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Assessment of CYP2C9 Structural Models for Site of Metabolism Prediction
Author(s) -
Zhang Xiaoxiao,
Xu Minjie,
Wu Zengrui,
Liu Guixia,
Tang Yun,
Li Weihua
Publication year - 2021
Publication title -
chemmedchem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.817
H-Index - 100
eISSN - 1860-7187
pISSN - 1860-7179
DOI - 10.1002/cmdc.202000964
Subject(s) - heme , computational biology , molecular dynamics , active site , chemistry , drug discovery , quantitative structure–activity relationship , drug target , flexibility (engineering) , biochemistry , stereochemistry , enzyme , biology , computational chemistry , mathematics , statistics
Structure‐based prediction of a compound's potential sites of metabolism (SOMs) mediated by cytochromes P450 (CYPs) is highly advantageous in the early stage of drug discovery. However, the accuracy of the SOMs prediction can be influenced by several factors. CYP2C9 is one of the major drug‐metabolizing enzymes in humans and is responsible for the metabolism of ∼13 % of clinically used drugs. In this study, we systematically evaluated the effects of protein crystal structure models, scoring functions, heme forms, conserved active‐site water molecules, and protein flexibility on SOMs prediction of CYP2C9 substrates. Our results demonstrated that, on average, ChemScore and GlideScore outperformed four other scoring functions: Vina, GoldScore, ChemPLP, and ASP. The performance of the crystal structure models with pentacoordinated heme was generally superior to that of the hexacoordinated iron‐oxo heme (referred to as Compound I) models. Inclusion of the conserved active‐site water molecule improved the prediction accuracy of GlideScore, but reduced the accuracy of ChemScore. In addition, the effect of the conserved water on SOMs prediction was found to be dependent on the receptor model and the substrate. We further found that one of snapshots from molecular dynamics simulations on the apo form can improve the prediction accuracy when compared to the crystal structural model.