Network controllability analysis reveals the antiviral potential of Etravirine against hepatitis E virus infection

Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in lower- and middle-income countries. HEV infection may lead to acute liver failure, chronic liver disease, and high mortality in pregnant women. Antiviral therapy is not a standard treatment for HEV patients. Computational biology tools promise to revolutionize the antiviral drug discovery. Here, we analyzed the transcriptome data of HEV-infected primary human hepatocyte cells through the connectivity map database and applied control theory on the functional network to identify antiviral targets against HEV. The above analyses predicted PKCβ, PKB/AKT, and CK1ε as potential antiviral targets against HEV. The antiviral function of PKB/AKT and CK1ε was experimentally validated by using respective biochemical inhibitors in g3 (genotype 3)-HEV replicon and Huh7 cell-based model of g3 and g1-HEV infection. Furthermore, knockdown of CK1ε showed a similar effect. These data confirmed that CK1ε is an antiviral target for HEV. At present, there are no Food and Drug Administration (FDA)-approved drugs targeting CK1ε. Etravirine is an FDA-approved non-nucleoside reverse transcriptase inhibitor drug, used for the treatment of AIDS patients. An in silico study predicted Etravirine to be a potent inhibitor of CK1ε. Our experiments revealed potent antiviral activity of Etravirine against HEV, which was mediated via its ability to inhibit the activity of CK1ε. Taken together, the current study demonstrates that PKB/AKT and CK1ε are bona fide antiviral targets for HEV and paves the way for repurposing Etravirine for the treatment of HEV-infected patients.IMPORTANCEAntiviral treatment is not the standard care for acute viral hepatitis E patients. Unbiased identification of antiviral targets or large-scale screening of antiviral compounds against the hepatitis E virus (HEV) has not been reported. Here, a computational biology approach was followed to unbiasedly identify antiviral targets of HEV. Transcriptome data of HEV-infected primary human hepatocyte cells were analyzed to identify modulators of the network and generate directional networks. Network controllability analysis identified PKCβ, PKB/AKT, and CK1ε as potential antiviral targets against HEV. Antiviral function of PKB/AKT and CK1ε was confirmed using cell-based models of genotype 1 (g1)- and g3-HEV infection. Further experiments demonstrated the antiviral activity of Etravirine against HEV, mediated via its ability to inhibit the CK1ε activity. Etravirine is a Food and Drug Administration-approved non-nucleoside reverse transcriptase inhibitor, used for the treatment of AIDS patients. This study reveals the potential of repurposing Etravirine for the treatment of HEV patients and illustrates the importance of computational biology in antiviral drug discovery.