Structural basis for RNA replication by the hepatitis C virus polymerase

  title={Structural basis for RNA replication by the hepatitis C virus polymerase},
  author={Todd C. Appleby and Jason K. Perry and Eisuke Murakami and Ona Barauskas and Joy Y. Feng and Aesop Cho and David Fox and Diana R. Wetmore and Mary E. Mcgrath and Adrian S. Ray and Michael J. Sofia and Swami Swaminathan and Thomas E Edwards},
  pages={771 - 775}
A view of the HCV polymerase at work More than 3% of the world's population is infected with hepatitis C virus (HCV), a predisposing factor for life-threatening liver diseases such as cirrhosis and cancer. HCV encodes a polymerase called NS5B that catalyzes replication of the viral RNA genome. Drugs inhibiting NS5B have shown impressive antiviral activity in recent clinical trials. Appleby et al. (see the Perspective by Bressanelli) reveal the inner workings of HCV RNA replication by analyzing… 

Using the Hepatitis C Virus RNA-Dependent RNA Polymerase as a Model to Understand Viral Polymerase Structure, Function and Dynamics

The structural and functional properties of the HCV RNA-dependent RNA polymerase (NS5B) are reviewed in order to understand the fundamental processes underlying the replication of viral genomes.

Kickstarting a viral RNA polymerase

New crystal structures of HCV NS5B are described that are a major advance both in the basic understanding of RdRp activity and in the way sofosbuvir can inhibit HCV replication.

Evidence for Internal Initiation of RNA Synthesis by the Hepatitis C Virus RNA-Dependent RNA Polymerase NS5B In Cellulo

The data indicate that the HCV replicase is capable of internal initiation in its natural environment, although functional replication likely requires only terminal initiation.

Structure of the RNA-dependent RNA polymerase from COVID-19 virus

The structure of the COVID-19 virus polymerase essential for viral replication provides a basis for the design of new antiviral drugs that target viral RdRp, also named nsp12, and it appears to be a primary target for the antiviral drug remdesivir.

Akt Phosphorylation of Hepatitis C Virus NS5B Regulates Polymerase Activity and Hepatitis C Virus Infection

In this work, several amino acids of NS5B that are phosphorylated by Akt are identified, with positions S27, T53, T267, and S282 giving the most robust results, and phosphorylation of NS 5B by cellular kinases is a mechanism of viral polymerase inactivation.

Targeting the RdRp of Emerging RNA Viruses: The Structure-Based Drug Design Challenge

This work overviews the main sequence and structural features of the RdRp of emerging RNA viruses, as well as inhibition strategies implemented so far, and provides examples of success stories such as for HCV and SARS-CoV-2.

Recapitulating Trafficking of Nucleosides Into the Active Site of Polymerases of RNA Viruses: The Challenge and the Prize

An account of ribose-modified nucleoside analogs as inhibitors of viral RdRPS and of why taking into account the dynamics of these polymerases is necessary to understand nucleotide selection by RdRps is given.

Inhibition of Viral RNA-Dependent RNA Polymerases by Nucleoside Inhibitors: An Illustration of the Unity and Diversity of Mechanisms

  • S. Barik
  • Biology
    International journal of molecular sciences
  • 2022
A molecular commentary on the molecular structural basis of synthetic nucleoside analogs' inhibitory interactions with RdRP is offered, revealing both traditional and novel mechanisms including a delayed chain termination effect.

HCV Molecular Virology and Animal Models

This chapter is divided into two parts and begins with a short introduction to HCV and its life cycle and reviews insights into biochemical and functional characteristics of HCV RNA elements and proteins.

The hepatitis C virus RNA-dependent RNA polymerase directs incoming nucleotides to its active site through magnesium-dependent dynamics within its F motif

This work used molecular modeling and molecular dynamics simulations, starting from the available crystal structures of HCV NS5B in ternary complex with template-primer duplexes and nucleotides, to address the question of ribonucleotide entry into the active site of viral RdRp and provide further details on the original nucleotide selection mechanism operating in RdRps of RNA viruses.



Structure of Hepatitis C Virus Polymerase in Complex with Primer-Template RNA

The removal of an autoinhibitory β-hairpin loop from genotype 2a HCV NS5B increases de novo RNA synthesis by >100-fold, promotes RNA binding, and facilitated the determination of the first crystallographic structures of HCV polymerase in complex with RNA primer-template pairs.

Two Crucial Early Steps in RNA Synthesis by the Hepatitis C Virus Polymerase Involve a Dual Role of Residue 405

In vitro dissections of de novo synthesis for J6 and JFH1 NS5B proteins, as well as for mutants at position 405 of several genotype 1 and 2 strains, show that an isoleucine at position405 can promote both dinucleotide formation and the transition to elongation.

Nucleotide prodrugs for the treatment of HCV infection.

  • M. Sofia
  • Biology, Medicine
    Advances in pharmacology
  • 2013

A Comprehensive Structure-Function Comparison of Hepatitis C Virus Strain JFH1 and J6 Polymerases Reveals a Key Residue Stimulating Replication in Cell Culture across Genotypes

A structural comparison of JFH1 and J6 at high resolution indicated a clear correlation of a closed-thumb conformation of the RdRp and the efficiency of the enzyme at de novo RNA synthesis, in accordance with the proposal that I405 enhances de noovo initiation.

Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus.

This superposition reveals the majority of the amino acid residues of the hepatitis C virus enzyme that are likely to be implicated in binding to the replicating RNA molecule and to the incoming NTP and suggests a rearrangement of the thumb domain as well as a possible concerted movement of thumb and fingertips during translocation of the RNA template-primer in successive polymerization rounds.

General Catalytic Deficiency of Hepatitis C Virus RNA Polymerase with an S282T Mutation and Mutually Exclusive Resistance towards 2′-Modified Nucleotide Analogues

The determination of the molecular mechanism by which the S282T mutation confers resistance to 2′-modified nucleotide analogues suggests not only that “2′-conformer” analogues target distinct steps in RNA synthesis but also that these analogues have interesting potential in combination therapies.

Further Insights into the Roles of GTP and the C Terminus of the Hepatitis C Virus Polymerase in the Initiation of RNA Synthesis*

A combined structural and functional analysis of genotype 1 HCV-NS5b of strains H77, for which no structure has been previously reported, and J4, finds that GTP specifically stimulates this transition irrespective of its incorporation in neosynthesized RNA.

Inhibition of Hepatitis C Virus RNA Replication by 2′-Modified Nucleoside Analogs*

The identification of 2′-substituted nucleosides as inhibitors of HCV replication is described, with significantly higher concentrations of 2-C-methyladenosine triphosphate than 2-O-methylcytidine triph phosphate detected, consistent with the greater potency of 2‐C- methyl adenosine in the replicon assay, despite similar inhibition of NS5B by the triph phosphate in the in vitroenzyme assays.

Template/Primer Requirements and Single Nucleotide Incorporation by Hepatitis C Virus Nonstructural Protein 5B Polymerase

Specific template/primer requirements for efficient RNA synthesis by HCV NS5B were investigated and it was found that HCVNS5B utilized di- or trinucleotides efficiently to initiate RNA replication.