic activation and drug design: challenges and opportunities in chemical toxicology. Chem Res Toxicol;19:889893.
  • 16
    Kalgutkar A.S., Obach R.S., Maurer T.S. (2007) Mechanism-based inactivation of cytochrome P450 enzymes: chemical mechanisms, structure-activity relationships and relationship to clinical drug-drug interactions and idiosyncratic adverse drug reactions. Curr Drug Metab;8:407447.
  • 17
    Sinz M., Wallace G., Sahi J. (2008) Current industrial practices in assessing CYP450 enzyme induction: preclinical and clinical. AAPS J;10:391400.
  • 18
    Fowler S., Zhang H. (2008) In vitro evaluation of reversible and irreversible cytochrome P450 inhibition: current status on methodologies and their utility for predicting drug-drug interactions. AAPS J;10:410424.
  • 19
    Hollenberg P.F., Kent U.M., Bumpus N.N. (2008) Mechanism-based inactivation of human cytochromes p450s: experimental characterization, reactive intermediates, and clinical implications. Chem Res Toxicol;21:189205.
  • 20
    Jorgensen W.L. (2004) The many roles of computation in drug discovery. Science;303:18131818.
  • 21
    Schames J.R., Henchman R.H., Siegel J.S., Sotriffer C.A., Ni H., McCammon J.A. (2004) Discovery of a novel binding trench in HIV integrase. J Med Chem;47:18791881.
  • 22
    Wester M.R., Johnson E.F., Marques-Soares C., Dansette P.M., Mansuy D., Stout C.D. (2003) Structure of a substrate complex of mammalian cytochrome P450 2C5 at 2.3 A resolution: evidence for multiple substrate binding modes. Biochemistry;42:63706379.
  • 23
    Kuhn B., Jacobsen W., Christians U., Benet L.Z., Kollman P.A. (2001) Metabolism of sirolimus and its derivative everolimus by cytochrome P450 3A4: insights from docking, molecular dynamics, and quantum chemical calculations. J Med Chem;44:20272034.
  • 24
    Kroemer R.T. (2007) Structure-based drug design: docking and scoring. Curr Protein Pept Sci;8:312328.
  • 25
    Ito Y., Kondo H., Goldfarb P.S., Lewis D.F. (2008) Analysis of CYP2D6 substrate interactions by computational methods. J Mol Graph Model;26:947956.
  • 26
    Ahlstrom M.M., Ridderstrom M., Zamora I. (2007) CYP2C9 structure-metabolism relationships: substrates, inhibitors, and metabolites. J Med Chem;50:53825391.
  • 27
    Kitchen D.B., Decornez H., Furr J.R., Bajorath J. (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov;3:935949.
  • 28
    Bazeley P.S., Prithivi S., Struble C.A., Povinelli R.J., Sem D.S. (2006) Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: predicting affinity and conformational sampling. J Chem Inf Model;46:26982708.
  • 29
    Muralidhara B.K., Negi S., Chin C.C., Braun W., Halpert J.R. (2006) Conformational flexibility of mammalian cytochrome P450 2B4 in binding imidazole inhibitors with different ring chemistry and side chains. J Biol Chem;281:80518061.
  • 30
    De Graaf C., Vermeulen N.P., Feenstra K.A. (2005) Cytochrome p450 in silico: an integrative modeling approach. J Med Chem;48:27252755.
  • 31
    Bathelt C.M., Mulholland A.J., Harvey J.N. (2008) QM/MM modeling of benzene hydroxylation in human cytochrome P450 2C9. J Phys Chem A;112:1314913156.
  • 32
    Cohen S., Kozuch S., Hazan C., Shaik S. (2006) Does substrate oxidation determine the regioselectivity of cyclohexene and propene oxidation by cytochrome p450?. J Am Chem Soc;128:1102811029.
  • 33
    Hirao H., Kumar D., Thiel W., Shaik S. (2005) Two states and two more in the mechanisms of hydroxylation and epoxidation by cytochrome P450. J Am Chem Soc;127:1300713018.
  • 34
    Fishelovitch D., Hazan C., Hirao H., Wolfson H.J., Nussinov R., Shaik S. (2007) QM/MM study of the active species of the human cytochrome P450 3A4, and the influence thereof of the multiple substrate binding. J Phys Chem B;111:1382213832.
  • 35
    Iori F., Da Fonseca R., Ramos M.J., Menziani M.C. (2005) Theoretical quantitative structure-activity relationships of flavone ligands interacting with cytochrome P450 1A1 and 1A2 isozymes. Bioorg Med Chem;13:43664374.
  • 36
    De Graaf C., Oostenbrink C., Keizers P.H., Van Der Wijst T., Jongejan A., Vermeulen N.P. (2006) Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking. J Med Chem;49:24172430.
  • 37
    Yano J.K., Wester M.R., Schoch G.A., Griffin K.J., Stout C.D., Johnson E.F. (2004) The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-A resolution. J Biol Chem;279:3809138094.
  • 38
    De Groot M.J., Ackland M.J., Horne V.A., Alex A.A., Jones B.C. (1999) A novel approach to predicting P450 mediated drug metabolism. CYP2D6 catalyzed N-dealkylation reactions and qualitative metabolite predictions using a combined protein and pharmacophore model for CYP2D6. J Med Chem;42:40624070.
  • 39
    De Groot M.J., Ackland M.J., Horne V.A., Alex A.A., Jones B.C. (1999) Novel approach to predicting P450-mediated drug metabolism: development of a combined protein and pharmacophore model for CYP2D6. J Med Chem;42:15151524.
  • 40
    Langowski J., Long A. (2002) Computer systems for the prediction of xenobiotic metabolism. Adv Drug Deliv Rev;54:407415.
  • 41
    Zhang J.W., Ge G.B., Liu Y., Wang L.M., Liu X.B., Zhang Y.Y., Li W., He Y.Q., Wang Z.T., Sun J., Xiao H.B., Yang L. (2008) Taxane’s substituents at C3′ affect its regioselective metabolism: different in vitro metabolism of cephalomannine and paclitaxel. Drug Metab Dispos;36:418426.
  • 42
    Oh W.S., Kim D.N., Jung J., Cho K.H., No K.T. (2008) New combined model for the prediction of regioselectivity in cytochrome P450/3A4 mediated metabolism. J Chem Inf Model;48:591601.
  • 43
    Sykes M.J., McKinnon R.A., Miners J.O. (2008) Prediction of metabolism by cytochrome P450 2C9: alignment and docking studies of a validated database of substrates. J Med Chem;51:780791.
  • 44
    Lafite P., Andre F., Zeldin D.C., Dansette P.M., Mansuy D. (2007) Unusual regioselectivity and active site topology of human cytochrome P450 2J2. Biochemistry;46:1023710247.
  • 45
    Keizers P.H., De Graaf C., De Kanter F.J., Oostenbrink C., Feenstra K.A., Commandeur J.N., Vermeulen N.P. (2005) Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towards 3,4-methylenedioxy-N-alkylamphetamines: in silico predictions and experimental validation. J Med Chem;48:61176127.
  • 46
    Perrin L., Aninat C., Hamon V., Hayashi Y., Abadie C., Heyd B. et al. (2008) Metabolism of phenylahistin enantiomers by cytochromes P450: a possible explanation for their different cytotoxicity. Drug Metab Dispos;36:23812392.
  • 47
    Bikadi Z., Hazai E. (2008) In silico description of differential enantioselectivity in methoxychlor O-demethylation by CYP2C enzymes. Biochim Biophys Acta;1780:10701079.
  • 48
    Julsing M.K., Vasilev N.P., Schneidman-Duhovny D., Muntendam R., Woerdenbag H.J., Quax W.J. et al. (2008) Metabolic stereoselectivity of cytochrome P450 3A4 towards deoxypodophyllotoxin: in silico predictions and experimental validation. Eur J Med Chem;43:11711179.
  • 49
    Koymans L., Van Lenthe J.H., Donne-op Den Kelder G.M., Vermeulen N.P. (1990) Mechanisms of activation of phenacetin to reactive metabolites by cytochrome P-450: a theoretical study involving radical intermediates. Mol Pharmacol;37:452460.
  • 50
    Loew G.H., Goldblum A. (1985) Metabolic activation and toxicity of acetaminophen and related analogs. A theoretical study. Mol Pharmacol;27:375386.
  • 51
    Potter D.W., Hinson J.A. (1987) Mechanisms of acetaminophen oxidation to N-acetyl-P-benzoquinone imine by horseradish peroxidase and cytochrome P-450. J Biol Chem;262:966973.
  • 52
    Hata M., Tanaka Y., Kyoda N., Osakabe T., Yuki H., Ishii I. et al. (2008) An epoxidation mechanism of carbamazepine by CYP3A4. Bioorg Med Chem;16:51345148.
  • 53
    Erve J.C., Svensson M.A., Von Euler-Chelpin H., Klasson-Wehler E. (2004) Characterization of glutathione conjugates of the remoxipride hydroquinone metabolite NCQ-344 formed in vitro and detection following oxidation by human neutrophils. Chem Res Toxicol;17:564571.
  • 54
    Kalgutkar A.S., Vaz A.D., Lame M.E., Henne K.R., Soglia J., Zhao S.X., Abramov Y.A, Lombardo F., Collin C., Hendsch Z.S., Hop C.E. (2005) Bioactivation of the nontricyclic antidepressant nefazodone to a reactive quinone-imine species in human liver microsomes and recombinant cytochrome P450 3A4. Drug Metab Dispos;33:243253.
  • 55
    McLaughlin L.A., Paine M.J., Kemp C.A., Marechal J.D., Flanagan J.U., Ward C.J., Sutcliffe M.J., Roberts G.C., Wolf C.R. (2005) Why is quinidine an inhibitor of cytochrome P450 2D6? The role of key active-site residues in quinidine binding J Biol Chem;280:3861738624.
  • 56
    Lill M.A., Dobler M., Vedani A. (2006) Prediction of small-molecule binding to cytochrome P450 3A4: flexible docking combined with multidimensional QSAR. ChemMedChem;1:7381.
  • 57
    Marechal J.D., Yu J., Brown S., Kapelioukh I., Rankin E.M., Wolf C.R., Roberts G.C., Paine M.J., Sutcliffe M.J. (2006) In silico and in vitro screening for inhibition of cytochrome P450 CYP3A4 by comedications commonly used by patients with cancer. Drug Metab Dispos;34:534538.
  • 58
    Isin E.M., Sohl C.D., Eoff R.L., Guengerich F.P. (2008) Cooperativity of cytochrome P450 1A2: interactions of 1,4-phenylene diisocyanide and 1-isopropoxy-4-nitrobenzene. Arch Biochem Biophys;473:6975.
  • 59
    Li W., Tang Y., Liu H., Cheng J., Zhu W., Jiang H. (2008) Probing ligand binding modes of human cytochrome P450 2J2 by homology modeling, molecular dynamics simulation, and flexible molecular docking. Proteins;71:938949.
  • 60
    Xue Y., Chao E., Zuercher W.J., Willson T.M., Collins J.L., Redinbo M.R. (2007) Crystal structure of the PXR-T1317 complex provides a scaffold to examine the potential for receptor antagonism. Bioorg Med Chem;15:21562166.
  • 61
    Gao Y.D., Olson S.H., Balkovec J.M., Zhu Y., Royo I., Yabut J., Evers R., Tan E.Y., Tang W., Hartley D.P., Mosley R.T. (2007) Attenuating pregnane X receptor (PXR) activation: a molecular modelling approach. Xenobiotica;37:124138.
  • 62
    Yukinaga H., Takami T., Shioyama S.H., Tozuka Z., Masumoto H., Okazaki O., Sudo K. (2007) Identification of cytochrome P450 3A4 modification site with reactive metabolite using linear ion trap-Fourier transform mass spectrometry. Chem Res Toxicol;20:13731378.
  • 63
    Baer B.R., Wienkers L.C., Rock D.A. (2007) Time-dependent inactivation of P450 3A4 by raloxifene: identification of Cys239 as the site of apoprotein alkylation. Chem Res Toxicol;20:954964.
  • 64
    Pearson J.T., Wahlstrom J.L., Dickmann L.J., Kumar S., Halpert J.R., Wienkers L.C., Foti R.S, Rock D.A. (2007) Differential time-dependent inactivation of P450 3A4 and P450 3A5 by raloxifene: a key role for C239 in quenching reactive intermediates. Chem Res Toxicol;20:17781786.
  • 65
    Kang P., Liao M., Wester M.R., Leeder J.S., Pearce R.E., Correia M.A. (2008) CYP3A4-Mediated carbamazepine (CBZ) metabolism: formation of a covalent CBZ-CYP3A4 adduct and alteration of the enzyme kinetic profile. Drug Metab Dispos;36:490499.
  • 66
    Kent U.M., Lin H.L., Noon K.R., Harris D.L., Hollenberg P.F. (2006) Metabolism of bergamottin by cytochromes P450 2B6 and 3A5. J Pharmacol Exp Ther;318:9921005.
  • 67
    Kent U.M., Sridar C., Spahlinger G., Hollenberg P.F. (2008) Modification of serine 360 by a reactive intermediate of 17-alpha-ethynylestradiol results in mechanism-based inactivation of cytochrome P450s 2B1 and 2B6. Chem Res Toxicol;21:19561963.
  • 68
    Keseru G.M., Makara G.M. (2006) Hit discovery and hit-to-lead approaches. Drug Discov Today;11:741748.
  • 69
    Katharine Holloway M., McGaughey G.B., Coburn C.A., Stachel S.J., Jones K.G., Stanton E.L. et al. (2007) Evaluating scoring functions for docking and designing beta-secretase inhibitors. Bioorg Med Chem Lett;17:823827.
  • 70
    Davis A.M., Keeling D.J., Steele J., Tomkinson N.P., Tinker A.C. (2005) Components of successful lead generation. Curr Top Med Chem;5:421439.
  • 71
    Joseph-McCarthy D., Baber J.C., Feyfant E., Thompson D.C., Humblet C. (2007) Lead optimization via high-throughput molecular docking. Curr Opin Drug Discov Devel;10:264274.
  • 72
    Shaikh S.A., Jain T., Sandhu G., Latha N., Jayaram B. (2007) From drug target to leads–sketching a physicochemical pathway for lead molecule design in silico. Curr Pharm Des;13:34543470.
  • 73
    Ahlstrom M.M., Ridderstrom M., Zamora I., Luthman K. (2007) CYP2C9 structure-metabolism relationships: optimizing the metabolic stability of COX-2 inhibitors. J Med Chem;50:44444452.
  • 74
    Armour D., De Groot M.J., Edwards M., Perros M., Price D.A., Stammen B.L. et al. (2006) The discovery of CCR5 receptor antagonists for the treatment of HIV infection: hit-to-lead studies. ChemMedChem;1:706709.
  • 75
    Wang X., Kolasa T., El Kouhen O.F., Chovan L.E., Black-Shaefer C.L., Wagenaar F.L. et al. (2007) Rapid hit to lead evaluation of pyrazolo[3,4-d]pyrimidin-4-one as selective and orally bioavailable mGluR1 antagonists. Bioorg Med Chem Lett;17:43034307.
  • 76
    Zeevaart J.G., Wang L., Thakur V.V., Leung C.S., Tirado-Rives J., Bailey C.M. et al. (2008) Optimization of azoles as anti-human immunodeficiency virus agents guided by free-energy calculations. J Am Chem Soc;130:94929499.
  • 77
    Rowland P., Blaney F.E., Smyth M.G., Jones J.J., Leydon V.R., Oxbrow A.K. et al. (2006) Crystal structure of human cytochrome P450 2D6. J Biol Chem;281:76147622.
  • 78
    Williams P.A., Cosme J., Vinkovic D.M., Ward A., Angove H.C., Day P.J. et al. (2004) Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone. Science;305:683686.
  • 79
    Ekroos M., Sjogren T. (2006) Structural basis for ligand promiscuity in cytochrome P450 3A4. Proc Natl Acad Sci USA;103:1368213687.
  • 80
    Schoch G.A., Yano J.K., Sansen S., Dansette P.M., Stout C.D., Johnson E.F. (2008) Determinants of cytochrome P450 2C8 substrate binding: structures of complexes with montelukast, troglitazone, felodipine, and 9-cis-retinoic acid. J Biol Chem;283:1722717237.
  • 81
    Schoch G.A., Yano J.K., Wester M.R., Griffin K.J., Stout C.D., Johnson E.F. (2004) Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. J Biol Chem;279:94979503.
  • 82
    Yano J.K., Hsu M.H., Griffin K.J., Stout C.D., Johnson E.F. (2005) Structures of human microsomal cytochrome P450 2A6 complexed with coumarin and methoxsalen. Nat Struct Mol Biol;12:822823.
  • 83
    Sansen S., Yano J.K., Reynald R.L., Schoch G.A., Griffin K.J., Stout C.D., Johnson E.F. (2007) Adaptations for the oxidation of polycyclic aromatic hydrocarbons exhibited by the structure of human P450 1A2. J Biol Chem;282:1434814355.
  • 84
    Smith B.D., Sanders J.L., Porubsky P.R., Lushington G.H., Stout C.D., Scott E.E. (2007) Structure of the human lung cytochrome P450 2A13. J Biol Chem;282:1730617313.
  • 85
    Wester M.R., Yano J.K., Schoch G.A., Yang C., Griffin K.J., Stout C.D., Johnson E.F. (2004) The structure of human cytochrome P450 2C9 complexed with flurbiprofen at 2.0-A resolution. J Biol Chem;279:3563035637.
  • 86
    Kartha J.S., Skordos K.W., Sun H., Hall C., Easterwood L.M., Reilly C.A., Yost G.S. (2008) Single mutations change CYP2F3 from a dehydrogenase of 3-methylindole to an oxygenase. Biochemistry;47:97569770.
  • 87
    Kartha J.S., Yost G.S. (2008) Mechanism-based inactivation of lung-selective cytochrome P450 CYP2F enzymes. Drug Metab Dispos;36:155162.
  • 88
    Kassahun K., Skordos K., McIntosh I., Slaughter D., Doss G.A., Baillie T.A., Yost G.S. (2005) Zafirlukast metabolism by cytochrome P450 3A4 produces an electrophilic alpha,beta-unsaturated iminium species that results in the selective mechanism-based inactivation of the enzyme. Chem Res Toxicol; 18:14271437.
  • 89
    Levesque J.F., Day S.H., Chauret N., Seto C., Trimble L., Bateman K.P., Silva J. M., Berthelette C., Lachance N., Boyd M., Li L., Sturino C.F., Wang Z., Zamboni R., Young R.N., Nicoll-Griffith D.A. (2007) Metabolic activation of indole-containing prostaglandin D2 receptor 1 antagonists: impacts of glutathione trapping and glucuronide conjugation on covalent binding. Bioorg Med Chem Lett;17:30383043.
  • 90
    Sun H., Yost G.S. (2008) Metabolic activation of a novel 3-substituted indole-containing TNF-alpha inhibitor: dehydrogenation and inactivation of CYP3A4. Chem Res Toxicol;21:374385.
  • 91
    Ring B.J., Patterson B.E., Mitchell M.I., Vandenbranden M., Gillespie J., Bedding A.W., Jewell H., Payne C.D., Forgue S.T., Eckstein J., Wrighton S.A., Phillips D.L. (2005) Effect of tadalafil on cytochrome P450 3A4-mediated clearance: studies in vitro and in vivo. Clin Pharmacol Ther;77:6375.
  • 92
    Sun H., Sharma R., Bauman J., Walker D.P., Aspnes G.E., Zawistoski M.P., Kalgutkar A.S. (2009) Differences in CYP3A4 catalyzed bioactivation of 5-aminooxindole and 5-aminobenzsultam scaffolds in proline-rich tyrosine kinase 2 (PYK2) inhibitors: retrospective analysis by CYP3A4 molecular docking, quantum chemical calculations and glutathione adduct detection using linear ion trap/orbitrap mass spectrometry. Bioorg Med Chem Lett;19:31773182.
  • 93
    Maiorov V., Sheridan R.P. (2005) Enhanced virtual screening by combined use of two docking methods: getting the most on a limited budget. J Chem Inf Model;45:10171023.