Plant-derived novel MurA inhibitors against Pantoea sp. NSTU24 causing rice grain discoloration: an integrated in-vitro and in-silico approach

Antimicrobial resistance among phytopathogens poses a growing threat to sustainable crop production, highlighting the need for environmentally compatible antibacterial strategies. This study integrated in vitro antibacterial screening and structure-based computational analyses to investigate plant-derived candidates against Pantoea sp. NSTU24 associated with rice grain discoloration. A pathogenic Pantoea isolate from infected rice grains in Bangladesh was characterized by biochemical and 16 S rRNA analyses and evaluated against antibiotics and thirteen ethanolic plant extracts. Piper betle , Albizia procera , and Moringa oleifera exhibited measurable antibacterial activity, with P. betle showing the strongest concentration-dependent inhibition (21.4 ± 0.1 mm at 400 mg/mL). Quantitative assays further confirmed its activity, with both MIC and MBC determined at 1.95 mg/mL, whereas definitive MIC and MBC endpoints were not obtained for A. procera and M. oleifera within the tested range. The isolate was resistant to fosfomycin but susceptible to most other antibiotics tested. Subsequent MurA-targeted molecular docking identified phytochemicals with stronger predicted binding affinities (− 11.2 to − 7.6 kcal/mol) than fosfomycin (− 4.5 kcal/mol). Quantum chemical analysis and 100-ns molecular dynamics simulations further supported favorable interaction profiles. Luteolin, genistein, ellagic acid, and piperbetol emerged as potential MurA inhibitors, providing candidates for further biochemical and biological validation.