NS3 Peptide, a Novel Potent Hepatitis C Virus NS3 Helicase Inhibitor: Its Mechanism of Action and Antiviral Activity in the Replicon System

Abstract

Hepatitis C virus (HCV) chronic infections represent one of the major and still unresolved health problems because of low efficiency and high cost of current therapy. Therefore, our studies centered on a viral protein, the NS3 helicase, whose activity is indispensable for replication of the viral RNA, and on its peptide inhibitor that corresponds to a highly conserved arginine-rich sequence of domain 2 of the helicase. The NS3 peptide (p14) was expressed in bacteria. Its 50% inhibitory activity in a fluorometric helicase assay corresponded to 725 nM, while the ATPase activity of NS3 was not affected. Nuclear magnetic resonance (NMR) studies of peptide-protein interactions using the relaxation filtering technique revealed that p14 binds directly to the full-length helicase and its separately expressed domain 1 but not to domain 2. Changes in the NMR chemical shift of backbone amide nuclei ( 1 H and 15 N) of domain 1 or p14, measured during complex formation, were used to identify the principal amino acids of both domain 1 and the peptide engaged in their interaction. In the proposed interplay model, p14 contacts the clefts between domains 1 and 2, as well as between domains 1 and 3, preventing substrate binding. This interaction is strongly supported by cross-linking experiments, as well as by kinetic studies performed using a fluorometric assay. The antiviral activity of p14 was tested in a subgenomic HCV replicon assay that showed that the peptide at micromolar concentrations can reduce HCV RNA replication.Hepatitis C virus (HCV) is a positive-strand RNA virus of the Flaviviridae family (11). HCV infection, affecting 3% of the world population, leads to chronic hepatitis in up to 85% of the cases, in 10 to 20% of the cases it develops into cirrhosis that requires constant treatment and provokes permanent infirmity, while 1 to 5% of chronically infected patients are diagnosed with hepatocellular carcinoma (9). No efficient treatment exists; even the new dual therapy with pegylated interferon alpha 2a or 2b and ribavirin is effective only in up to 60% of the cases, depending on the genotype of the virus and the duration of the treatment (21). To date, no vaccine against HCV has been developed in spite of numerous attempts and advanced trials, principally because of the high variability of the RNA genome and association of HCV particles with host lipoproteins and immunoglobulins (1, 15). Thus, nonstructural proteins involved in viral replication are being examined as targets of antiviral therapy. One of them is NS3 (serine protease/RNA helicase), whose helicase activity is indispensable for replication of the viral RNA (25). The helicase part of NS3 folds into three domains of comparable size (domains 1, 2, and 3) that form a triangular molecule. Five structures of the NS3 helicase have been resolved by X-ray crystallography. The latest resolved structure shows two helicases bound to a single DNA molecule and reveals an apparent interface between two protein molecules (33). The existence of oligomeric structures o...

RNA helicases in infection and disease

“…212 HCV helicase activity is inhibited in vitro by recombinant antibodies, 213,214 by RNA aptamers 215,216 and by peptides. 217,218 Targeting the nucleotide binding site of HCV-NS3 has proven exceedingly difficult, 219 although nucleotide-mimicking competitive inhibitors have been identified. 220,221 Ring-expanded nucleoside and nucleotide analogs have been shown to selectively inhibit HCV, West Nile Virus, and Japanese encephalitis virus NS3 helicases in vitro without affecting the activity of a control host helicase.…”

Alphavirus Antiviral Drug Development: Scientific Gap Analysis and Prospective Research Areas

“…49 Helicase activity has been exploited therapeutically, with drug candidates in preclinical development for both HCV and herpes simplex virus (HSV). 50,51 Helicase ALPHAVIRUS ANTIVIRAL DRUG DEVELOPMENT activity of nsP2 may be amenable to HTS, as fluorometric assays have been developed for the HCV NS3 helicase. 51 Nonstructural protein 3 (nsP3) is a phosphoprotein that is essential for virus replication.…”

Spectroscopic studies on the irreversible heat-induced structural transition of Pin1

“…To some proteins, thermal unfolding follow partially [12] or highly [13,14] reversible steps, and the reversibility may decrease in the presence of denaturants or high pH values. To some other proteins, especially the multi-domain proteins, thermal unfoldings are usually irreversible [23,24].…”