In silico prediction and structural profiling of human CYP2E1 missense variants implicated in hepatotoxic injuries

Abstract

CYP2E1 sits at the crossroads of xenobiotic metabolism and oxidative-stress generation, yet the functional consequences of most coding variants are unknown. We developed a structure-aware in silico pipeline to prioritize and mechanistically profile human CYP2E1 nsSNPs. From 490 missense SNPs collected, a consensus cascade of 27 prediction tools and evolutionary conservation filters yielded 24 high-confidence candidates, six highly conserved substitutions were subjected to all-atom MD. Trajectories analysis revealed variant-specific atomistic phenotypes spanning core collapse, access-tunnel rigidification, and localized electrostatic destabilization. G300R produced the largest structural disruption, while R359P induced pronounced rigidification of access-region dynamics, both emerged as top candidates for altered coupling efficiency and hepatotoxic risk. We provided a ranked variant list and mechanistic hypotheses linking coding substitutions to altered heme positioning and potential increases in ROS leakage. This structure-based prioritization framework is intended to guide experimental biochemical, cellular and pharmacogenetic follow-up in studies of drug-induced and chronic liver injury.