International Science Community Association International Research Journal of Biological Sciences 15 3 2026 08 10 Exploring Antiviral Chemical Space for the Discovery of Novel RNA-Dependent RNA Polymerase inhibitors against Japanese Encephalitis Virus 15 27 EN Auddya Deblina 1 Department of Botany, Raghunathpur College, Raghunathpur, Purulia, WB-723133, India and Department of Botany, Sidho Kanho Birsha University, Purulia, WB -723104, India Sinha Anjan Kumar 2 Department of Botany, Raghunathpur College, Raghunathpur, Purulia, WB-723133, India Puttaswamy Rajeshwari 1 Department of Botany Government Science College, Chitradurga, Karnataka, India Shukla Akshay Kumar 1 Department of Biological Sciences, Faculty of Science and Environment, Mahatma Gandhi Chitrakoot Gramodaya Vishwavidyalaya, Chitrakoot, Satna, India Saeed Mohd 2 Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia Dwivedi Vivek Dhar 3 Bioinformatics Research Division, Quanta Calculus, Greater Noida, UP, India Tripathi Ramesh Chandra 4 Department of Biological Sciences, Faculty of Science and Environment, Mahatma Gandhi Chitrakoot Gramodaya Vishwavidyalaya, Chitrakoot, Satna, India > Research Paper 2026 6 20 2026 08 10 This research focuses on Japanese encephalitis virus (JEV), one of the most serious mosquito-borne flaviviruses that cause neuroinvasive disease in humans. Despite the wide use of vaccines, there is still a high burden of JEV infections for which there are no good therapies. One of the main enzymes responsible for viral replication is the RNA-dependent RNA polymerase (RdRp), and it could be a good drug target. Thus, in the current research, we employed a structure-based virtual screening strategy to predict inhibitors of the JEV RdRp enzyme using the enzyme's crystal structure and Life Chemicals' antiviral library. Fifteen candidates were identified during the screening process and then re-scored using MM/GBSA calculations. After scoring using MM/GBSA values, the three top-ranking molecules (F3217-0045, F1951-0385, and F1951-0396), together with the reference inhibitor Galidesivir, underwent detailed analysis via molecular dynamics simulations. All three selected molecules interacted stably with the catalytically active sites in the ATP-binding pocket and exhibited higher binding affinity than the reference inhibitor. The trajectory analysis and trajectory-based MM/GBSA calculations indicated that all three selected compounds formed stable protein-ligand complexes over 100 ns of MD. Particularly, F3217-0045 had the best binding free energy (-84.95 ± 5.71 kcal/mol) among the three molecules, and F1951-0396 had the highest stability during the molecular dynamics simulation. Overall, the results presented constitute the discovery of promising lead molecules that inhibit JEV-RdRp and provide a basis for further experimental studies. Copyright@ International Science Community Association