title: Development of two-dimensional template system for the prediction of CYP2B6-mediated reaction sites.
abstract: We developed a template-based system for predicting the regioselectivity of CYP2B6-mediated oxidation of chemicals. Two planar templates consisting of hexagonal blocks (A and B) were deduced from the overlapping regions of polyaromatic hydrocarbon-type substrates. Substrate atoms were placed only on the corners of the hexagonal blocks in the simulated interaction with the CYP2B6 templates. Through the application of various substrates having non-planar structures to Templates A and B, these templates were found to link to each other at specific positions (pinching points). The occupancy rates at each position of the templates were evaluated using more than 40 substrates, and a heavily utilized area (trigger region) was identified on Template A. This CYP2B6 template system is suggested to interact with substrates in at least three positions (trigger, pinching/bending and oxidation sites). In the present method, chemicals drawn as two or three-dimensional structures were directly overlaid on the templates to verify the feasibility of the simulated interaction. Both CYP2B6 substrates and non-substrates were applied to assess the validity of this template system. Results were consistent between the predicted and the in vitro experimental data with high accuracy, indicating the potential use of this system for studies on drug metabolism and new drug development.
authors.affiliation: Division of Drug Metabolism & Molecular Toxicology, Graduate School of Pharmaceutical Science, Tohoku University, Japan. n_koyama@research.otsuka.co.jp
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Koyama
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Yamazoe
mesh_terms: D015127:9,10-Dimethyl-1,2-benzanthracene / Q000737:chemistry*; D001189:Aryl Hydrocarbon Hydroxylases / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D002273:Carcinogens / Q000737:chemistry*; D020134:Catalytic Domain; D003198:Computer Simulation / Q000706:statistics & numerical data*; D065702:Cytochrome P-450 CYP2B6; D015195:Drug Design; D006801:Humans; D006900:Hydroxylation; D006899:Mixed Function Oxygenases / Q000378:metabolism*; D008956:Models, Chemical; D008968:Molecular Conformation; D010084:Oxidation-Reduction; D010089:Oxidoreductases, N-Demethylating / Q000737:chemistry* / Q000378:metabolism*; D021281:Quantitative Structure-Activity Relationship; D015203:Reproducibility of Results; D012984:Software; D013379:Substrate Specificity
chemical_list: D002273:Carcinogens; D015127:9,10-Dimethyl-1,2-benzanthracene; D006899:Mixed Function Oxygenases; D001189:Aryl Hydrocarbon Hydroxylases; C585599:CYP2B6 protein, human; D065702:Cytochrome P-450 CYP2B6; D010089:Oxidoreductases, N-Demethylating