Molecular Modeling and simulation-based identification of inhibitors against new Delhi Metallo-Lactamase 1: Implications for bacterial antibiotic resistance

Abstract

Objectives: Bacterial infections expressing New Delhi metallo-lactamase-1 (NDM-1) pose an escalating global threat to healthcare systems. NDM-1 is an enzyme that renders β-lactam antibiotics ineffective, leading to resistance against numerous antibiotics used in clinical practice. Therefore, there is an urgent need to identify and develop a clinically relevant inhibitor for NDM-1. Methods: Vitas-M laboratory database was screened for small molecules with abilities to bind NDM-1, by generating structure-based pharmacophore hypothesis. Thereafter, molecular docking was performed between NDM-1 and the potential small molecule inhibitors. The outcomes of molecular docking were validated by molecular dynamics simulation and MM-GBSA protocols. Results: Based upon initial NDM-1-binding characteristics, two ligands (STK115225 and STK107343) were nominated for further analyses for stability and affinity of protein–ligand interactions. Assessment of conformational change parameters indicated that these showed tight and stable binding to the active site pocket of NDM-1 protein. Principal component analysis (PCA) further illustrated that the protein ligand complexes were highly stable. Molecular dynamics simulation along with high numbers of static hydrogen bonds signifies the potency of STK115225 and STK107343 in inhibiting NDM-1. Further, MM-GBSA-based binding free energy maps verified favorable energy changes for the binding of the two small molecules, indicating their abilities for high affinity-binding with NDM-1. Conclusions: This study has significant implications for addressing antibiotic resistance mediated by NDM-1. The identification of STK115225 and STK107343 as high-affinity binding ligands against NDM-1 provides a strong foundation for developing new therapeutic agents. However, to fully ascertain their clinical relevance, these findings must be validated through in vitro and in vivo experiments. If successful, these inhibitors could restore the efficacy of β-lactam antibiotics and offer a new approach to combat NDM-1 mediated antibiotic resistance, ultimately improving patient outcomes and reducing the global burden of resistant bacterial infections.

Keywords

• NDM-1
• Vitas-M laboratory
• Structure-based pharmacophore
• Virtual screening
• MM-GBSA