Cytochrome P450s (CYPs) are membrane-associated heme proteins and hepatic microsomal enzymes participating in drug metabolism and detoxification. Among the human CYPs, CYP3A4 is the most important enzyme because of its participation in a wide range of drug metabolism and high level of expression in the human liver.1,2) On the other hand, in the CYP2C subfamily, CYP2C9 (e.g. fluoxetine, losartan, phenytoin, tolbutamide, torsemide, S-warfarin, and NSAIDs 3) ) and CYP2C19 (e.g. antidepressants, proton pump inhibitors, benzodiazepines, S-mephenytoin, and proguanil [4][5][6] ) are known to catalyze reactions for a lot of therapeutic agents. However, recently it has become clear that the contribution of CYP2C8 to drug metabolism has been underestimated, and CYP2C8 and CYP3A4 share some of their substrates (e.g. repaglinide, paclitaxel, morphine, carbamazepine, verapamil, zopiclone, and cerivastatin. 7-13) ). The crystal structure of mammalian CYP2C5 reported by Williams et al. 14) has enabled modeling of human CYPs. Thus, we have constructed CYP2C8, CYP2C9, and CYP2C19 models based on the CYP2C5 crystallographic coordinates, and compared them with the previously constructed CYP3A4 model 15) to elucidate the differences in their active sites. These models could be used to obtain helpful hints for avoiding undesirable drug-drug interactions.
ExperimentalHomology Modeling The amino acid sequences of CYP2C8, CYP2C9, and CYP2C19 were taken from the ExPASy web site (http://tw.expasy.org/). The amino acid sequence alignment used for the homology modeling was obtained by ClustalW.16) According to the alignment (Fig. 1), homology models of CYP2C8, CYP2C9, and CYP2C19 were constructed based on the mammalian CYP2C5 crystal structure (PDB code:1DT6) using the homology module of Insight II (ver. 2000, Accelrys Inc., San Diego, California, U.S.A.). Using the Search/Generate-Loops function of Insight II, conformations of the insertion parts in the alignment were generated. After some manual adjustments to remove large steric hindrances, the whole structure was subjected to energy minimization over 1000 steps with the steepest descent minimizer and then 5000 steps with the conjugate gradient minimizer, to a maximum gradient of 0.1 kcal/mol Ϫ1 Å Ϫ1 , using the Discover-ESFF force field (ver. 980, Accelrys Inc., San Diego, California, U.S.A.). During the minimization procedure, the following conditions were adopted. The dielectric constant was set to 4*r, where r is the distance between two interacting atoms. The force constant of tethering constraints for the backbone of structurally conserved regions (SCRs, asterisks in Fig. 1) and heme was set to 40 kcal/Å 2 to prevent a large movement from the initial positions. Docking of Paclitaxel Paclitaxel, an anticancer drug from a natural compound, was docked into the CYP2C8 model using Gold (ver. 2.0, the To compare the features of the active sites of CYP2C8, CYP2C9, and CYP2C19, homology modeling was performed based on the crystallographic coordinates of mammalian CYP2C5. It was foun...