Prediction of cytochrome P450 xenobiotic metabolism: tethered docking and reactivity derived from ligand molecular orbital analysis.

Metabolism of xenobiotic and endogenous compounds is frequently complex, not completely elucidated, and therefore often ambiguous. The prediction of sites of metabolism (SoM) can be particularly helpful as a first step toward the identification of metabolites, a process especially relevant to drug discovery. This paper describes a reactivity approach for predicting SoM whereby reactivity is derived directly from the ground state ligand molecular orbital analysis, calculated using Density Functional Theory, using a novel implementation of the average local ionization energy. Thus each potential SoM is sampled in the context of the whole ligand, in contrast to other popular approaches where activation energies are calculated for a predefined database of molecular fragments and assigned to matching moieties in a query ligand. In addition, one of the first descriptions of molecular dynamics of cytochrome P450 (CYP) isoforms 3A4, 2D6, and 2C9 in their Compound I state is reported, and, from the representative protein structures obtained, an analysis and evaluation of various docking approaches using GOLD is performed. In particular, a covalent docking approach is described coupled with the modeling of important electrostatic interactions between CYP and ligand using spherical constraints. Combining the docking and reactivity results, obtained using standard functionality from common docking and quantum chemical applications, enables a SoM to be identified in the top 2 predictions for 75%, 80%, and 78% of the data sets for 3A4, 2D6, and 2C9, respectively, results that are accessible and competitive with other recently published prediction tools.