Constructing xenobiotic maps of metabolism to predict enzymes catalyzing metabolites capable of binding to DNA

Mael Conan,Sophie Langouet,Anne Siegel,Nathalie Théret

doi:10.1186/s12859-021-04363-6

Abstract

BackgroundThe liver plays a major role in the metabolic activation of xenobiotics (drugs, chemicals such as pollutants, pesticides, food additives...). Among environmental contaminants of concern, heterocyclic aromatic amines (HAA) are xenobiotics classified by IARC as possible or probable carcinogens (2A or 2B). There exist little information about the effect of these HAA in humans. While HAA is a family of more than thirty identified chemicals, the metabolic activation and possible DNA adduct formation have been fully characterized in human liver for only a few of them (MeIQx, PhIP, AalphaC).ResultsWe have developed a modeling approach in order to predict all the possible metabolites of a xenobiotic and enzymatic profiles that are linked to the production of metabolites able to bind DNA. Our prediction of metabolites approach relies on the construction of an enriched and annotated map of metabolites from an input metabolite.The pipeline assembles reaction prediction tools (SyGMa), sites of metabolism prediction tools (Way2Drug, SOMP and Fame 3), a tool to estimate the ability of a xenobotics to form DNA adducts (XenoSite Reactivity V1), and a filtering procedure based on Bayesian framework. This prediction pipeline was evaluated using caffeine and then applied to HAA. The method was applied to determine enzymes profiles associated with the maximization of metabolites derived from each HAA which are able to bind to DNA. The classification of HAA according to enzymatic profiles was consistent with their chemical structures.ConclusionsOverall, a predictive toxicological model based on an in silico systems biology approach opens perspectives to estimate the genotoxicity of various chemical classes of environmental contaminants. Moreover, our approach based on enzymes profile determination opens the possibility of predicting various xenobiotics metabolites susceptible to bind to DNA in both normal and physiopathological situations.

Highlights

Heterocyclic Aromatic Amines (HAA) and their metabolites The liver plays a major role in the metabolic activation of xenobiotics
Contribution To advance the ability to predict the formation of DNA adducts by heterocyclic aromatic amines (HAA), we have introduced a new method which combines the concept of a filtered metabolic map introduced in [36] and the concept of ranked pathways introduced in [35]
In enriched metabolic maps, nodes are labeled by SMILES formula, DNA reactivity label and production probability score and edges are labeled by rule name, atom number, rank label, enzyme name and enzyme family

Summary

Introduction

The liver plays a major role in the metabolic activation of xenobiotics (drugs, chemicals such as pollutants, pesticides, food additives...). Among environmental contaminants of concern, heterocyclic aromatic amines (HAA) are xenobiotics classified by IARC as possible or probable carcinogens (2A or 2B). While HAA is a family of more than thirty identified chemicals, the metabolic activation and possible DNA adduct formation have been fully characterized in human liver for only a few of them (MeIQx, PhIP, A αC). Heterocyclic Aromatic Amines (HAA) and their metabolites The liver plays a major role in the metabolic activation of xenobiotics (drugs, pollutants, pesticides, food additives...). Aminoimidazoarene HAA, such as MeIQx (2-amino3,8-dimethylimidazo[4,5-f]quinoxaline), PhIP (2-amino-1-methyl-6-phenylimidazo[4,5b]pyridine) and IQ (2-amino-3-methylimidazo[4,5-f]quinoline), are formed by Maillard reaction between hexose and amino acids at a temperature greater than 150C [5]

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