A Mechanism-Based Model for the Prediction of the Metabolic Sites of Steroids Mediated by Cytochrome P450 3A4.

Zi-Ru Dai,Yu-Qi He,Jia-Yue Wang,Yan Jia,Hui-Zi Man,Ling Yang,Guang-Bo Ge,Jing-Jing Wu,Chun-Zhi Ai

doi:10.3390/ijms160714677

Abstract

Early prediction of xenobiotic metabolism is essential for drug discovery and development. As the most important human drug-metabolizing enzyme, cytochrome P450 3A4 has a large active cavity and metabolizes a broad spectrum of substrates. The poor substrate specificity of CYP3A4 makes it a huge challenge to predict the metabolic site(s) on its substrates. This study aimed to develop a mechanism-based prediction model based on two key parameters, including the binding conformation and the reaction activity of ligands, which could reveal the process of real metabolic reaction(s) and the site(s) of modification. The newly established model was applied to predict the metabolic site(s) of steroids; a class of CYP3A4-preferred substrates. 38 steroids and 12 non-steroids were randomly divided into training and test sets. Two major metabolic reactions, including aliphatic hydroxylation and N-dealkylation, were involved in this study. At least one of the top three predicted metabolic sites was validated by the experimental data. The overall accuracy for the training and test were 82.14% and 86.36%, respectively. In summary, a mechanism-based prediction model was established for the first time, which could be used to predict the metabolic site(s) of CYP3A4 on steroids with high predictive accuracy.

Highlights

Identification of the metabolic pathways of a given compound is important for the lead optimization in the early stage of drug discovery and development [1]
All of the 50 cytochrome P450 3A4 (CYP3A4) substrates were docked into this CYP3A4 crystallographic structure, while the CYP3A4 crystal structure was treated as rigid yet substrates as flexible
N-dealkylation and aliphatic hydroxylation of CYP3A4 substrates. These findings suggested that it is necessary to evaluate the binding accessibility and activation energy simultaneously together, for the precise prediction of the metabolic site(s) of substrates in CYP3A4

Summary

Introduction

Identification of the metabolic pathways of a given compound is important for the lead optimization in the early stage of drug discovery and development [1]. It is well known that CYP3A4 displays a weak substrate specificity and poor regioselectivity, due to its large active cavity, which makes it a huge challenge to predict the metabolic site(s) on CYP3A4 substrates, especially for those compounds with rigid structures [3,4]. CYP3A4 prefers to catalyze 6-hydroxylation on steroids with 3-keto-4-ene, such as testosterone and medroxyprogesterone acetate (MPA), due to the pharmacophoric features and the electronic reactivity of H atoms at the C-6 site [7,8,9,10,11].

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Conclusion