STRUCTURAL CHARACTERIZATION AND COMPARATIVE IN SILICO SCREENING OF POTENTIAL LIGANDS AGAINST ANTIMICROBIAL RESISTANCE PROTEINS IDENTIFIED FROM THE RIVER VARUNA

Abstract

Antimicrobial resistance (AMR) in aquatic environments represent an important environmental dimension of the global AMR load, specifically in the polluted river systems receiving diverse anthropogenic inputs. The present study investigated selected abundant AMR proteins identified at four sites (VR1-VR4) of the river Varuna using a whole-genome shotgun metagenomic approach. Further, a computational screening-ligand-associated study was performed. AMR protein sequences were subjected to BLASTp analysis for sequence-level identification, followed by conserved domain analysis to confirm their functional properties. The proteins identified were Sul1, Sul4, blaOXA, and blaVEB-9 from sites VR1, VR2, VR3, and VR4. Conserved domain analysis identified dihydropteroate synthase domain in Sul1 and Sul4, and a class D ß-lactamase domain in blaOXA and a class A ß-lactamase related serine hydrolase domain in blaVEB-9. Experimentally determined 3D protein structures were retrieved from the Protein Data Bank termed as 7S2I, 1TWS, 1M6K, and 6NVT. Comparative cavity-guided molecular docking was performed using CB-Dock2 with sulfamethoxazole (FDA-approved drug) and thymol (natural compound). Thymol showed predicted docking scores ranging from -6.3 to -8.1kcal/mol. The most favorable predicted interaction for both ligands was observed with blaVEB-9. This finding provides preliminary structural insights into ligand-binding patterns of environment-derived AMR (Antimicrobial resistance) proteins and identifies protein-ligand combinations to analyze further biochemical and microbiological validation.