Integrated proteomics and connectivity map‐based analysis reveal compounds with a potential antiviral effect against Japanese encephalitis virus infection in a mouse model

Japanese encephalitis virus (JEV) is the leading causative agent of viral encephalitis in India and contributes to a significant disease burden in South Asian countries. However, no antiviral treatment is available against JEV‐induced encephalitis, highlighting the urgent need for novel therapeutic approaches. Repurposing or repositioning drugs was found to be more economical and practical in the current drug development scenario. The present study aimed to develop a host‐directed strategy through a computational drug repurposing approach. As part of the strategy, we first generated a dynamic signature of differentially expressed JEV infection‐associated proteins in mice brains through a semiquantitative proteomics approach. With the help of the Connectivity Map (CMap) analysis, we narrowed down the lists of drugs with a high negative CMap score (−70 or lower). Based on the CMap score, we chose the top three compounds (Tipifarnib, Ly303511 and MDL11939) with CMap scores of −91.83, −88.18 and −91.15, respectively. The antiviral potential of these three compounds was further compared in both JEV‐infected mouse neuroblastoma cells and C57BL/6 mice. Oral administration of Ly303511 and MDL11939, alone or in combination, showed improved outcomes (e.g. delayed death, increased survival, and less viral load than Tipifarnib alone or combined). The JEV‐infected mice survived upon drug treatment, effectively reducing viral load and reversing the antiviral signature. Our results highlight Ly303511 and MDL11939 as promising host‐targeted inhibitors of JEV infection and pathogenesis. Moreover, our results favor the combination of Ly303511 and MDL11939 therapy to improve clinical symptoms and reduce JEV‐induced damage, thus warranting inclusion in clinical studies.