References
- Bayly CI, Ciepllak P, Cornell W, Kollman PA. (1993). A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges. The RESP model. J Phys Chem 97:10269–80
- Bogaards JJP, Bertrand M, Jackson P, et al. (2000). Determining the best animal model for human cytochrome P450 activities: a comparison of mouse, rat, rabbit, dog, micropig, monkey and man. Xenobiotica 30:1131–52
- Born SL, Caudill D, Smith BJ, Lehman-McKeeman LD. (2000). In vitro kinetics of coumarin 3,4-epoxidation: application to species differences in toxicity and carcinogenicity. Toxicol Sci 58:23–31
- Concannon S, Ramachandran VN, Smyth WF. (2000). A study of the electronspray ionization of selected coumarin derivatives and their subsequent fragmentation using an ion trap mass spectrometer. Rapid Commun Mass Spectrom 14:1157–66
- Cruciani G. (2013). Metabolites: structure determination and prediction. Drug Discov Today 10:e145–6
- Dalgaard L. (2015). Comparison of minipig, dog, monkey and human drug metabolism and disposition, J Pharmacol Toxicol Methods. [Epub ahead of print]. doi:10.1016/jvascn2014.12.005
- DeLisle RK, Otten J, Rhodes S. (2011). In silico modeling of P450 substrates, inhibitors, activators, and inducers. Combin Chem High Throughput Screen 14:396–416
- Foti RS, Wienkers LC, Wahlstrom JL. (2010). Application of cytochrome P450 drug interaction screening in drug discovery. Combin Chem High Throughput Screen 13:145–58
- Giammona DA. (1984). Force field modifications for united atom heme plus flexible water N.B. the parameters around the iron are appropriate for five-coordinated (deoxy) heme. PhD thesis. Davis: University of California
- Gohlke H, Case DA. (2004). Converging free energy estimates: MM-PB(GB)SA studies on the protein–protein complex Ras-Raf. J Comput Chem 25:238–50
- Hou T, Wang J, Li Y, Wang W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods: 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inform Model 51:69–82
- Johnson MS, Overington J. (1993). A structural basis for sequence comparisons: an evaluation of scoring methodologies. J Mol Biol 233:716–38
- Juvonen RO, Gynther J, Pasanen M, et al. (2000). Pronounced differences in inhibition potency of lactone and non-lactone compounds for mouse and human coumarin 7-hydroxylases (CYP2A5 and CYP2A6). Xenobiotica 30:81–92
- Kaipainen P, Koivusaari U, Lang M. (1985). Catalytic and immunological comparison of coumarin 7-hydroxylation in different species. Comp Biochem Physiol Part C, Comp 81:293–6
- Kirchmair J, Williamson MJ, Tyzack JD, et al. (2012). Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. J Chem Inform Model 52:617–48
- Korb O, Stützle T, Exner TE. (2009). Empirical scoring functions for advanced protein–ligand docking with plants. J Chem Inform Model 49:84–96
- Lake BG, Gray TJB, Evans JG, et al. (1989). Studies on the mechanism of coumarin-induced toxicity in rat hepatocytes: comparison with dihydrocoumarin and other coumarin metabolites. Toxicol Appl Pharmacol 97:311–23
- Lang MA, Gielen JE, Nebert DW. (1981). Genetic evidence for many unique liver microsomal P-450-mediated monooxygenase activities in heterogeneic stock mice. J Biol Chem 256:12068–75
- Lehtonen JV, Still DJ, Rantanen VV, et al. (2004). BODIL: a molecular modeling environment for structure-function analysis and drug design. J Comput Aided Mol Des 18:401–19
- Long A. (2013). Drug metabolism in silico – the knowledge-based expert system approach. Historical perspectives and current strategies. Drug Discov Today: Technol 10:e147–53
- Makaji E, Trambitas CS, Shen P, et al. (2009). Effects of cytochrome P450 inhibitors on the biotransformation of fluorogenic substrates by adult male rat liver microsomes and cDNA-expressed rat cytochrome P450 isoforms. Toxicol Sci 113:293–304
- Miller III BR, McGee TD, Swails JM, et al. (2012). MMPBSA.py: an efficient program for end-state free energy calculations. J Chem Theory Comput 8:3314–21
- Morreel K, Kim H, Lu F, et al. (2010). Mass spectrometry-based fragmentation as an identification tool in lignomics. Anal Chem 89:8095–105
- Niinivehmas SP, Virtanen SI, Lehtonen JV, et al. (2011). Comparison of virtual high-throughput screening methods for the identification of phosphodiesterase-5 inhibitors. J Chem Inform Model 51:1353–63
- Onufriev A, Bashford D, Case DA. (2004). Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55:383–94
- Pelkonen O, Rautio A, Raunio H, Pasanen M. (2000). CYP2A6: a human coumarin 7-hydroxylase. Toxicology 144:139–47
- Phillips JC, Braun R, Wang W, et al. (2005). Scalable molecular dynamics with NAMD. J Comp Chem 26:1781–802
- Rahnasto M, Raunio H, Poso A, Juvonen RO. (2003). More potent inhibition of human CYP2A6 than mouse CYP2A5 enzyme activities by derivatives of phenylethylamine and benzaldehyde. Xenobiotica 33:529–39
- Rahnasto M, Raunio H, Poso A, et al. (2005). Quantitative structure–activity relationship analysis of inhibitors of the nicotine metabolizing CYP2A6 enzyme. J Med Chem 48:440–9
- Rahnasto MK, Raunio HA, Wittekindt C, et al. (2011). Identification of novel CYP2A6 inhibitors by virtual screening. Bioorg Med Chem 19:7186–93
- Raner GM, Chiang EW, Vaz ADN, Coon MJ. (1997). Mechanism-based inactivation of cytochrome P450 2B4 by aldehydes: relationship to aldehyde deformylation via a peroxyhemiacetal intermediate. Biochemistry 36:4895–902
- Rastelli G, Del Rio A, Degliesposti G, Sgobba M. (2010). Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. J Comput Chem 31:797–810
- Raunio H, Juvonen R, Pasanen M, et al. (1998). Cytochrome P4502A6 (CYP2A6) expression in human hepatocellular carcinoma. Hepatology 27:427–32
- Raunio H, Rahnasto-Rilla M. (2012). CYP2A6: genetics, structure, regulation, and function. Drug Metab Drug Interact 27:73–88
- Roe DR, Cheatham TE. (2013). PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput 9:3084–95
- Sali A, Blundell TL. (1993). Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779–815
- Sevior DK, Pelkonen O, Ahokas JT. (2012). Hepatocytes: the powerhouse of biotransformation. Int J Biochem Cell Biol 44:257–61
- Skaanild MT. (2006). Porcine cytochrome P450 and metabolism. Curr Pharm Design 12:1421–7
- Soucek P. (1999). Expression of cytochrome P450 2A6 in Escherichia coli: purification, spectral and catalytic characterization, and preparation of polyclonal antibodies. Arch Biochem Biophys 370:190–200
- Stepan AF, Walker DP, Bauman J, et al. (2011). Structural alert/reactive metabolite concept as applied in medicinal chemistry to mitigate the risk of idiosyncratic drug toxicity: a perspective based on the critical examination of trends in the top 200 drugs marketed in the United States. Chem Res Toxicol 24:1345–410
- Tani N, Juvonen RO, Raunio H, et al. (2014). Rational design of novel CYP2A6 inhibitors. Bioorg Med Chem 22:6655–64
- Testa B, Pedretti A, Vistoli G. (2012). Reactions and enzymes in the metabolism of drugs and other xenobiotics. Drug Discov Today 17:549–60
- Timonen J, Romppanen R, Aulaskari P, Jänis J. (2013). Low-energy collision-induced dissociation tandem mass spectrometry of 7-acetonyloxycoumarins. Rapid Commun Mass Spectrom 27:2665–75
- Tsui V, Case DA. (2000). Theory and applications of the Generalized Born solvation model in macromolecular simulations. Biopolymers 56:275–91
- Turpeinen M, Korhonen LE, Tolonen A, et al. (2006). Cytochrome P450 (CYP) inhibition screening: comparison of three tests. Eur J Pharm Sci 29:130–8
- Wang JM, Wang W, Kollman PA. (2001). Antechamber: an accessory software package for molecular mechanical calculations. Abstracts of papers of the American Chemical Society 222:U403
- Word JM, Lovell SC, Richardson JS, Richardson DC. (1999). Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285:1735–47
- Yano JK, Denton TT, Cerny MA, et al. (2006). Synthetic inhibitors of cytochrome P-450 2A6: inhibitory activity, difference spectra, mechanism of inhibition, and protein cocrystallization. J Med Chem 49:6987–7001
- Yano JK, Hsu MH, Griffin KJ, et al. (2005). Structures of human microsomal cytochrome P450 2A6 complexed with coumarin and methoxsalen. Nat Struct Mol Biol 12:822–3
- Ylilauri M, Pentikäinen OT. (2013). MMGBSA as a tool to understand the binding affinities of filamin–peptide interactions. J Chem Inform Model 53:2626–33
- Ylilauri M, Pentikäinen OT. (2012). Structural mechanism of N-methyl-D-aspartate receptor type 1 partial agonism. PLoS One 7:e47604
- Zanger UM, Schwab M. (2013). Cytochrome P450 enzymes in drug metabolism: regulation of gene expression, enzyme activities, and impact of genetic variation. Pharmacol Ther 138:103–41