Nonstructural protein 5A (NS5A) of hepatitis C virus (HCV) is an indispensable component of the HCV replication and assembly machineries. Although its precise mechanism of action is not yet clear, current evidence indicates that its structure and function are regulated by the cellular peptidylprolyl isomerase cyclophilin A (CyPA). CyPA binds to proline residues in the C-terminal half of NS5A, in a distributed fashion, and modulates the structure of the disordered domains II and III. Cyclophilin inhibitors (CPIs), including cyclosporine (CsA) and its nonimmunosuppressive derivatives, inhibit HCV infection of diverse genotypes, both in vitro and in vivo. Here we report a mechanism by which CPIs inhibit HCV infection and demonstrate that CPIs can suppress HCV assembly in addition to their well-documented inhibitory effect on RNA replication. Although the interaction between NS5A and other viral proteins is not affected by CPIs, RNA binding by NS5A in cell culture-based HCV (HCVcc)-infected cells is significantly inhibited by CPI treatment, and sensitivity of RNA binding is correlated with previously characterized CyPA dependence or CsA sensitivity of HCV mutants. Furthermore, the difference in CyPA dependence between a subgenomic and a full-length replicon of JFH-1 was due, at least in part, to an additional role that CyPA plays in HCV assembly, a conclusion that is supported by experiments with the clinical CPI alisporivir. The host-directed nature and the ability to interfere with more than one step in the HCV life cycle may result in a higher genetic barrier to resistance for this class of HCV inhibitors.
Hepatitis C virus (HCV) is a positive-strand RNA virus encoding a polyprotein that is cleaved into 10 proteins, including three structural proteins (core, E1, and E2), a putative ion channel (p7), and six nonstructural proteins (NS2, NS3, NS4A, NS4B, NS5A, and NS5B) (42). Propelled by the development of both subgenomic replicons (8, 31) and a cell culture-based infection system (HCVcc) (9,29,49,54), research has garnered a wealth of information on the role of each of these proteins in the life cycle of the virus. The structural proteins and p7 are needed for virion assembly but not RNA replication, whereas the nonstructural proteins are probably involved in both replication and infectious virus production. In addition to the requisite protease and polymerase activities, HCV also encodes proteins that perform specialized functions, such as deforming the membranes (to generate a microenvironment for RNA replication) or scaffolding (to bring the appropriate proteins together for virion assembly) (14,24,37,41).HCV infects ϳ3% of the world's population and is a major risk factor for liver cirrhosis and hepatocellular carcinoma (5, 47). Current treatment comprises pegylated interferon (IFN), the nucleoside analog ribavirin, and recently approved direct-acting antivirals (DAAs) that inhibit the HCV NS3 protease. Despite the success of this triple therapy, drug resistance against the DAAs develops quickly (38), presuma...