Phytochemical Screening Targeting DNA Gyrase-B of Aeromonas hydrophila: An In Silico Approach for Sustainable Fish Disease Management

• 513 phytochemicals were screened against DNA gyrase-B using an integrated in silico workflow • Lupeol and Epicatechin-3-O-(3-O-methylgallate) showed strong predicted binding and stability • 100-ns MD simulations indicated stable occupancy of the ATP-binding pocket • Multi-parameter analysis (MM-GBSA, QM, QSAR, ADME/T) supported candidate prioritization • Findings identify promising computational hits for further experimental validation Aeromonas hydrophila is a widespread Gram-negative pathogen that infects diverse aquaculture species and causes substantial mortality and economic losses. Antibiotics remain widely used, but rising antimicrobial resistance has reduced their effectiveness, highlighting the need for alternative approaches. DNA gyrase-B, a key enzyme involved in bacterial DNA replication, represents a promising molecular target for controlling A. hydrophila . Medicinal plants offer accessible, economical, and environmentally friendly sources of bioactive compounds suitable for sustainable aquaculture. In this study, 513 phytochemicals were virtually screened against DNA gyrase-B using PyRx, followed by detailed docking analysis in BIOVIA Discovery Studio. ADME/T profiling, HOMO–LUMO analysis and PASS-based bioactivity prediction identified Lupeol (CID-259846) and Epicatechin-3-O-(3-O-methylgallate) (CID-467296) as the most promising candidates. A 100-ns molecular dynamics simulation revealed stable binding of both compounds within the binding pocket, with Lupeol exhibiting lower RMSD values, reduced residue flexibility and greater structural compactness, while the Epicatechin analog showed stronger polar interactions and more favorable MM-GBSA binding energy. Overall, Lupeol and Epicatechin-3-O-(3-O-methylgallate) were identified as promising computational hits targeting DNA gyrase-B, indicating their potential as phytobiotic candidates for further experimental evaluation in the management of A. hydrophila in aquaculture. This study integrates virtual screening, molecular docking, ADME/T, QSAR, QM, and 100-ns MD simulation to identify candidate phytochemical hits with multi-target potential (computationally predicted) against DNA gyrase-B and provides a computational framework that may support sustainable aquaculture disease management by reducing reliance on conventional antibiotics.