Expression and purification of a hepatitis C virus NS3/4A complex, and characterization of its helicase activity with the Scintillation Proximity Assay system

New hepatitis C virus drug discovery strategies and model systems

INTRODUCTION

Hepatitis C virus (HCV) is a major cause of liver disease worldwide and the leading indication for liver transplantation in the United States. Current treatment options are expensive, not effective in all patients and are associated with serious side effects. Although preclinical, anti-HCV drug screening is still hampered by the lack of readily infectable small animal models, the development of cell culture HCV experimental model systems has driven a promising new wave of HCV antiviral drug discovery.

AREAS COVERED

This review contains a concise overview of current HCV treatment options and limitations with a subsequent in-depth focus on the available experimental models and novel strategies that have, and continue to enable, important advances in HCV drug development.

EXPERT OPINION

With a large cohort of chronically HCV-infected patients progressively developing liver disease that puts them at risk for hepatocellular carcinoma and hepatic decompensation, there is an urgent need to develop effective therapeutics that are well tolerated and effective in all patients and against all HCV genotypes. Significant advances in HCV experimental model development have expedited drug discovery; however, additional progress is needed. Importantly, the current trends and momentum in the field suggests that we will continue to overcome critical experimental challenges to reach this end goal.

Fuel specificity of the hepatitis C virus NS3 helicase

The hepatitis C virus (HCV) NS3 protein is a helicase capable of unwinding duplex RNA or DNA. This study uses a newly developed molecular-beacon-based helicase assay (MBHA) to investigate how nucleoside triphosphates (NTPs) fuel HCV helicase-catalyzed DNA unwinding. The MBHA monitors the irreversible helicase-catalyzed displacement of an oligonucleotide-bound molecular beacon so that rates of helicase translocation can be directly measured in real time. The MBHA reveals that HCV helicase unwinds DNA at different rates depending on the nature and concentration of NTPs in solution, such that the fastest reactions are observed in the presence of CTP followed by ATP, UTP, and GTP. 3'-Deoxy-NTPs generally support faster DNA unwinding, with dTTP supporting faster rates than any other canonical (d)NTP. The presence of an intact NS3 protease domain makes HCV helicase somewhat less specific than truncated NS3 bearing only its helicase region (NS3h). Various NTPs bind NS3h with similar affinities, but each NTP supports a different unwinding rate and processivity. Studies with NTP analogs reveal that specificity is determined by the nature of the Watson-Crick base-pairing region of the NTP base and the nature of the functional groups attached to the 2' and 3' carbons of the NTP sugar. The divalent metal bridging the NTP to NS3h also influences observed unwinding rates, with Mn(2+) supporting about 10 times faster unwinding than Mg(2+). Unlike Mg(2+), Mn(2+) does not support HCV helicase-catalyzed ATP hydrolysis in the absence of stimulating nucleic acids. Results are discussed in relation to models for how ATP might fuel the unwinding reaction.

Understanding helicases as a means of virus control

Helicases are promising antiviral drug targets because their enzymatic activities are essential for viral genome replication, transcription, and translation. Numerous potent inhibitors of helicases encoded by herpes simplex virus, severe acute respiratory syndrome coronavirus, hepatitis C virus, Japanese encephalitis virus, West Nile virus, and human papillomavirus have been recently reported in the scientific literature. Some inhibitors have also been shown to decrease viral replication in cell culture and animal models. This review discusses recent progress in understanding the structure and function of viral helicases to help clarify how these potential antiviral compounds function and to facilitate the design of better inhibitors. The above helicases and all related viral proteins are classified here based on their evolutionary and functional similarities, and the key mechanistic features of each group are noted. All helicases share a common motor function fueled by ATP hydrolysis, but differ in exactly how the motor moves the protein and its cargo on a nucleic acid chain. The helicase inhibitors discussed here influence rates of helicase-catalyzed DNA (or RNA) unwinding by preventing ATP hydrolysis, nucleic acid binding, nucleic acid release, or by disrupting the interaction of a helicase with a required cofactor.

Viral and cellular RNA helicases as antiviral targets

To date, although many viral infections can be successfully prevented via vaccination, we lack effective knowledge of vaccines for numerous important human pathogens, including hepatitis C virus (HCV) and human immunodeficiency virus (HIV). Accordingly, antiviral drugs will be needed to treat many viral diseases. Virally encoded enzymes and cellular enzymes adapted for use by viruses for replication might represent useful targets for antiviral drugs.

Drugs that target either a viral or cellular polypeptide hold different implications. Inhibitors of unique viral functions have a lower risk of toxicity, whereas inhibitors of cellular enzymes that are used by viruses have a narrower window for efficacy without creating toxicity.

All viruses seem to require a helicase function for replication. HCV encodes a viral RNA helicase, and recent findings have shown that HIV-1 adapts a cellular RNA helicase for its viral lifecycle. These observations raise the possibility of small-molecule helicase inhibitors as a general mode of antiviral therapy.

Helicases fall into three super-families (SF1, SF2 and SF3) with conserved motifs. The conserved motifs are associated with conserved helicase function. However, outside of the conserved motifs the primary sequences and tertiary structures between helicases are differ greatly. In this regard, differences in primary sequence and tertiary structure between the helicase of a viral pathogen and that of cellular helicases can be exploited to confer specificity to an antiviral inhibitor.

The conformation of an active helicase can be broadly divided into an 'open' and a 'closed' complex. Strategies for identifying small-molecule helicase inhibitors include: inhibiting NTPase activity by direct competition with NTP binding; competitively inhibit nucleic-acid binding; inhibiting NTP hydrolysis or NDP release by blocking the movement of domain 2; inhibiting the process that couples NTP hydrolysis to translocation and unwinding of nucleic acid; inhibiting unwinding by sterically blocking helicase translocation; and inhibiting unwinding. Other potential inhibitory mechanisms include those that change the physical conformation of the helicase, or those that disrupt helicase turnover, or those that inhibit helicase interaction with other crucial proteins.

Preclinical proof of concept for helicase inhibitors as antiviral agents has been obtained for HSV. This breakthrough finding provides the best evidence to date that it is possible to develop selective, potent inhibitors of a viral helicase as antiviral agents. Searches are ongoing for antihelicase molecules that have activity against HCV or HIV-1.

Although there has been considerable progress in the development of antiviral agents in recent years, there is still a pressing need for new drugs both to improve on the properties of existing agents and to combat the problem of viral resistance. Helicases, both viral and human, have recently emerged as novel targets for the treatment of viral infections. Here, we discuss the role of these enzymes, factors affecting their potential as drug targets and progress in the development of agents that inhibit their activity using the hepatitis C virus-encoded helicase NS3 and the cellular helicase DDX3 adopted for use by HIV-1 as examples.