Japanese encephalitis (JE) is a viral neurologic disease of global public health importance. JE is caused by an RNA virus - the Japanese encephalitis virus (JEV) belonging to genus Flavivirus in the family Flaviviridae. JE is endemic in many parts of Asia and western pacific. Annually, approximately 50,000 JE cases are reported with case fatality rates as high as 30-35% resulting in ~15,000 deaths. Presently, there are no successful drugs against JE. Docking of JEV NS3 helicase/NTPase helicase domain with 10 compounds was performed in iGEMDOCK v2.1. Integrated docking, screening, post- analysis and visualization were performed using RasMol software. The drug susceptibility was evaluated by virus yield reduction assay. Three ligands out of 10 antibiotic compounds studied showed highest binding affinity with receptor protein. Kanamycin, Rolitetracycline and Doxycycline showed better binding energy compared to two study standards- Ribavirin and Minocycline. Interacting bonds were formed in all three domains of NS3 helicase/NTPase. The interactions in motifs I, II and VI of helicase are important; these would have possibly inhibited viral replication. Biological assay showed that Kanamycin (Inhibitory concentration, IC - 70 µg/ml), Rolitetracycline (IC - 76 µg/ml) and Doxycycline (IC - 22 µg/ml) inhibited plaque formation.
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