scholarly journals Effects of the Q80K Polymorphism on the Physicochemical Properties of Hepatitis C Virus Subtype 1a NS3 Protease

Viruses ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 691
Author(s):  
Allan Peres-da-Silva ◽  
Deborah Antunes ◽  
André Luiz Quintanilha Torres ◽  
Ernesto Raul Caffarena ◽  
Elisabeth Lampe
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Physicochemical Properties ◽  
Comparative Modeling ◽  
Amino Acid Residues ◽  
Structural Protein ◽  
Virus Genotype ◽  
Genetic Barriers ◽  
Dynamics Simulations ◽  
Ns3 Protease

Hepatitis C virus genotype 1a (HCV-1a) comprises clades I and II. The Q80K polymorphism is found predominantly in clade I but rarely in clade II. Here, we investigated whether natural polymorphisms in HCV-1a clade II entailed structural protein changes when occurrence of the Q80K variant was simulated. Based on HCV-1a clade I and II protein sequences, the structure of the HCV-1a Q80K mutant NS3-4A was obtained by comparative modeling. Its physicochemical properties were studied by molecular dynamics simulations and network analysis. Results demonstrate that, in the presence of the K80 variant, clade II protease polymorphisms A91 and S/G174 led to variations in hydrogen bond occupancies. Structural analyses revealed differences in (i) flexibility of the H57 catalytic residue on the NS3 protease and (ii) correlations between amino acids on the NS3 protease and the NS4A cofactor. The latter indicated possible destabilization of interactions, resulting in increased separation of these proteins. The present findings describe how the relationships between different HCV-1a NS3 protease amino acid residues could affect the appearance of viral variants and the existence of distinct genetic barriers to HCV-1a isolates.

scholarly journals Viral Resistance in Hepatitis C Virus Genotype 1-Infected Patients Receiving the NS3 Protease Inhibitor Faldaprevir (BI 201335) in a Phase 1b Multiple-Rising-Dose Study

2013 ◽  
Vol 57 (10) ◽  
pp. 4928-4936 ◽  
Author(s):  
Kristi L. Berger ◽  
Lisette Lagacé ◽  
Ibtissem Triki ◽  
Mireille Cartier ◽  
Martin Marquis ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Protease Inhibitor ◽  
Genotype 1 ◽  
Resistance Mutations ◽  
Virus Genotype ◽  
Drug Pressure ◽  
Phase 1B ◽  
Ns3 Protease ◽  
Emergence Of Resistance

ABSTRACTFaldaprevir (BI 201335) is a selective NS3/4A protease inhibitor under development for the treatment of chronic hepatitis C virus (HCV) infection. NS3/4A genotyping and NS3 protease phenotyping analyses were performed to monitor the emergence of resistance in patients with HCV genotype 1 infection receiving faldaprevir alone or combined with pegylated interferon alfa 2a and ribavirin (PegIFN-RBV) during a phase 1b study. Among all baseline variants, a maximum 7-fold reduction inin vitrosensitivity to faldaprevir was observed for a rare NS3 (V/I)170T polymorphism. During faldaprevir monotherapy in treatment-naive patients, virologic breakthrough was common (77%, 20/26) and was associated with the emergence of resistance mutations predominantly carrying NS3 substitutions R155K in GT1a and D168V in GT1b. D168V conferred a greater reduction in faldaprevir sensitivity (1,800-fold) than R155K (330-fold); however, D168V was generally less fit than R155K in the absence of selective drug pressure. Treatment-experienced patients treated with faldaprevir-PegIFN-RBV triple therapy showed higher viral load reductions, lower rates of breakthrough (8%, 5/62), and less frequent emergence of resistance-associated variants compared with faldaprevir monotherapy. (This study has been registered at ClinicalTrials.gov under registration no. NCT00793793.)

NS3 protease resistance-associated substitutions in liver tissue and plasma samples from patients infected by hepatitis C virus genotype 1A or 1B

2017 ◽  
Vol 162 (8) ◽  
pp. 2271-2277 ◽  
Author(s):  
Giulia Morsica ◽  
Andrea Andolina ◽  
Marco Merli ◽  
Emanuela Messina ◽  
Hamid Hasson ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Liver Tissue ◽  
Plasma Samples ◽  
Virus Genotype ◽  
Protease Resistance ◽  
Genotype 1A ◽  
Ns3 Protease

scholarly journals Impact of Preexisting Hepatitis C Virus Genotype 6 NS3, NS5A, and NS5B Polymorphisms on theIn VitroPotency of Direct-Acting Antiviral Agents

2019 ◽  
Vol 63 (4) ◽  
Author(s):  
Fiona McPhee ◽  
Joseph Ueland ◽  
Vincent Vellucci ◽  
Scott Bowden ◽  
William Sievert ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Antiviral Agents ◽  
Virologic Response ◽  
Virus Genotype ◽  
Direct Acting Antiviral ◽  
East And Southeast Asia ◽  
Direct Acting ◽  
Ns3 Protease

ABSTRACTHCV genotype 6 (GT-6) is found predominantly in East and Southeast Asia. Clinical studies have focused on patients infected with hepatitis C virus (HCV) GT-6a, where high sustained virologic response (SVR) rates to direct-acting antivirals (DAAs) have been achieved. However, GT-6 is highly diverse, with 29 reported subtypes. We explored the diversity of GT-6 polymorphisms at residues associated with DAA resistance, their impact on DAAin vitropotency when evaluated in a GT-6a consensus replicon, and their association with specific GT-6 subtypes. GT-6 sequences from 25 patient-derived samples and 105 sequences from the U.S. HCV database were compared, and substitutions at resistance-associated residue positions were phenotyped against different DAAs. Preexisting resistance-associated substitutions (RASs) to NS3 protease (A156V and D168E) and NS5B nucleotide (L159F and S282C) inhibitors were rare (<4%). Preexisting RASs to NS5A inhibitors were common, especially at L28 (A/F/G/M/T/V) and R30 (E/N/S).In vitrosusceptibilities of NS5A-L28A and -L28T were dramatically reduced against all tested NS5A drugs (90% effective concentration [EC90] range, 119 to 2,032 nM) compared with susceptibilities against a GT-6a consensus replicon (EC90range, 0.1 to 19 nM). These L28 RASs preexisted in combination with R30S (EC90[L28A-R30S] of ≥720 nM or EC90[L28T-R30S] of ≥128 nM against tested DAAs) or as L28T-L31I (EC90[tested DAAs] of >5,000 nM) and were detected in evaluated GT-6b and -6f sequences. NS5A-L28A-R30A, observed in GT-6r, did not replicate. In conclusion, HCV GT-6b, GT-6f, and GT-6r sequences harbored highly resistant RASs to all evaluated NS5A drugs. Therefore, monitoring SVR in patients infected with these GT-6 subtypes treated with NS5A drug-containing regimens is suggested to confirm any association between noted NS5A polymorphisms and treatment failure.

scholarly journals Infectious cDNA clone of the hepatitis C virus genotype 1 prototype sequence

2001 ◽  
Vol 82 (6) ◽  
pp. 1291-1297 ◽  
Author(s):  
Robert E. Lanford ◽  
Helen Lee ◽  
Deborah Chavez ◽  
Bernadette Guerra ◽  
Kathleen M. Brasky
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Cdna Clone ◽  
Infectious Cdna Clone ◽  
Full Length ◽  
Cdna Clones ◽  
Amino Acid Residues ◽  
Genotype 1 ◽  
Virus Genotype ◽  
Hcv Genotype 1

A full-length cDNA clone of the hepatitis C virus (HCV) genotype 1 prototype (subtype 1a) sequence was constructed. Synthetic RNA produced from the initial cDNA clone was not infectious following intrahepatic inoculation of a chimpanzee. A consensus clone was prepared by comparison with multiple full-length HCV sequences of genotypes 1, 2 and 3. A total of 11 non-consensus amino acid residues were altered by mutagenesis. Synthetic RNA from the repaired clone initiated a typical, acute-resolving HCV infection following intrahepatic inoculation of a chimpanzee. In addition, at least one of three chimeric cDNA clones constructed between the HCV-1 and H77 genotype 1a strains of HCV was infectious in a chimpanzee. This is the first example of an infectious chimeric HCV clone. An infectious cDNA clone of HCV-1 will be of particular value, since it is the prototype HCV sequence and many commonly used reagents are based on this sequence.

Genetic heterogeneity of the NS3 protease gene in hepatitis C virus genotype 1 from untreated infected patients

2005 ◽  
Vol 75 (4) ◽  
pp. 528-537 ◽  
Author(s):  
Sophie Vallet ◽  
Stephanie Gouriou ◽  
Jean-Baptiste Nousbaum ◽  
Marie-Christine Legrand-Quillien ◽  
Alain Goudeau ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Genetic Heterogeneity ◽  
Protease Gene ◽  
Genotype 1 ◽  
Virus Genotype ◽  
Ns3 Protease

scholarly journals Hepatitis C virus non-structural protein NS3 interacts with LMP7, a component of the immunoproteasome, and affects its proteasome activity

2004 ◽  
Vol 384 (2) ◽  
pp. 401-409 ◽  
Author(s):  
Yee-Ling KHU ◽  
Yee-Joo TAN ◽  
Seng Gee LIM ◽  
Wanjin HONG ◽  
Phuay-Yee GOH
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Protease Activity ◽  
Immune Surveillance ◽  
Stable Cell Line ◽  
Helicase Domain ◽  
Structural Protein ◽  
Subgenomic Replicon ◽  
Ns3 Protease

NS3, a non-structural protein of the HCV (hepatitis C virus), contains a protease and a helicase domain and plays essential roles in the processing of the viral polyprotein, viral RNA replication and translation. LMP7 (low-molecular-mass protein 7), a component of the immunoproteasome, was identified as an NS3-binding protein from yeast two-hybrid screens, and this interaction was confirmed by in vitro binding and co-immunoprecipitation analysis. The minimal domain of interaction was defined to be between the pro-sequence region of LMP7 (amino acids 1–40) and the protease domain of NS3. To elucidate the biological importance of this interaction, we studied the effect of this interaction on NS3 protease activity and on LMP7 immunoproteasome activity. Recombinant LMP7 did not have any effect on NS3 protease activity in vitro. The peptidase activities of LMP7 immunoproteasomes, however, were markedly reduced when tested in a stable cell line containing a HCV subgenomic replicon. The down-regulation of proteasome peptidase activities could interfere with the processing of viral antigens for presentation by MHC class I molecules, and may thus protect HCV from host immune surveillance mechanisms to allow persistent infection by the virus.

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