A Pragmatic Approach Using First-Principle Methods to Address Site of Metabolism with Implications for Reactive Metabolite Formation

A majority of xenobiotics are metabolized by cytochrome P450 (CYP) enzymes. The discovery of drug candidates with low propensity to form reactive metabolites and low clearance can be facilitated by understanding CYP-mediated xenobiotic metabolism. Being able to predict the sites where reactive metabolites form is beneficial in drug design to produce drug candidates free of reactive metabolite issues. Herein, we report a pragmatic protocol using first-principle density functional theory (DFT) calculations for predicting sites of epoxidation and hydroxylation of aromatic substrates mediated by CYP. The method is based on the relative stabilities of the CYP-substrate intermediates or the substrate epoxides. Consequently, it concerns mainly the electronic reactivity of the substrates. Comparing to the experimental findings, the presented protocol gave excellent first-ranked epoxidation site predictions of 83%, and when the test was extended to CYP-mediated sites of aromatic hydroxylation, satisfactory results were also obtained (73%). This indicates that our assumptions are valid and also implies that the intrinsic reactivities of the substrates are in general more important than their binding poses in proteins, although the protocol may benefit from the addition of docking information.