In Silico Assisted Identification of Potential Inhibitors of D-Alanyl-D-Lactate Ligase in <i>Enterococcus faecium</i> Using a Molecular Modeling Approach

Background Enterococcus faecium is a major global health hazard, primarily associated with hospital-acquired infections in immunocompromised patients. E. faecium is well known for its high levels of antibiotic resistance, particularly to vancomycin. Methods In the present study, computational and advanced biophysical strategies were used for the identification of inhibitors against the vancomycin-resistant D-Alanyl-D-lactate ligase. Results Based on the lowest binding energy scores, the top three selected compounds were identified as computationally prioritized drug candidates, with binding affinity scores of -10.4, -10.2, and -10.0 kcal/mol for Top-1, Top-2, and Top-3, respectively. In comparison, the control ligand, D-alanyl-D-lactate, showed a binding affinity of -7.5 kcal/mol. These computational results specify the relative affinity of each compound for the active site, with lower (more negative) values reflecting stronger molecular interactions. The top-ranked docked complexes were then subjected to 200 ns molecular dynamics simulations to evaluate the behavior of the protein-ligand complexes under a dynamic environment. Analysis of the simulation trajectories suggested that the selected top-ranked ligands sustained favorable interactions within the binding pocket throughout the simulation period, supporting their potential as computational hits for further experimental assessment. Further, the ADMET properties analysis of the selected compounds was evaluated; according to Lipinski's rule of five, the selected compounds fall into the drug-likeness group. In the PCA analysis, the selected compounds stabilized the protein structure to varying degrees by reducing its intrinsic conformational flexibility compared to the control system. Salt bridge analysis showed that the selected compounds maintain structural integrity under physiological conditions. DFT calculations provided supportive insight into ligand electronic properties, including frontier orbital distribution, reactivity descriptors, and charge distribution, which may help rationalize interaction propensity. Conclusion Overall, the findings provide a theoretical framework for experimental biologists to formulate effective drug molecules for E. faecium.