Molecular Docking Study of Gentamicin against Dihydrofolate Reductase (DHFR) of Pseudomonas aeruginosa

Background: Pseudomonas aeruginosa is an important opportunistic pathogen associated with healthcare-associated infections and increasing antimicrobial resistance. Gentamicin is an aminoglycoside antibiotic commonly used against Gram-negative bacterial infections, including those caused by P. aeruginosa. Although its established antibacterial mechanism involves binding to the bacterial 30S ribosomal subunit, the possibility of additional interactions with other bacterial proteins remains insufficiently explored. Dihydrofolate reductase (DHFR), an essential enzyme involved in folate metabolism, represents a potential molecular target for antibacterial drug development. Objective: This study aimed to investigate the potential interaction of gentamicin with DHFR of P. aeruginosa using molecular docking and to determine its predicted binding affinity, docking score, interacting amino-acid residues, and major molecular interactions. Methods: An in silico molecular docking approach was used to evaluate the interaction between gentamicin and P. aeruginosa DHFR. The protein and ligand structures were prepared and optimized before docking. The predicted DHFR binding region was used to generate the docking grid, and multiple gentamicin poses were generated and ranked according to their docking scores. The highest-ranked structurally plausible pose was subsequently analyzed for amino-acid contacts and hydrogen-bonding, hydrophobic, electrostatic, and van der Waals interactions. Results: Gentamicin showed a favorable predicted interaction with P. aeruginosa DHFR, with a best docking score of −6.37 kcal/mol and a predicted binding affinity of −6.37 kcal/mol. The ligand occupied the predicted DHFR binding region and formed interactions with eight principal residues: Asp27, Phe31, Lys32, Ile50, Asn51, Arg57, Ile102, and Tyr107. Three hydrogen bonds were identified with Asp27, Asn51, and Tyr107, while Phe31 and Ile50 contributed hydrophobic interactions. Electrostatic interactions were observed with Lys32 and Arg57, and Ile102 contributed a van der Waals contact. Conclusion: The molecular docking analysis suggests that gentamicin can adopt a favorable orientation within the predicted DHFR binding region of P. aeruginosa. The observed network of multiple non-covalent interactions provides computational evidence for a potential gentamicin–DHFR association. However, the findings are hypothesis-generating and do not establish direct DHFR inhibition or a contribution to gentamicin's antibacterial activity. Experimental enzyme-inhibition studies, molecular dynamics simulations, and biochemical validation are required to determine the biological significance of the predicted interaction.