Construction and assessment of models of CYP2E1: predictions of metabolism from docking, molecular dynamics, and density functional theoretical calculations

Abstract

3D models of CYP2E1 were constructed for the purpose of structure-based prediction of 2E1 metabolism of diverse substrates based on configuration sampling of ligand-atom-oxyferryl center distances and quantum chemical criteria. Models were constructed on the basis of sequence alignments of 2E1 with templates of known structure, including rabbit CYP2C5 (3LVdH) and bacterial CYP450s. Following geometric and energetic assessments, the utility of the model was tested in structure-based predictions of metabolism. Autodock was used to dock chlorzoxazone, p-nitrophenol, N-nitrosodimethylamine, acetominophen, caffeine, theophylline, and methoxyflurane into the model CYP2E1 employing a model oxyferryl heme with charges based on density functional theoretical parametrization. In all cases, the lowest energy bound docked configurations corresponded to ones with the substrate intimately associated with the oxyferryl center. Configurations among the lowest energy docked forms of each of the ligands had orientations relative to the oxyferryl center consistent with the experimentally observed metabolites. Docking of long-chain dialkylnitrosoamines revealed no heme binding site bound configurations, in agreement with the negligible metabolism of these ligands. The lowest energy docked configurations of chlorzoxazone, p-nitrophenol, and N-nitrosodimethylamine, high-affinity substrates of 2E1, were used to initiate 300 ps molecular dynamics (MD) trajectories. The MD-sampled ligand-oxyferryl heme reactant configurations were in good accord with density functional theoretical (DFT) optimized oxyferryl-heme-ligand geometries. Analysis of the MD-sampled ligand-2E1 configurations from multiple docked orientations indicates the configurations with closest exposure of reactive centers to the oxyferryl heme to be correlated with observed metabolites with proper consideration of H-abstraction energetics. DFT assessment of relative radical energetics is directly compared with differential H-abstraction activation energetics by compound I and by a p-nitrosophenoxy radical compound I surrogate for the specific case of methoxyflurane and is shown to be in good agreement