The molecular and structural basis of advanced antiviral therapy for hepatitis C virus infection

Key Points

  • Hepatitis C virus (HCV) infection is a major cause of chronic hepatitis, liver cirrhosis and hepatocellular carcinoma worldwide.

  • Cell culture systems for HCV, especially the replicon and cell culture-derived HCV (HCVcc) systems, have been essential for researchers to gain insights into the viral replication cycle and for the development of selective drugs.

  • Prime targets for direct-acting antiviral agents (DAAs) against HCV are the protease NS3-4A, the replicase factor NS5A and the RNA-dependent RNA polymerase NS5B.

  • Knowledge of the biochemical and structural properties of NS3-4A, NS5A and NS5B has been a key factor for the development of highly efficient drugs targeting these proteins.

  • Additional viral proteins, such as the ion channel formed by p7 or the membrane-active protein NS4B, represent alternative targets for antiviral therapy.

  • Drugs directed against certain host cell factors on which HCV is dependent, such as cyclophilin A or microRNA miR-122, are highly efficient in vitro and in vivo.

  • New drug regimens based on the combination of DAAs and independent of interferon and, eventually, ribavirin (both of which drugs account for serious side effects) appear to be within reach in the near future.

Abstract

The availability of the first molecular clone of the hepatitis C virus (HCV) genome allowed the identification and biochemical characterization of two viral enzymes that are targets for antiviral therapy: the protease NS3-4A and the RNA-dependent RNA polymerase NS5B. With the advent of cell culture systems that can recapitulate either the intracellular steps of the viral replication cycle or the complete cycle, additional drug targets have been identified, most notably the phosphoprotein NS5A, but also host cell factors that promote viral replication, such as cyclophilin A. Here, we review insights into the structures of these proteins and the mechanisms by which they contribute to the HCV replication cycle, and discuss how these insights have facilitated the development of new, directly acting antiviral compounds that have started to enter the clinic.

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Figure 1: Hepatitis C virus genome organization and the membrane topology of cleaved viral proteins.
Figure 2: The hepatitis C virus replication cycle.
Figure 3: Membrane topology of NS3-4A and positions of mutations that confer resistance to NS3-4A inhibitors.
Figure 4: Structure of the NS5A dimer.
Figure 5: Structure of NS5B and positions of resistance mutations.
Figure 6: Alternative targets for hepatitis C virus-specific therapy.

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Acknowledgements

The authors apologize to all colleagues whose work could not be cited owing to space limitations. Research in the R.B. and V.L. laboratories is supported by the Deutsche Forschungsgemeinschaft (grants SFB/TRR 83 (TP 13), SFB 638 (TP A1), SFB/TRR77 (TP A1) and FOR1202 (TP1) to R.B.; and grants LO1556/1-2, SFB/TRR77 (TP A1) and FOR1202 (TP3) to V.L.). F.P. is supported by the French National Agency for Research on AIDS and Viral Hepatitis (ANRS).

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Correspondence to Ralf Bartenschlager.

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R.B. and V.L. are co-founders of ReBLikon GmbH, which holds commercial rights to hepatitis C virus replicon technology. F.P. declares no competing financial interests.

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Glossary

Internal ribosome entry site

An RNA sequence that allows ribosomes to bind an mRNA internally, independently of a cap structure, and that thus mediates translation of a downstream ORF.

Low-density and very-low-density lipoproteins

Lipoproteins that are made in the liver from triglycerides, cholesterol and apolipoproteins and are used to transport lipids in the blood.

Membranous web

Originally, a term describing a discrete accumulation of the membranous vesicles that have been detected in cells containingreplicating hepatitis C virus (HCV) RNA. More recent studies have shown that this web is composed of single-, double- and multi-membraned vesicles, complex ER membrane rearrangements and lipid droplets. However, in most reports, the term is used as a synonym for the membranous HCV replication compartment, although firm proof of exactly where HCV RNA replication takes place is not available.

Cyclophilin A

A highly abundant protein that catalyses the cis–trans isomerization of peptide bonds at Pro residues and thus facilitates protein folding. Cyclophilin A binds to the immunosuppressive drug cyclosporin A and is involved in numerous biological processes.

miR-122

A short, non-coding RNA that is highly expressed in hepatocytes, where it regulates the translation and turnover of mRNAs involved in numerous activities, such as iron and cholesterol homeostasis. In addition, miR-122 was found to act as a tumour suppressor.

MAVS

(Mitochondrial antiviral-signalling protein). An important factor involved in the activation of a rapid interferon response following the triggering of intracellular RNA sensors such as RIG-I or MDA5.

TRIF

(TIR domain-containing adaptor inducing interferon-β). A protein involved in the induction of an interferon response following the activation of certain Toll-like receptors, for example Toll-like receptor 3.

Phosphatidylinositol 4-kinase IIIα

(PtdIns4KIIIα). A lipid kinase that generates PtdIns 4-phosphate by adding a phosphate group to the 4-hydroxy group of PtdIns. PtdIns phosphates are membrane-localized metabolites that have important roles in intracellular signalling and membrane trafficking.

Sustained virological response rates

The percentages of patients with undetectable hepatitis C virus RNA in the blood at least 6 months after the completion of antiviral therapy.

Viroporin

A virally encoded membrane protein that localizes mainly to the ER or the cell membrane of the host cell and forms an ion channel or pore.

RNA-induced silencing complex

A multiprotein complex that incorporates a microRNA to recognize complementary sequences in mRNAs and block protein expression.

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Bartenschlager, R., Lohmann, V. & Penin, F. The molecular and structural basis of advanced antiviral therapy for hepatitis C virus infection. Nat Rev Microbiol 11, 482–496 (2013). https://doi.org/10.1038/nrmicro3046

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