Mechanisms of action and efficacy of HCV direct-acting antiviral agents and the host-targeting agent Cyclosporin A

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Hepatitis C virus (HCV) remains a significant public health burden worldwide, with an approximated 170 million people infected globally. Chronic HCV infection is associated with increased risk of liver fibrosis, cirrhosis and hepatocellular carcinoma. In developed countries, it is the leading cause of liver transplantation. The previous standard of care (SOC) for HCV was composed of pegylated interferon alpha (pegIFN-[alpha]) and ribavirin (RBV) for 48 weeks. This SOC is associated with about 50% virologic response rate and with severe side effects leading to treatment discontinuation. Since 2011, several direct-acting antiviral agents (DAAs) have been approved, aiming for interferon (IFN)-sparing regimens with shorter duration and fewer side effects. However, the mechanism of action (MOA) and the kinetics of DAAs are still not known. In this Ph.D. thesis work, we first established a multiplex assay approach to compare the relative efficacy of various DAAs and the kinetics of their antiviral activities, as a potential pre-clinical measure of their clinical utility. This approach employs flow cytometry, a Gaussia luciferase reporter system, western blot analysis, quantitative reverse transcription polymerase chain reaction (RT-qPCR), limited dilution assay [tissue culture infectious dose 50 (TCID50)], and an image profiling assay that quantifies the NS5A redistribution in response to drug treatment. Using this multiplex assay approach, we evaluated three classes of DAAs, including NS5A inhibitors ledipasvir (LDV) and daclatasvir (DCV), the NS3/4A inhibitor danoprevir (DNV), and the NS5B inhibitor sofosbuvir (SOF). Our results suggest that the NS5A inhibitor LDV, followed closely by DCV, has the fastest effect on suppression of viral proteins and RNA and on redistribution of NS5A. In terms of MOA, our data demonstrate that LDV has a more pronounced effect than DCV on viral replication, assembly, and infectivity of released virus. In contrast to DAAs, host-targeting agents (HTAs) affect host factors that are involved in the viral life cycle, conferring a higher barrier to viral resistance. Using the previously established multiplex assay approach plus a strand-specific nucleic acid visualization method, we compared the inhibition kinetics, MOA, and relative potency of cyclosporin A (CsA), an HTA that targets host factor cyclophilin A (CypA), to DAAs, including LDV, DCV, DNV and SOF. Our data show that CsA suppresses viral protein production more rapidly than other DAAs and causes lipid droplets (LDs) enlarged in size. However, LDV has the fastest effect on viral RNA and NS5A redistribution and disrupts the association of double-stranded RNA (dsRNA) with NS5A. Furthermore, inhibitors of NS5A, NS3/4A, but not of NS5B, suppressed the infectivity of released virus. NS5A inhibitors LDV and DCV rapidly suppressed the infectivity of intracellular virus,suggesting that they exert effects on HCV assembly. CypA inhibitor CsA rapidly suppressed the infectivity of extracellular virus, but significantly less efficient in inhibiting the infectivity of intracellular virus, indicating that it blocks a step of the viral life cycle after viral assembly, but before, or at the step of virus release. Taken together, my Ph.D. thesis work has led to the establishment of a multiplex assay approach and shed light on the MOA and efficacy of HCV antivirals. We used this approach to compare the kinetics and the MOA of DAAs and HTA. In addition, this approach can be used to facilitate the study of the biological processes involved in HCV replication and help identify optimal drug combinations for therapeutic interventions.