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Abstract <p><b>Objective:</b> The aim of this study was to explore the potential of humic substances (HS) as non-β-lactam inhibitors for β-lactamase, using molecular modeling to understand the interaction between humic-like molecules and β-lactamase, particularly TEM-1. <b>Methods:</b> Molecular dereplication of humic-like inhibitors was performed by comparing their molecular formulas, derived from high-resolution mass spectrometry, to known compounds in the ChEMBL database. The interaction of selected humic-like molecules with β-lactamase was studied using docking and molecular dynamics simulations with Chimera v.1.15 and Amber14 software. <b>Results and Discussion:</b> From dereplication, 156 unique structures were identified as β-lactamase inhibitors. Three molecules were selected for molecular modeling based on their lipophilicity and similarity to HS. Docking simulations revealed that the humic-like molecules interacted with the enzyme through non-competitive inhibition, binding to an allosteric site, and also showed aggregation behavior on the protein surface. Molecular dynamics simulations suggested that the aggregation of humic-like ligands could block the active site of β-lactamase, enhancing the synergistic effect on sulbactam. <b>Conclusions:</b> This study demonstrates that humic-like molecules can interact with β-lactamase through non-competitive inhibition and aggregation, potentially improving the efficacy of existing β-lactamase inhibitors. The dereplication method proved valuable for identifying active components within humic substances, offering a novel approach to discovering non-β-lactam inhibitors.</p>

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Development of Approaches to Molecular Modeling of the Interaction Between Biologically Active Components of Humic Substances and β-Lactamases on the Example of Humic-Like Low-Molecular Weight Analogues

  • 期刊论文

  • 发表日期：

    2025年12月15日

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  • S. A. Vladimirov,
  • G. D. Rukhovich,
  • E. V. Radchenko,
  • I. V. Perminova

摘要

Abstract

Objective: The aim of this study was to explore the potential of humic substances (HS) as non-β-lactam inhibitors for β-lactamase, using molecular modeling to understand the interaction between humic-like molecules and β-lactamase, particularly TEM-1. Methods: Molecular dereplication of humic-like inhibitors was performed by comparing their molecular formulas, derived from high-resolution mass spectrometry, to known compounds in the ChEMBL database. The interaction of selected humic-like molecules with β-lactamase was studied using docking and molecular dynamics simulations with Chimera v.1.15 and Amber14 software. Results and Discussion: From dereplication, 156 unique structures were identified as β-lactamase inhibitors. Three molecules were selected for molecular modeling based on their lipophilicity and similarity to HS. Docking simulations revealed that the humic-like molecules interacted with the enzyme through non-competitive inhibition, binding to an allosteric site, and also showed aggregation behavior on the protein surface. Molecular dynamics simulations suggested that the aggregation of humic-like ligands could block the active site of β-lactamase, enhancing the synergistic effect on sulbactam. Conclusions: This study demonstrates that humic-like molecules can interact with β-lactamase through non-competitive inhibition and aggregation, potentially improving the efficacy of existing β-lactamase inhibitors. The dereplication method proved valuable for identifying active components within humic substances, offering a novel approach to discovering non-β-lactam inhibitors.