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In Silico Assessment of Interactions Between Pharmaceutical Contaminants and Human Metabolic Enzymes Using Molecular Docking
* 1 , 2 , 3
1  Graduate Program in Environmental Sciences, São Paulo State University (UNESP), Brazil
2  Department of Environmental Sciences, São Paulo State University (UNESP), Sorocaba, Brazil
3  Department of Biothecnology, São Paulo State University (UNESP), Assis 19806-900, Brazil
Academic Editor: Stefano Magni

Abstract:

The increasing presence of pharmaceutical compounds in aquatic environments has raised concerns regarding their potential impacts on human health and ecosystems. Many of these substances are considered emerging contaminants due to their persistence, high solubility, and continuous introduction into the environment through industrial effluents and wastewater. Computational approaches have become valuable tools for evaluating the potential interactions between xenobiotics and biological targets, allowing the preliminary assessment of toxicological risks associated with environmental exposure.

This study aimed to investigate the interactions between selected pharmaceutical contaminants and human metabolic enzymes using molecular docking simulations. Protein structures were obtained from the Protein Data Bank and included Cytochrome P450 3A4 (CYP3A4), a key enzyme involved in xenobiotic metabolism, and N-acetyltransferase 2 (NAT2), responsible for acetylation reactions in drug metabolism. Ligand structures were retrieved from public chemical databases and prepared for docking using standard molecular modeling protocols. Docking simulations were performed using AutoDock Vina, and binding affinities and structural orientations were analyzed to evaluate potential interactions.

The results showed that amoxicillin presented a favorable binding affinity with CYP3A4 (approximately −8.7 kcal/mol). However, structural analysis indicated a relatively large distance (~6.5 Å) between the ligand and the heme iron atom, suggesting that although the molecule can occupy the active site, its orientation may not favor efficient catalytic biotransformation. For sulfamethoxazole, docking simulations revealed binding affinities around −7.8 kcal/mol with NAT2 and stable binding poses with RMSD values below 2 Å, suggesting a possible interaction near the catalytic region associated with acetylation.

Overall, the findings suggest that pharmaceutical contaminants may interact with human metabolic enzymes, highlighting the importance of evaluating their potential toxicological effects in scenarios of chronic environmental exposure. Computational approaches such as molecular docking represent useful tools for preliminary risk assessment of emerging contaminants.

Keywords: Environmental toxicology; Xenobiotics; Molecular docking; Emerging contaminants; Pharmaceutical pollutants
Comments on this paper
Keith Brunt
This is particularly interesting, as it will enable large scale computational predictive analytics and in silico screening of compounds that are already grandfathered in by historical use, and then can serve as a reference library for new emerging compounds or detected waste chemicals of concern in the environment.

For this model it might be of interest to also look at the metabolites of Amoxicillin, two major metabolites: amoxicilloic acid (AMA) and amoxicillin diketopiperazine-2',5'-dione (DIKETO), to identify whether these get closer to the heme in CYP3A4.

Well organized poster!
Gabriel Ribeiro
I agree that extending the analysis to amoxicillin metabolites, such as amoxicilloic acid (AMA) and diketopiperazine (DIKETO), could provide important additional insights. Since amoxicillin showed favorable binding but a relatively large Fe–ligand distance in Cytochrome P450 3A4, evaluating these metabolites may help determine whether they adopt conformations closer to the heme center and potentially better reflect metabolic susceptibility. This is an excellent suggestion for expanding the predictive framework of this study. Thank you for your valuable feedback. We'll take a look into it too.
Vitória de Oliveira
While the assessment of major metabolites would certainly add value, it is also important to consider that the parent compound remains environmentally relevant and can be present alongside transformation products. Comparing docking profiles across the parent molecule and its metabolites may therefore help elucidate how chemical modifications affect binding orientation, active-site accessibility, and potential metabolic susceptibility.
Vitória de Oliveira
While the assessment of major metabolites would certainly add value, it is also important to consider that the parent compound remains environmentally relevant and can be present alongside transformation products. Comparing docking profiles across the parent molecule and its metabolites may therefore help elucidate how chemical modifications affect binding orientation, active-site accessibility, and potential metabolic susceptibility.



 
 
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