Identification of Novel Inhibitors of JEV RdRp as Potent Antiviral Drugs: Targeting NS5-NS3 Protein Interaction

Japanese Encephalitis Virus (JEV) belongs to the Flavivirus family, and the RNA-dependent RNA polymerase (RdRp) domain located at the C-terminus of non-structural protein 5 (NS5) regulates de novo viral genome synthesis. The conserved priming loop inserted in the thumb domain of RDRP initiates de novo genome synthesis. Interestingly, the reported replication process initiates with an interaction between NS5 (methyltransferase/RDRP) and NS3 (protease/helicase), and inhibiting this interaction directly correlates with the inhibition of viral replication. The function of the priming loop in the context of the NS5-NS3 interaction is not yet known. In this study, we studied the priming loop function in the NS5-NS3 interaction and viral replication. Using a structure-based drug design approach, we screened the Maybridge compound library against the RdRp priming loop and identified 15 candidate compounds based on binding energy. Among them, DSHS00151 showed significant dose-dependent inhibition of the NS5-NS3 interaction with an IC50 of 3.5 µM in the mammalian two-hybrid assay, inhibited viral infectivity with an IC50 of 2.54 µM, and reduced viral RNA load with an IC50 of 2.9 µM, compared to CD10712. Molecular Dynamics (MD) simulations revealed that DSHS00151 exhibits stronger and more stable binding with the priming loop residues (790–812) compared to CD10712. The molecular mechanism suggested by the docking of the NS5-NS3 proteins showed that the priming loop tends to rotate toward the NS3 protein to stabilize the complex, and compound binding restricts this loop rotation, thus compromising the stability of the NS5-NS3 complex and affecting viral replication. Overall, our study validated the function of the NS5 priming loop as an allosteric site, and compounds binding to this allosteric site belong to the Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTI) class of inhibitors, which disrupt the NS5-NS3 interaction and could be developed as novel anti-JEV therapeutics.