A Computational Approach for Identification and Validation of Antibacterial Compounds Targeting DHFR Enzyme Using Molecular Docking and Dynamics

Antimicrobial drugs are essential to combat bacterial pathogens responsible for millions of deaths annually. However, the global rise in antibiotic resistance has rendered many treatment strategies ineffective, necessitating the urgent discovery of novel antibacterial agents. In this study, we investigated gut bacterial strains as potential sources of bioactive compounds, given their emerging role as prolific producers of antimicrobial substances. Secondary metabolites were initially isolated from Bacillus subtilis, a strain previously obtained from the human gut. These metabolites were evaluated for their antibacterial activity against three pathogenic bacteria—Escherichia coli, Salmonella typhi, and Staphylococcus aureus—using in vitro assays. Our findings demonstrated significant antibacterial activity. GC-MS analysis of B. subtilis identified 18 bioactive compounds and further exploration of the B. subtilis metabolome identified 75 additional compounds in public databases. These compounds were docked against DHFR, as inhibitors of DHFR is proven effective for treating bacterial infections. Among these compounds, one compound, CID: 99896 (pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro-3-(phenylmethyl)), displayed superior binding energy (-8.680 kcal/mol) against S. aureus DHFR compared to the standard drug trimethoprim (-7.895 kcal/mol).Protein-ligands complex were subjected to MD simulations for 100 ns to confirm their rigidity and stability by exploring root mean square deviations, root mean square fluctuations, solvent accessible surface area, radius of gyration and hydrogen bond analysis from simulation trajectories. MD simulation suggests that potential inhibitor of DHFR enzyme would prevent the bacteria from completing their life cycle. Further in vitro and in vivo studies are warranted to evaluate the therapeutic potential of this compound for treating multidrug-resistant bacterial infections.

• Supervision