title: Analysis of clinically relevant substrates of CYP2B6 enzyme by computational methods.
abstract: Mounting evidence thus far indicates that human cytochrome P450 2B6 (CYP2B6), an enzyme expressed at a relatively low level functionally, is primarily responsible for the metabolism of several clinically relevant drugs, including propofol, efavirenz, bupropion, mephobarbital, and the propofol analog 2,6-di-sec-butyl phenol. We used molecular dynamics and molecular docking methods to predict such interactions and to compare with experimentally measured metabolisms. Insight II and Discover Studio 2.5 were used to carry out the docking of these substrates into CYP2B6 to explore the critical residues and interaction energies of the complexes. Phe297, Glu301, Thr302 and Val367 were identified as major drug-binding residues, which is consistent with previous data on site-directed mutagenesis, crystallography structure, and from modeling and docking studies. In addition, our docking results suggest that nonpolar amino acid clusters and heme also participate in binding to mediate drug oxidative metabolism. The binding modes of the five clinically relevant substrates mentioned above for metabolism on CYP2B6 are presented.
authors.affiliation: State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China.
authors.forename: Rui-Juan
authors.initials: RJ
authors.lastname: Niu
authors.forename: Qing-Chuan
authors.initials: QC
authors.lastname: Zheng
authors.forename: Ji-Long
authors.initials: JL
authors.lastname: Zhang
authors.forename: Hong-Xing
authors.initials: HX
authors.lastname: Zhang
mesh_terms: D000480:Alkynes; D048588:Benzoxazines / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D016642:Bupropion / Q000737:chemistry / Q000378:metabolism; D002073:Butanes / Q000737:chemistry / Q000378:metabolism; D003521:Cyclopropanes; D065702:Cytochrome P-450 CYP2B6; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D006860:Hydrogen Bonding; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D004364:Pharmaceutical Preparations / Q000737:chemistry* / Q000378:metabolism; D010636:Phenols / Q000737:chemistry / Q000378:metabolism; D015742:Propofol / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D013379:Substrate Specificity
chemical_list: D000480:Alkynes; D048588:Benzoxazines; D002073:Butanes; D003521:Cyclopropanes; D004364:Pharmaceutical Preparations; D010636:Phenols; C509539:di-sec-butyl phenol; D016642:Bupropion; D003577:Cytochrome P-450 Enzyme System; C585599:CYP2B6 protein, human; D065702:Cytochrome P-450 CYP2B6; C098320:efavirenz; D015742:Propofol