Combined three-dimensional quantitative structure-activity relationship analysis of cytochrome P450 2B6 substrates and protein homology modeling.
Understanding the basis of the substrate specificity of cytochrome P450 2B6 (CYP2B6) is important for determining the role of this enzyme in drug metabolism and for predicting new substrates. Pharmacophores were generated for 16 structurally diverse CYP2B6 substrates with Catalyst after overlapping the reaction sites. Two pharmacophores were determined for the CYP2B6 binding site. Both include two hydrophobes and one hydrogen bond acceptor. The three-dimensional structure of CYP2B6 was then modeled based on the crystal structure of CYP2C5. Benzyloxyresorufin and 7-ethoxy-4-trifluoromethylcoumarin, the two lowest K(m) substrates in the training set, were then docked in the active site of CYP2B6. The pharmacophores were combined with the CYP2B6 model by comparing the docking results and the mapping of the two substrates with the pharmacophores. The results indicated that the active site of CYP2B6 complements the pharmacophores. The pharmacophores and the CYP2B6 model were used in conjunction to predict the K(m) values of substrates in a test set of five compounds and yielded satisfactory predictions for benzphetamine, cinnarizine, bupropion, and verapamil but not lidocaine. The CYP2B6 model, the pharmacophores, and the combination of the model with these pharmacophores provide insight into the interactions of CYP2B6 with substrates. The pharmacophores may be used as queries to search a database to predict new substrates for CYP2B6 when the reaction site is known (N- or O-dealkylation). For C-hydroxylation, the CYP2B6 model is helpful in evaluating the possible reaction sites in order for the pharmacophores to predict corresponding K(m) values.
Wang
Qinmi
Q
Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-1031, USA.
Halpert
James R
JR
D000595:Amino Acid Sequence; D001189:Aryl Hydrocarbon Hydroxylases; D001665:Binding Sites; D065702:Cytochrome P-450 CYP2B6; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry* / Q000378:metabolism; D015195:Drug Design; D006801:Humans; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010089:Oxidoreductases, N-Demethylating / Q000737:chemistry* / Q000378:metabolism; D004364:Pharmaceutical Preparations / Q000737:chemistry* / Q000378:metabolism; D021281:Quantitative Structure-Activity Relationship; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
D004364:Pharmaceutical Preparations; D003577:Cytochrome P-450 Enzyme System; D001189:Aryl Hydrocarbon Hydroxylases; C585599:CYP2B6 protein, human; D065702:Cytochrome P-450 CYP2B6; D010089:Oxidoreductases, N-Demethylating