1
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Frericks N, Brown RJP, Reinecke BM, Herrmann M, Brüggemann Y, Todt D, Miskey C, Vondran FWR, Steinmann E, Pietschmann T, Sheldon J. Unraveling the dynamics of hepatitis C virus adaptive mutations and their impact on antiviral responses in primary human hepatocytes. J Virol 2024; 98:e0192123. [PMID: 38319104 PMCID: PMC10949430 DOI: 10.1128/jvi.01921-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Hepatitis C virus (HCV) infection progresses to chronicity in the majority of infected individuals. Its high intra-host genetic variability enables HCV to evade the continuous selection pressure exerted by the host, contributing to persistent infection. Utilizing a cell culture-adapted HCV population (p100pop) which exhibits increased replicative capacity in various liver cell lines, this study investigated virus and host determinants that underlie enhanced viral fitness. Characterization of a panel of molecular p100 clones revealed that cell culture adaptive mutations optimize a range of virus-host interactions, resulting in expanded cell tropism, altered dependence on the cellular co-factor micro-RNA 122 and increased rates of virus spread. On the host side, comparative transcriptional profiling of hepatoma cells infected either with p100pop or its progenitor virus revealed that enhanced replicative fitness correlated with activation of endoplasmic reticulum stress signaling and the unfolded protein response. In contrast, infection of primary human hepatocytes with p100pop led to a mild attenuation of virion production which correlated with a greater induction of cell-intrinsic antiviral defense responses. In summary, long-term passage experiments in cells where selective pressure from innate immunity is lacking improves multiple virus-host interactions, enhancing HCV replicative fitness. However, this study further indicates that HCV has evolved to replicate at low levels in primary human hepatocytes to minimize innate immune activation, highlighting that an optimal balance between replicative fitness and innate immune induction is key to establish persistence. IMPORTANCE Hepatitis C virus (HCV) infection remains a global health burden with 58 million people currently chronically infected. However, the detailed molecular mechanisms that underly persistence are incompletely defined. We utilized a long-term cell culture-adapted HCV, exhibiting enhanced replicative fitness in different human liver cell lines, in order to identify molecular principles by which HCV optimizes its replication fitness. Our experimental data revealed that cell culture adaptive mutations confer changes in the host response and usage of various host factors. The latter allows functional flexibility at different stages of the viral replication cycle. However, increased replicative fitness resulted in an increased activation of the innate immune system, which likely poses boundary for functional variation in authentic hepatocytes, explaining the observed attenuation of the adapted virus population in primary hepatocytes.
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Affiliation(s)
- Nicola Frericks
- Institute for Experimental Virology, TWINCORE, Hannover, Germany
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Richard J. P. Brown
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
- Division of Veterinary Medicine, Paul Ehrlich Institute, Langen, Germany
| | | | - Maike Herrmann
- Division of Veterinary Medicine, Paul Ehrlich Institute, Langen, Germany
| | - Yannick Brüggemann
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Daniel Todt
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
- European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Florian W. R. Vondran
- Department for General, Visceral and Transplant Surgery, Hannover Medical School, Hannover, Germany
- Clinic for General, Visceral and Transplant Surgery, University Hospital RWTH Aachen, Aachen, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Eike Steinmann
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Thomas Pietschmann
- Institute for Experimental Virology, TWINCORE, Hannover, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Julie Sheldon
- Institute for Experimental Virology, TWINCORE, Hannover, Germany
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2
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Farouk F, Ibrahim IM, Sherif S, Abdelhamed HG, Sharaky M, Al-Karmalawy AA. Investigating the effect of polymerase inhibitors on cellular proliferation: Computational studies, cytotoxicity, CDK1 inhibitory potential, and LC-MS/MS cancer cell entrapment assays. Chem Biol Drug Des 2024; 103:e14500. [PMID: 38467555 DOI: 10.1111/cbdd.14500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 02/04/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
Directly acting antivirals (DAAs) are a breakthrough in the treatment of HCV. There are controversial reports on their tendency to induce hepatocellular carcinoma (HCC) in HCV patients. Numerous reports have concluded that the HCC is attributed to patient-related factors while others are inclined to attribute this as a DAA side-effect. This study aims to investigate the effect of polymerase inhibitor DAAs, especially daclatasivir (DLT) on cellular proliferation as compared to ribavirin (RBV). The interaction of DAAs with variable cell-cycle proteins was studied in silico. The binding affinities to multiple cellular targets were investigated and the molecular dynamics were assessed. The in vitro effect of the selected candidate DLT on cancer cell proliferation was determined and the CDK1 inhibitory potential in was evaluated. Finally, the cellular entrapment of the selected candidates was assessed by an in-house developed and validated LC-MS/MS method. The results indicated that polymerase inhibitor antiviral agents, especially DLT, may exert an anti-proliferative potential against variable cancer cell lines. The results showed that the effect may be achieved via potential interaction with the multiple cellular targets, including the CDK1, resulting in halting of the cellular proliferation. DLT exhibited a remarkable cell permeability in the liver cancer cell line which permits adequate interaction with the cellular targets. In conclusion, the results reveal that the polymerase inhibitor (DLT) may have an anti-proliferative potential against liver cancer cells. These results may pose DLT as a therapeutic choice for patients suffering from HCV and are liable to HCC development.
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Affiliation(s)
- Faten Farouk
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
| | - Ibrahim M Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Salma Sherif
- Faculty of Women for Arts, Science and Education, Ain Shams University, Cairo, Egypt
| | | | - Marwa Sharaky
- Pharmacology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
- Biochemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
| | - Ahmed A Al-Karmalawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta, Egypt
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3
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Frericks N, Brown RJP, Reinecke BM, Herrmann M, Brüggemann Y, Todt D, Miskey C, Vondran FWR, Steinmann E, Pietschmann T, Sheldon J. Hepatitis C virus cell culture adaptive mutations enhance cell culture propagation by multiple mechanisms but boost antiviral responses in primary human hepatocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568224. [PMID: 38045248 PMCID: PMC10690267 DOI: 10.1101/2023.11.22.568224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Hepatitis C virus (HCV) infection progresses to chronicity in the majority of infected individuals. Its high intra-host genetic variability enables HCV to evade the continuous selection pressure exerted by the host, contributing to persistent infection. Utilizing a cell culture adapted HCV population (p100pop) which exhibits increased replicative capacity in various liver cell lines, this study investigated virus and host determinants which underlie enhanced viral fitness. Characterization of a panel of molecular p100 clones revealed that cell culture adaptive mutations optimize a range of virus-host interactions, resulting in expanded cell tropism, altered dependence on the cellular co-factor micro-RNA 122 and increased rates of virus spread. On the host side, comparative transcriptional profiling of hepatoma cells infected either with p100pop or its progenitor virus revealed that enhanced replicative fitness correlated with activation of endoplasmic reticulum stress signaling and the unfolded protein response. In contrast, infection of primary human hepatocytes with p100pop led to a mild attenuation of virion production which correlated with a greater induction of cell-intrinsic antiviral defense responses. In summary, long-term passage experiments in cells where selective pressure from innate immunity is lacking improves multiple virus-host interactions, enhancing HCV replicative fitness. However, this study further indicates that HCV has evolved to replicate at low levels in primary human hepatocytes to minimize innate immune activation, highlighting that an optimal balance between replicative fitness and innate immune induction is key to establishing persistence. Author Summary HCV infection remains a global health burden with 58 million people currently chronically infected. However, the detailed molecular mechanisms which underly persistence are incompletely defined. We utilized a long-term cell culture adapted HCV, exhibiting enhanced replicative fitness in different human liver cell lines, in order to identify molecular principles by which HCV optimizes its replication fitness. Our experimental data revealed that cell culture adaptive mutations confer changes in the host response and usage of various host factors. The latter allows functional flexibility at different stages of the viral replication cycle. However, increased replicative fitness resulted in an increased activation of the innate immune system, which likely poses boundary for functional variation in authentic hepatocytes, explaining the observed attenuation of the adapted virus population in primary hepatocytes.
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4
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Mamatis JE, Gallardo-Flores CE, Sangwan U, Tooley TH, Walsh T, Colpitts CC. Induction of antiviral gene expression by cyclosporine A, but not inhibition of cyclophilin A or B, contributes to its restriction of human coronavirus 229E infection in a lung epithelial cell line. Antiviral Res 2023; 219:105730. [PMID: 37805057 DOI: 10.1016/j.antiviral.2023.105730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/09/2023]
Abstract
The development of antivirals with an extended spectrum of activity is an attractive possibility to protect against future emerging coronaviruses (CoVs). Cyclosporine A (CsA), a clinically approved immunosuppressive drug, has established antiviral activity against diverse unrelated viruses, including several CoVs. However, its antiviral mechanisms of action against CoV infection have remained elusive, precluding the rational design of non-immunosuppressive derivatives with improved antiviral activities. In this study, we evaluated the mechanisms of CsA against HCoV-229E infection in a human lung epithelial cell line. We demonstrate that the antiviral activity of CsA against HCoV-229E is independent of classical CsA target proteins, cyclophilin A or B, which are not required host factors for HCoV-229E in A549 cells. Instead, CsA treatment induces expression of antiviral genes in a manner dependent on interferon regulatory factor 1, but independent of classical interferon responses, which contributes to its inhibitory effect against HCoV-229E infection. Our results also point to a role for the HCoV-229E nucleoprotein in antagonizing activation of type I interferon, but we show that CsA treatment does not affect evasion of innate immune signalling pathways by HCoV-229E. Overall, our findings further the understanding of the antiviral mechanisms of CsA against CoV infection and highlight a novel immunomodulatory strategy to inhibit CoV infection that may inform future drug development efforts.
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Affiliation(s)
- John E Mamatis
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Carla E Gallardo-Flores
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Ujjwal Sangwan
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Trinity H Tooley
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Taylor Walsh
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Che C Colpitts
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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5
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Stauffer W, Bobardt M, Ure D, Foster R, Gallay P. The Cyclophilin Inhibitor Rencofilstat Decreases HCV-Induced Hepatocellular Carcinoma Independently of Its Antiviral Activity. Viruses 2023; 15:2099. [PMID: 37896876 PMCID: PMC10612079 DOI: 10.3390/v15102099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
There is an urgent need for the identification of new drugs that inhibit HCV-induced hepatocellular carcinoma (HCC). Our work demonstrates that cyclophilin inhibitors (CypIs) represent such new drugs. We demonstrate that the nonimmunosuppressive cyclosporine A (CsA) analog (CsAa) rencofilstat possesses dual therapeutic activities for the treatment of HCV infection and HCV-induced HCC. Specifically, we show that the HCV infection of humanized mice results in the progressive development of HCC. This is true for the four genotypes tested (1 to 4). Remarkably, we demonstrate that rencofilstat inhibits the development of HCV-induced HCC in mice even when added 16 weeks after infection when HCC is well established. Importantly, we show that rencofilstat drastically reduces HCC progression independently of its anti-HCV activity. Indeed, the CypI rencofilstat inhibits HCC, while other anti-HCV agents such as NS5A (NS5Ai) and NS5B (NS5Bi) fail to reduce HCC. In conclusion, this study shows for the first time that the CypI rencofilstat represents a potent therapeutic agent for the treatment of HCV-induced HCC.
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Affiliation(s)
- Winston Stauffer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (W.S.); (M.B.)
| | - Michael Bobardt
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (W.S.); (M.B.)
| | - Daren Ure
- Hepion Pharmaceuticals Inc., Edison, NJ 08837, USA; (D.U.); (R.F.)
| | - Robert Foster
- Hepion Pharmaceuticals Inc., Edison, NJ 08837, USA; (D.U.); (R.F.)
| | - Philippe Gallay
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (W.S.); (M.B.)
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6
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Stauffer W, Bobardt M, Ure D, Foster R, Gallay P. The Cyclophilin Inhibitor Rencofilstat Decreases HCV-induced Hepatocellular Carcinoma Independently of Its Antiviral Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553982. [PMID: 37645728 PMCID: PMC10462172 DOI: 10.1101/2023.08.19.553982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
There is an urgent need for the identification of new drugs that inhibit HCV-induced hepatocellular carcinoma (HCC). Our work demonstrates that cyclophilin inhibitors (CypI) represent such new drugs. We demonstrated that the non-immunosuppressive cyclosporine A (CsA) analog (CsAa) rencofilstat possesses dual therapeutic activities for the treatment of HCV infection and HCV-induced HCC. Specifically, we showed that HCV infection of humanized mice results in the progressive development of HCC. This was true for four genotypes tested (1 to 4). Remarkably, we demonstrated that rencofilstat inhibits the development of HCV-induced HCC in mice even when added 16 weeks post-infection when HCC is well established. Importantly, we showed that rencofilstat drastically reduces HCC progression independently of its anti-HCV activity. Indeed, the CypI rencofilstat inhibits HCC while other anti-HCV agents such as NS5A (NS5Ai) and NS5B (NS5Bi) fail to reduce HCC. In conclusion, this study shows for the first time that the CypI rencofilstat represents a potent therapeutic agent for the treatment of HCV-induced HCC.
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Affiliation(s)
- Winston Stauffer
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Michael Bobardt
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Daren Ure
- Hepion Pharmaceuticals Inc., Edison, New Jersey, USA
| | - Robert Foster
- Hepion Pharmaceuticals Inc., Edison, New Jersey, USA
| | - Philippe Gallay
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, California, USA
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7
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Liu D, Ndongwe TP, Ji J, Huber AD, Michailidis E, Rice CM, Ralston R, Tedbury PR, Sarafianos SG. Mechanisms of Action of the Host-Targeting Agent Cyclosporin A and Direct-Acting Antiviral Agents against Hepatitis C Virus. Viruses 2023; 15:981. [PMID: 37112961 PMCID: PMC10143304 DOI: 10.3390/v15040981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Several direct-acting antivirals (DAAs) are available, providing interferon-free strategies for a hepatitis C cure. In contrast to DAAs, host-targeting agents (HTAs) interfere with host cellular factors that are essential in the viral replication cycle; as host genes, they are less likely to rapidly mutate under drug pressure, thus potentially exhibiting a high barrier to resistance, in addition to distinct mechanisms of action. We compared the effects of cyclosporin A (CsA), a HTA that targets cyclophilin A (CypA), to DAAs, including inhibitors of nonstructural protein 5A (NS5A), NS3/4A, and NS5B, in Huh7.5.1 cells. Our data show that CsA suppressed HCV infection as rapidly as the fastest-acting DAAs. CsA and inhibitors of NS5A and NS3/4A, but not of NS5B, suppressed the production and release of infectious HCV particles. Intriguingly, while CsA rapidly suppressed infectious extracellular virus levels, it had no significant effect on the intracellular infectious virus, suggesting that, unlike the DAAs tested here, it may block a post-assembly step in the viral replication cycle. Hence, our findings shed light on the biological processes involved in HCV replication and the role of CypA.
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Affiliation(s)
- Dandan Liu
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Tanya P. Ndongwe
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Juan Ji
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Andrew D. Huber
- CS Bond Life Sciences Center, Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65201, USA
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Biochemical Pharmacology, Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Robert Ralston
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Philip R. Tedbury
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
- Laboratory of Biochemical Pharmacology, Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Stefan G. Sarafianos
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
- Laboratory of Biochemical Pharmacology, Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
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8
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Schiene‐Fischer C, Fischer G, Braun M. Non-Immunosuppressive Cyclophilin Inhibitors. Angew Chem Int Ed Engl 2022; 61:e202201597. [PMID: 35290695 PMCID: PMC9804594 DOI: 10.1002/anie.202201597] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Indexed: 01/05/2023]
Abstract
Cyclophilins, enzymes with peptidyl-prolyl cis/trans isomerase activity, are relevant to a large variety of biological processes. The most abundant member of this enzyme family, cyclophilin A, is the cellular receptor of the immunosuppressive drug cyclosporine A (CsA). As a consequence of the pathophysiological role of cyclophilins, particularly in viral infections, there is a broad interest in cyclophilin inhibition devoid of immunosuppressive activity. This Review first gives an introduction into the physiological and pathophysiological roles of cyclophilins. The presentation of non-immunosuppressive cyclophilin inhibitors will commence with drugs based on chemical modifications of CsA. The naturally occurring macrocyclic sanglifehrins have become other lead structures for cyclophilin-inhibiting drugs. Finally, de novo designed compounds, whose structures are not derived from or inspired by natural products, will be presented. Relevant synthetic concepts will be discussed, but the focus will also be on biochemical studies, structure-activity relationships, and clinical studies.
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Affiliation(s)
- Cordelia Schiene‐Fischer
- Institute of Biochemistry and BiotechnologyMartin-Luther-University Halle-Wittenberg06099Halle (Saale)Germany
| | - Gunter Fischer
- Max Planck Institute for Biophysical Chemistry37077GöttingenGermany
| | - Manfred Braun
- Institute of Organic and Macromolecular ChemistryHeinrich-Heine-University Düsseldorf40225DüsseldorfGermany
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9
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Han J, Kyu Lee M, Jang Y, Cho WJ, Kim M. Repurposing of cyclophilin A inhibitors as broad-spectrum antiviral agents. Drug Discov Today 2022; 27:1895-1912. [PMID: 35609743 PMCID: PMC9123807 DOI: 10.1016/j.drudis.2022.05.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/30/2022] [Accepted: 05/18/2022] [Indexed: 12/28/2022]
Abstract
Cyclophilin A (CypA) is linked to diverse human diseases including viral infections. With the worldwide emergence of severe acute respiratory coronavirus 2 (SARS-CoV-2), drug repurposing has been highlighted as a strategy with the potential to speed up antiviral development. Because CypA acts as a proviral component in hepatitis C virus, coronavirus and HIV, its inhibitors have been suggested as potential treatments for these infections. Here, we review the structure of cyclosporin A and sanglifehrin A analogs as well as synthetic micromolecules inhibiting CypA; and we discuss their broad-spectrum antiviral efficacy in the context of the virus lifecycle.
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Affiliation(s)
- Jinhe Han
- College of Pharmacy, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Myoung Kyu Lee
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Yejin Jang
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Won-Jea Cho
- College of Pharmacy, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Meeheyin Kim
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea; Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea.
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10
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Braun M, Schiene-Fischer C, Fischer G. Non‐Immunosuppressive Cyclophilin Inhibitors. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Manfred Braun
- Heinrich-Heine-Universität Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Organic CHemistry Universitätsstr. 1 40225 Düsseldorf GERMANY
| | - Cordelia Schiene-Fischer
- Martin-Luther-Universität Halle-Wittenberg: Martin-Luther-Universitat Halle-Wittenberg Institute of Biochemistry and Biotechnology, GERMANY
| | - Gunter Fischer
- Max-Planck-Institut für Biophysikalische Chemie Abteilung Meiosis: Max-Planck-Institut fur Multidisziplinare Naturwissenschaften Abteilung Meiosis Max Planck Institute for Biophysical Chemistry GERMANY
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11
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Mamatis JE, Pellizzari-Delano IE, Gallardo-Flores CE, Colpitts CC. Emerging Roles of Cyclophilin A in Regulating Viral Cloaking. Front Microbiol 2022; 13:828078. [PMID: 35242122 PMCID: PMC8886124 DOI: 10.3389/fmicb.2022.828078] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/26/2022] [Indexed: 12/24/2022] Open
Abstract
Cellular cyclophilins (Cyps) such as cyclophilin A (CypA) have emerged as key players at the virus-host interface. As host factors required for the replication of many unrelated viruses, including human immunodeficiency virus (HIV), hepatitis C virus (HCV) and coronaviruses (CoVs), Cyps are attractive targets for antiviral therapy. However, a clear understanding of how these viruses exploit Cyps to promote their replication has yet to be elucidated. Recent findings suggest that CypA contributes to cloaking of viral replication intermediates, an evasion strategy that prevents detection of viral nucleic acid by innate immune sensors. Furthermore, Cyps are emerging to have roles in regulation of cellular antiviral signaling pathways. Recruitment of Cyps by viral proteins may interfere with their ability to regulate these signaling factors. Consistent with disruption of viral cloaking and innate immune evasion, treatment with Cyp inhibitors such as cyclosporine A (CsA) restores antiviral innate immunity and induces expression of a subset of antiviral genes that restrict viral infection, which may help to explain the broad antiviral spectrum of CsA. In this review, we provide an overview of the roles of CypA in viral cloaking and evasion of innate immunity, focusing on the underlying mechanisms and new perspectives for antiviral therapies.
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Affiliation(s)
- John E Mamatis
- Department of Biomedical and Molecular Sciences, Faculty of Health Sciences, Queen's University, Kingston, ON, Canada
| | - Isabella E Pellizzari-Delano
- Department of Biomedical and Molecular Sciences, Faculty of Health Sciences, Queen's University, Kingston, ON, Canada
| | - Carla E Gallardo-Flores
- Department of Biomedical and Molecular Sciences, Faculty of Health Sciences, Queen's University, Kingston, ON, Canada
| | - Che C Colpitts
- Department of Biomedical and Molecular Sciences, Faculty of Health Sciences, Queen's University, Kingston, ON, Canada
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12
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Stanciu C, Muzica CM, Girleanu I, Cojocariu C, Sfarti C, Singeap AM, Huiban L, Chiriac S, Cuciureanu T, Trifan A. An update on direct antiviral agents for the treatment of hepatitis C. Expert Opin Pharmacother 2021; 22:1729-1741. [PMID: 33896315 DOI: 10.1080/14656566.2021.1921737] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: The development of direct-acting antiviral (DAA) agents for the treatment of hepatitis C virus (HCV) infection has completely transformed the management of this disease. The advantages of using DAA therapies include high efficacy (sustained virological response (SVR) rate >95%) with minimal side effects, good tolerability, easy drug administration (once daily oral dosing), and short duration of treatment (8-12 weeks). This transformative nature of DAA therapy underpins the goal of the World Health Organization to eliminate HCV infection as a public health threat by 2030.Areas covered: This review seeks to address the current status of DAA therapies, including recent developments, current limitations, and future challenges.Expert opinion: The current DAA regimens, with their high effectiveness and safety profiles, have changed patient perception of HCV infection from a disease that requires complex evaluation and long-term monitoring to a disease that can be cured after one visit to the general practitioner. Despite the remarkably high success rate of DAAs, few patients (4-5%) fail to obtain SVR even after treatment. Five years ahead, the landscape of HCV treatment will undoubtedly continue to evolve, and more pan-genotypic treatment options will be available to all patients.
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Affiliation(s)
- Carol Stanciu
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, ST. SpiridonEmergency Hospital, Iasi, Romania
| | - Cristina Maria Muzica
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, ST. SpiridonEmergency Hospital, Iasi, Romania
| | - Irina Girleanu
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, ST. SpiridonEmergency Hospital, Iasi, Romania
| | - Camelia Cojocariu
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, ST. SpiridonEmergency Hospital, Iasi, Romania
| | - Catalin Sfarti
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, ST. SpiridonEmergency Hospital, Iasi, Romania
| | - Ana-Maria Singeap
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, ST. SpiridonEmergency Hospital, Iasi, Romania
| | - Laura Huiban
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, ST. SpiridonEmergency Hospital, Iasi, Romania
| | - Stefan Chiriac
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, ST. SpiridonEmergency Hospital, Iasi, Romania
| | - Tudor Cuciureanu
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, ST. SpiridonEmergency Hospital, Iasi, Romania
| | - Anca Trifan
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, ST. SpiridonEmergency Hospital, Iasi, Romania
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Gallardo-Flores CE, Colpitts CC. Cyclophilins and Their Roles in Hepatitis C Virus and Flavivirus Infections: Perspectives for Novel Antiviral Approaches. Pathogens 2021; 10:pathogens10070902. [PMID: 34358052 PMCID: PMC8308494 DOI: 10.3390/pathogens10070902] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/07/2021] [Accepted: 07/15/2021] [Indexed: 12/19/2022] Open
Abstract
Cyclophilins are cellular peptidyl-prolyl isomerases that play an important role in viral infections, with demonstrated roles in the replication of hepatitis C virus (HCV) and other viruses in the Flaviviridae family, such as dengue virus (DENV) and yellow fever virus (YFV). Here, we discuss the roles of cyclophilins in HCV infection and provide a comprehensive overview of the mechanisms underlying the requirement for cyclophilins during HCV replication. Notably, cyclophilin inhibitor therapy has been demonstrated to be effective in reducing HCV replication in chronically infected patients. While the roles of cyclophilins are relatively well-understood for HCV infection, cyclophilins are more recently emerging as host factors for flavivirus infection as well, providing potential new therapeutic avenues for these viral infections which currently lack antiviral therapies. However, further studies are required to elucidate the roles of cyclophilins in flavivirus replication. Here, we review the current knowledge of the role of cyclophilins in HCV infection to provide a conceptual framework to understand how cyclophilins may contribute to other viral infections, such as DENV and YFV. Improved understanding of the roles of cyclophilins in viral infection may open perspectives for the development of cyclophilin inhibitors as effective antiviral therapeutics for HCV and related viruses.
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Bobardt M, Ramirez CM, Baum MM, Ure D, Foster R, Gallay PA. The combination of the NS5A and cyclophilin inhibitors results in an additive anti-HCV inhibition in humanized mice without development of resistance. PLoS One 2021; 16:e0251934. [PMID: 34014993 PMCID: PMC8136729 DOI: 10.1371/journal.pone.0251934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/05/2021] [Indexed: 12/12/2022] Open
Abstract
We and others previously reported that the direct-acting agents (DAA) NS5A inhibitors (NS5Ai) and the host-targeting agents cyclophilin inhibitors (CypIs) inhibit HCV replication in vitro. In this study, we investigated whether the combination of NS5Ai and CypI offers a potent anti-HCV effect in vivo. A single administration of NS5Ai or CypI alone to HCV-infected humanized-mice inhibits HCV replication. The combination of NS5Ai with CypI suppresses HCV (GT1a, GT2a, GT3a and GT4a) replication in an additive manner. NS5Ai/CypI combinations provide a statistically more profound anti-HCV inhibition for GT2a and GT3a than GT1a and GT4a, leading to a fastest and deepest inhibition of GT2a and GT3a replications. Combining CypI with NS5Ai prevents the viral rebound normally observed in mice treated with NS5Ai alone. Results were confirmed in mice implanted with human hepatocytes from different donors. Therefore, the combination of NS5Ai with CypI may serve as a regimen for the treatment of HCV patients with specific genotypes and disorder conditions, which diminish sustain viral response levels to DAA, such as GT3a infection, cirrhosis, and DAA resistance associated with the selection of resistance-associated substitutions present at baseline or are acquired during treatment.
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Affiliation(s)
- Michael Bobardt
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Christina M. Ramirez
- Los Angeles (UCLA) Fielding School of Public Health, University of California, Center for Health Sciences, Los Angeles, CA, United States of America
| | - Marc M. Baum
- Department of Chemistry, Oak Crest Institute of Science, Monrovia, CA, United States of America
| | - Daren Ure
- Hepion Pharmaceuticals, Edison, New Jersey
| | | | - Philippe A. Gallay
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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15
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Li HC, Yang CH, Lo SY. Hepatitis C Viral Replication Complex. Viruses 2021; 13:v13030520. [PMID: 33809897 PMCID: PMC8004249 DOI: 10.3390/v13030520] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 12/16/2022] Open
Abstract
The life cycle of the hepatitis C virus (HCV) can be divided into several stages, including viral entry, protein translation, RNA replication, viral assembly, and release. HCV genomic RNA replication occurs in the replication organelles (RO) and is tightly linked to ER membrane alterations containing replication complexes (proteins NS3 to NS5B). The amplification of HCV genomic RNA could be regulated by the RO biogenesis, the viral RNA structure (i.e., cis-acting replication elements), and both viral and cellular proteins. Studies on HCV replication have led to the development of direct-acting antivirals (DAAs) targeting the replication complex. This review article summarizes the viral and cellular factors involved in regulating HCV genomic RNA replication and the DAAs that inhibit HCV replication.
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Affiliation(s)
- Hui-Chun Li
- Department of Biochemistry, Tzu Chi University, Hualien 97004, Taiwan;
| | - Chee-Hing Yang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan;
| | - Shih-Yen Lo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan;
- Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien 97004, Taiwan
- Correspondence: ; Tel.: +886-3-8565301 (ext. 2322)
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16
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Liao Y, Luo D, Peng K, Zeng Y. Cyclophilin A: a key player for etiological agent infection. Appl Microbiol Biotechnol 2021; 105:1365-1377. [PMID: 33492451 PMCID: PMC7829623 DOI: 10.1007/s00253-021-11115-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 12/13/2022]
Abstract
Abstract Cyclophilin A (CypA), a key member of the immunophilin family, is the most abundantly expressed isozyme of the 18 known human cyclophilins. Besides acting as an intracellular receptor for cyclosporine A, CypA plays a vital role in microorganismal infections, cardiovascular diseases, liver diseases, kidney diseases, neurodegeneration, cancer, rheumatoid arthritis, periodontitis, sepsis, asthma, and aging. This review focuses on the pivotal roles of CypA in the infection of etiological agents, which manifests mainly in promoting or inhibiting viral replication based on the host cell type and viral species. CypA can interact with viral proteins and thus regulate the replication cycle of the virus. CypA is involved in pathogenic bacterial infections by regulating the formation of host actin skeleton or membrane translocation of bacterial toxins, or mediated the adhesion of Mycoplasma genitalium during the infection processes by acting as a cellular receptor of M. genitalium. CypA also plays a critical role in infection or the life cycle of certain parasites or host immune regulation. Moreover, we summarized the current understanding of CypA inhibitors acting as host-targeting antiviral agents, thus opening an avenue for the treatment of multiple viral infections due to their broad antiviral effects and ability to effectively prevent drug resistance. Therefore, the antiviral effect of CypA has the potential to promote CypA inhibitors as host-targeting drugs to CypA-involved etiological agent infections and human diseases. Key points • CypA is involved in the replication and infection of several viruses, pathogenic bacteria, mycoplasma, and parasites. • CypA inhibitors are in a strong position to inhibit the infection of viruses, bacterial, and mycoplasma.
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Affiliation(s)
- Yating Liao
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, No. 28, West Changsheng Road, Hengyang City, 421001 Hunan Province People’s Republic of China
| | - Dan Luo
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, No. 28, West Changsheng Road, Hengyang City, 421001 Hunan Province People’s Republic of China
| | - Kailan Peng
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, No. 28, West Changsheng Road, Hengyang City, 421001 Hunan Province People’s Republic of China
| | - Yanhua Zeng
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, No. 28, West Changsheng Road, Hengyang City, 421001 Hunan Province People’s Republic of China
- Department of Dermatology and Venereology, The First Affiliated Hospital, University of South China, Hengyang City, 421001 Hunan Province People’s Republic of China
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Chu JYK, Ou JHJ. Autophagy in HCV Replication and Protein Trafficking. Int J Mol Sci 2021; 22:ijms22031089. [PMID: 33499186 PMCID: PMC7865906 DOI: 10.3390/ijms22031089] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/11/2022] Open
Abstract
Autophagy is a catabolic process that is important for maintaining cellular homeostasis. It is also known to possess other functions including protein trafficking and anti-microbial activities. Hepatitis C virus (HCV) is known to co-opt cellular autophagy pathway to promote its own replication. HCV regulates autophagy through multiple mechanisms to control intracellular protein and membrane trafficking to enhance its replication and suppress host innate immune response. In this review, we discuss the current knowledge on the interplay between HCV and autophagy and the crosstalk between HCV-induced autophagy and host innate immune responses.
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Alzahrani N, Wu MJ, Shanmugam S, Yi M. Delayed by Design: Role of Suboptimal Signal Peptidase Processing of Viral Structural Protein Precursors in Flaviviridae Virus Assembly. Viruses 2020; 12:v12101090. [PMID: 32993149 PMCID: PMC7601889 DOI: 10.3390/v12101090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/04/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
The Flaviviridae virus family is classified into four different genera, including flavivirus, hepacivirus, pegivirus, and pestivirus, which cause significant morbidity and mortality in humans and other mammals, including ruminants and pigs. These are enveloped, single-stranded RNA viruses sharing a similar genome organization and replication scheme with certain unique features that differentiate them. All viruses in this family express a single polyprotein that encodes structural and nonstructural proteins at the N- and C-terminal regions, respectively. In general, the host signal peptidase cleaves the structural protein junction sites, while virus-encoded proteases process the nonstructural polyprotein region. It is known that signal peptidase processing is a rapid, co-translational event. Interestingly, certain signal peptidase processing site(s) in different Flaviviridae viral structural protein precursors display suboptimal cleavage kinetics. This review focuses on the recent progress regarding the Flaviviridae virus genus-specific mechanisms to downregulate signal peptidase-mediated processing at particular viral polyprotein junction sites and the role of delayed processing at these sites in infectious virus particle assembly.
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Colpitts CC, Ridewood S, Schneiderman B, Warne J, Tabata K, Ng CF, Bartenschlager R, Selwood DL, Towers GJ. Hepatitis C virus exploits cyclophilin A to evade PKR. eLife 2020; 9:e52237. [PMID: 32539931 PMCID: PMC7297535 DOI: 10.7554/elife.52237] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 05/28/2020] [Indexed: 12/12/2022] Open
Abstract
Counteracting innate immunity is essential for successful viral replication. Host cyclophilins (Cyps) have been implicated in viral evasion of host antiviral responses, although the mechanisms are still unclear. Here, we show that hepatitis C virus (HCV) co-opts the host protein CypA to aid evasion of antiviral responses dependent on the effector protein kinase R (PKR). Pharmacological inhibition of CypA rescues PKR from antagonism by HCV NS5A, leading to activation of an interferon regulatory factor-1 (IRF1)-driven cell intrinsic antiviral program that inhibits viral replication. These findings further the understanding of the complexity of Cyp-virus interactions, provide mechanistic insight into the remarkably broad antiviral spectrum of Cyp inhibitors, and uncover novel aspects of PKR activity and regulation. Collectively, our study identifies a novel antiviral mechanism that harnesses cellular antiviral immunity to suppress viral replication.
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Affiliation(s)
- Che C Colpitts
- Department of Biomedical and Molecular Sciences, Queen’s UniversityKingstonCanada
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Sophie Ridewood
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Bethany Schneiderman
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Justin Warne
- Wolfson Institute for Biomedical Research, UCLLondonUnited Kingdom
| | - Keisuke Tabata
- Department of Infectious Diseases, Molecular Virology, Heidelberg UniversityHeidelbergGermany
| | - Caitlin F Ng
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg UniversityHeidelbergGermany
- Division Virus-Associated Carcinogenesis, German Cancer Research CenterHeidelbergGermany
- German Center for Infection Research (DZIF), Heidelberg Partner SiteHeidelbergGermany
| | - David L Selwood
- Department of Medicine, Imperial College LondonLondonUnited Kingdom
| | - Greg J Towers
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
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20
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Wyles D, Mangia A, Cheng W, Shafran S, Schwabe C, Ouyang W, Hedskog C, McNally J, Brainard DM, Doehle BP, Svarovskaia E, Miller MD, Mo H, Dvory-Sobol H. Long-term persistence of HCV NS5A resistance-associated substitutions after treatment with the HCV NS5A inhibitor, ledipasvir, without sofosbuvir. Antivir Ther 2019. [PMID: 28650844 DOI: 10.3851/imp3181] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Data on persistence of NS5A resistance-associated substitutions (RASs) may have implications for resistance testing approaches and selection of initial and retreatment strategies. METHODS Long-term persistence of NS5A RASs in HCV genotype (GT) 1 infected subjects (n=76) who did not achieve sustained virological response after receiving ledipasvir (LDV) without sofosbuvir (SOF) and were subsequently enrolled in an ongoing 3-year follow-up registry study was investigated by population or deep sequencing. RESULTS Of the 76 subjects enrolled, 67 and 9 subjects had GT1a and GT1b infection, respectively. At pretreatment, NS5A RASs were detected in 14% of subjects (11/76) by population sequencing, with three subjects having >1 RAS. All RASs that were detected at pretreatment persisted and were observed at the 96 week visit in the follow-up study (FU96). For the remaining subjects with no detectable RASs at pretreatment, RASs were detected in 98% (63/64) of subjects at virological failure in the parent study and persisted at detectable levels through FU96 in 86% of subjects by deep sequencing (1% cutoff). However, a decline in the quasispecies frequency of most RASs and the number of RASs per subject was observed over time. Phenotypic analysis demonstrated that the majority of NS5A RASs confer similar levels of resistance to LDV and daclatasvir. CONCLUSIONS The majority of NS5A RASs can persist at detectable levels for >96 weeks post-treatment in subjects who failed treatment with regimens containing an NS5A inhibitor without SOF, suggesting relatively high fitness of NS5A RASs even in the absence of drug pressure.
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Affiliation(s)
- David Wyles
- Division of Infectious Diseases, Denver Health and Hospital Authority, Denver, CO, USA
| | - Alessandra Mangia
- Liver Unit, Department of Medical Sciences IRCCS 'Casa Sollievo della Sofferenza', San Giovanni Rotondo, Italy
| | - Wendy Cheng
- Gastroenterology and Hepatology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Stephen Shafran
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | | | - Wen Ouyang
- Gilead Sciences, Inc., Foster City, CA, USA
| | | | | | | | | | | | | | - Hongmei Mo
- Gilead Sciences, Inc., Foster City, CA, USA
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21
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Sofia MJ. The Discovery and Development of Daclatasvir: An Inhibitor of the Hepatitis C Virus NS5A Replication Complex. ACTA ACUST UNITED AC 2019. [PMCID: PMC7122418 DOI: 10.1007/7355_2018_47] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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22
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Adaptive Mutations in Replicase Transmembrane Subunits Can Counteract Inhibition of Equine Arteritis Virus RNA Synthesis by Cyclophilin Inhibitors. J Virol 2019; 93:JVI.00490-19. [PMID: 31243130 DOI: 10.1128/jvi.00490-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/19/2019] [Indexed: 12/18/2022] Open
Abstract
Previously, the cyclophilin inhibitors cyclosporine (CsA) and alisporivir (ALV) were shown to inhibit the replication of diverse RNA viruses, including arteriviruses and coronaviruses, which both belong to the order Nidovirales In this study, we aimed to identify arterivirus proteins involved in the mode of action of cyclophilin inhibitors and to investigate how these compounds inhibit arterivirus RNA synthesis in the infected cell. Repeated passaging of the arterivirus prototype equine arteritis virus (EAV) in the presence of CsA revealed that reduced drug sensitivity is associated with the emergence of adaptive mutations in nonstructural protein 5 (nsp5), one of the transmembrane subunits of the arterivirus replicase polyprotein. Introduction of singular nsp5 mutations (nsp5 Q21R, Y113H, or A134V) led to an ∼2-fold decrease in sensitivity to CsA treatment, whereas combinations of mutations further increased EAV's CsA resistance. The detailed experimental characterization of engineered EAV mutants harboring CsA resistance mutations implicated nsp5 in arterivirus RNA synthesis. Particularly, in an in vitro assay, EAV RNA synthesis was far less sensitive to CsA treatment when nsp5 contained the adaptive mutations mentioned above. Interestingly, for increased sensitivity to the closely related drug ALV, CsA-resistant nsp5 mutants required the incorporation of an additional adaptive mutation, which resided in nsp2 (H114R), another transmembrane subunit of the arterivirus replicase. Our study provides the first evidence for the involvement of nsp2 and nsp5 in the mechanism underlying the inhibition of arterivirus replication by cyclophilin inhibitors.IMPORTANCE Currently, no approved treatments are available to combat infections with nidoviruses, a group of positive-stranded RNA viruses, including important zoonotic and veterinary pathogens. Previously, the cyclophilin inhibitors cyclosporine (CsA) and alisporivir (ALV) were shown to inhibit the replication of diverse nidoviruses (both arteriviruses and coronaviruses), and they may thus represent a class of pan-nidovirus inhibitors. In this study, using the arterivirus prototype equine arteritis virus, we have established that resistance to CsA and ALV treatment is associated with adaptive mutations in two transmembrane subunits of the viral replication machinery, nonstructural proteins 2 and 5. This is the first evidence for the involvement of specific replicase subunits of arteriviruses in the mechanism underlying the inhibition of their replication by cyclophilin inhibitors. Understanding this mechanism of action is of major importance to guide future drug design, both for nidoviruses and for other RNA viruses inhibited by these compounds.
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Dujardin M, Madan V, Gandhi NS, Cantrelle FX, Launay H, Huvent I, Bartenschlager R, Lippens G, Hanoulle X. Cyclophilin A allows the allosteric regulation of a structural motif in the disordered domain 2 of NS5A and thereby fine-tunes HCV RNA replication. J Biol Chem 2019; 294:13171-13185. [PMID: 31315928 DOI: 10.1074/jbc.ra119.009537] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/28/2019] [Indexed: 12/13/2022] Open
Abstract
Implicated in numerous human diseases, intrinsically disordered proteins (IDPs) are dynamic ensembles of interconverting conformers that often contain many proline residues. Whether and how proline conformation regulates the functional aspects of IDPs remains an open question, however. Here, we studied the disordered domain 2 of nonstructural protein 5A (NS5A-D2) of hepatitis C virus (HCV). NS5A-D2 comprises a short structural motif (PW-turn) embedded in a proline-rich sequence, whose interaction with the human prolyl isomerase cyclophilin A (CypA) is essential for viral RNA replication. Using NMR, we show here that the PW-turn motif exists in a conformational equilibrium between folded and disordered states. We found that the fraction of conformers in the NS5A-D2 ensemble that adopt the structured motif is allosterically modulated both by the cis/trans isomerization of the surrounding prolines that are CypA substrates and by substitutions conferring resistance to cyclophilin inhibitor. Moreover, we noted that this fraction is directly correlated with HCV RNA replication efficiency. We conclude that CypA can fine-tune the dynamic ensemble of the disordered NS5A-D2, thereby regulating viral RNA replication efficiency.
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Affiliation(s)
- Marie Dujardin
- University of Lille, CNRS, UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Vanesa Madan
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Neha S Gandhi
- School of Mathematical Sciences and Institute for Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - François-Xavier Cantrelle
- University of Lille, CNRS, UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Hélène Launay
- University of Lille, CNRS, UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Isabelle Huvent
- University of Lille, CNRS, UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Guy Lippens
- University of Lille, CNRS, UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Xavier Hanoulle
- University of Lille, CNRS, UMR 8576, UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France.
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Gaska JM, Balev M, Ding Q, Heller B, Ploss A. Differences across cyclophilin A orthologs contribute to the host range restriction of hepatitis C virus. eLife 2019; 8:e44436. [PMID: 31074414 PMCID: PMC6510530 DOI: 10.7554/elife.44436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/15/2019] [Indexed: 12/22/2022] Open
Abstract
The restricted host tropism of hepatitis C virus (HCV) remains incompletely understood, especially post-entry, and has hindered developing an immunocompetent, small animal model. HCV replication in non-permissive species may be limited by incompatibilities between the viral replication machinery and orthologs of essential host factors, like cyclophilin A (CypA). We thus compared the ability of CypA from mouse, tree shrew, and seven non-human primate species to support HCV replication, finding that murine CypA only partially rescued viral replication in Huh7.5-shRNA CypA cells. We determined the specific amino acid differences responsible and generated mutants able to fully rescue replication. We expressed these mutants in engineered murine hepatoma cells and although we observed increases in HCV replication following infection, they remained far lower than those in highly permissive human hepatoma cells, and minimal infectious particle release was observed. Together, these data suggest additional co-factors remain unidentified. Future work to determine such factors will be critical for developing an immunocompetent mouse model supporting HCV replication.
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Affiliation(s)
- Jenna M Gaska
- Department of Molecular BiologyPrinceton UniversityPrincetonUnited States
| | - Metodi Balev
- Department of Molecular BiologyPrinceton UniversityPrincetonUnited States
| | - Qiang Ding
- Department of Molecular BiologyPrinceton UniversityPrincetonUnited States
| | - Brigitte Heller
- Department of Molecular BiologyPrinceton UniversityPrincetonUnited States
| | - Alexander Ploss
- Department of Molecular BiologyPrinceton UniversityPrincetonUnited States
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Alazard-Dany N, Denolly S, Boson B, Cosset FL. Overview of HCV Life Cycle with a Special Focus on Current and Possible Future Antiviral Targets. Viruses 2019; 11:v11010030. [PMID: 30621318 PMCID: PMC6356578 DOI: 10.3390/v11010030] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C infection is the leading cause of liver diseases worldwide and a major health concern that affects an estimated 3% of the global population. Novel therapies available since 2014 and 2017 are very efficient and the WHO considers HCV eradication possible by the year 2030. These treatments are based on the so-called direct acting antivirals (DAAs) that have been developed through research efforts by academia and industry since the 1990s. After a brief overview of the HCV life cycle, we describe here the functions of the different targets of current DAAs, the mode of action of these DAAs and potential future inhibitors.
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Affiliation(s)
- Nathalie Alazard-Dany
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
| | - Solène Denolly
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
| | - Bertrand Boson
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
| | - François-Loïc Cosset
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.
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Khan M, Imam H, Siddiqui A. Subversion of cellular autophagy during virus infection: Insights from hepatitis B and hepatitis C viruses. LIVER RESEARCH 2018; 2:146-156. [PMID: 31803515 PMCID: PMC6892584 DOI: 10.1016/j.livres.2018.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Autophagy is a self-eating process, in which the damaged or excessed cell organelles and misfolded protein aggregates are removed from the cellular microenvironment. Autophagy is generally thought of as a pro-survival mechanism which is not only important for balancing energy supply at times of nutrient deprivation but also in the removal of various stress stimuli to ensure homeostasis. In addition to the target materials of "self" origin, autophagy can also eliminate intracellular pathogens and acts as a defense mechanism to curb infections. In addition, autophagy is linked to the host cell's innate immune response. However, viruses have evolved various strategies to manipulate and overtake host cell machinery to establish productive replication and maintain infectious process. In fact, replication of many viruses has been found to be autophagy-dependent and suppression of autophagy can potentially affect the viral replication. Thus, autophagy can either serve as an anti-viral defense mechanism or a pro-viral process that supports viral replication. Hepatitis B virus (HBV) and hepatitis C virus (HCV) are known to co-opt cellular autophagy process as a pro-viral tool. Both viruses also induce mitophagy, which contributes to the establishment of chronic hepatitis. This review focuses on the roles of autophagy and mitophagy in the chronic liver disease pathogenesis associated with HBV and HCV infections.
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Shanmugam S, Nichols AK, Saravanabalaji D, Welsch C, Yi M. HCV NS5A dimer interface residues regulate HCV replication by controlling its self-interaction, hyperphosphorylation, subcellular localization and interaction with cyclophilin A. PLoS Pathog 2018; 14:e1007177. [PMID: 30036383 PMCID: PMC6072203 DOI: 10.1371/journal.ppat.1007177] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/02/2018] [Accepted: 06/25/2018] [Indexed: 12/12/2022] Open
Abstract
The HCV NS5A protein plays multiple roles during viral replication, including viral genome replication and virus particle assembly. The crystal structures of the NS5A N-terminal domain indicated the potential existence of the NS5A dimers formed via at least two or more distinct dimeric interfaces. However, it is unknown whether these different forms of NS5A dimers are involved in its numerous functions. To address this question, we mutated the residues lining the two different NS5A dimer interfaces and determined their effects on NS5A self-interaction, NS5A-cyclophilin A (CypA) interaction, HCV RNA replication and infectious virus production. We found that the mutations targeting either of two dimeric interfaces disrupted the NS5A self-interaction in cells. The NS5A dimer-interrupting mutations also inhibited both viral RNA replication and infectious virus production with some genotypic differences. We also determined that reduced NS5A self-interaction was associated with altered NS5A-CypA interaction, NS5A hyperphosphorylation and NS5A subcellular localization, providing the mechanistic bases for the role of NS5A self-interaction in multiple steps of HCV replication. The NS5A oligomers formed via different interfaces are likely its functional form, since the residues at two different dimeric interfaces played similar roles in different aspects of NS5A functions and, consequently, HCV replication. In conclusion, this study provides novel insight into the functional significance of NS5A self-interaction in different steps of the HCV replication, potentially, in the form of oligomers formed via multiple dimeric interfaces. HCV NS5A is a multifunctional protein involved in both viral RNA replication and infectious virus production, and is a target of one of the most potent antivirals available to date. However, the mode of action of NS5A inhibitors is still unclear due to the lack of mechanistic detail regarding NS5A functions during HCV life cycles. In this study, we have provided evidence that surface-exposed NS5A residues involved in two different dimeric interactions in crystal structures are indeed involved in NS5A self-interactions in cells. We also showed that these NS5A residues play critical role in HCV RNA replication and infectious virus production by regulating NS5A hyperphosphorylation, its subcellular localization and its interaction with host protein CypA. Overall, our data support the functional significance of “NS5A oligomers” formed via multiple interfaces in HCV replication. We speculate that the NS5A inhibitors exploited the NS5A oligomer-dependent functions during HCV replication, rather than targeting individual NS5A, which consequently resulted in their high potency.
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Affiliation(s)
- Saravanabalaji Shanmugam
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Alyssa K. Nichols
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Dhanaranjani Saravanabalaji
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Christoph Welsch
- Department of Internal Medicine I, Goethe University, Frankfurt/Main, Germany
| | - MinKyung Yi
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- * E-mail:
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de Wilde AH, Pham U, Posthuma CC, Snijder EJ. Cyclophilins and cyclophilin inhibitors in nidovirus replication. Virology 2018; 522:46-55. [PMID: 30014857 PMCID: PMC7112023 DOI: 10.1016/j.virol.2018.06.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/13/2018] [Accepted: 06/18/2018] [Indexed: 12/12/2022]
Abstract
Cyclophilins (Cyps) belong to the family of peptidyl-prolyl isomerases (PPIases). The PPIase activity of most Cyps is inhibited by the immunosuppressive drug cyclosporin A and several of its non-immunosuppressive analogs, which can also block the replication of nidoviruses (arteriviruses and coronaviruses). Cyclophilins have been reported to play an essential role in the replication of several other RNA viruses, including human immunodeficiency virus-1, hepatitis C virus, and influenza A virus. Likewise, the replication of various nidoviruses was reported to depend on Cyps or other PPIases. This review summarizes our current understanding of this class of nidovirus-host interactions, including the potential function of in particular CypA and the inhibitory effect of Cyp inhibitors. Also the involvement of the FK-506-binding proteins and parvulins is discussed. The nidovirus data are placed in a broader perspective by summarizing the most relevant data on Cyp interactions and Cyp inhibitors for other RNA viruses. Nidovirus replication is inhibited by cyclophilin inhibitors. Arterivirus replication depends on cyclophilin A. Cyclosporin A blocks arterivirus RNA synthesis. Using cyclophilin inhibitors against nidoviruses in vivo needs more investigation.
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Affiliation(s)
- Adriaan H de Wilde
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Uyen Pham
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Clara C Posthuma
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
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Characterization of the Anti-Hepatitis C Virus Activity of New Nonpeptidic Small-Molecule Cyclophilin Inhibitors with the Potential for Broad Anti-Flaviviridae Activity. Antimicrob Agents Chemother 2018; 62:AAC.00126-18. [PMID: 29760125 PMCID: PMC6021681 DOI: 10.1128/aac.00126-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/19/2018] [Indexed: 12/17/2022] Open
Abstract
Although members of the Flaviviridae display high incidence, morbidity, and mortality rates, the development of specific antiviral drugs for each virus is unlikely. Cyclophilins, a family of host peptidyl-prolyl cis-trans isomerases (PPIases), play a pivotal role in the life cycles of many viruses and therefore represent an attractive target for broad-spectrum antiviral development. We report here the pangenotypic anti-hepatitis C virus (HCV) activity of a small-molecule cyclophilin inhibitor (SMCypI). Mechanistic and modeling studies revealed that the SMCypI bound to cyclophilin A in competition with cyclosporine (CsA), inhibited its PPIase activity, and disrupted the CypA-nonstructural protein 5A (NS5A) interaction. Resistance selection showed that the lead SMCypI hardly selected amino acid substitutions conferring low-level or no resistance in vitro. Interestingly, the SMCypI selected D320E and Y321H substitutions, located in domain II of the NS5A protein. These substitutions were previously associated with low-level resistance to cyclophilin inhibitors such as alisporivir. Finally, the SMCypI inhibited the replication of other members of the Flaviviridae family with higher 50% effective concentrations (EC50s) than for HCV. Thus, because of its chemical plasticity and simplicity of synthesis, our new family of SMCypIs represents a promising new class of drugs with the potential for broad-spectrum anti-Flaviviridae activity as well as an invaluable tool to explore the role of cyclophilins in viral life cycles.
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Welte MA, Gould AP. Lipid droplet functions beyond energy storage. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:1260-1272. [PMID: 28735096 PMCID: PMC5595650 DOI: 10.1016/j.bbalip.2017.07.006] [Citation(s) in RCA: 331] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/17/2017] [Accepted: 07/17/2017] [Indexed: 02/07/2023]
Abstract
Lipid droplets are cytoplasmic organelles that store neutral lipids and are critically important for energy metabolism. Their function in energy storage is firmly established and increasingly well characterized. However, emerging evidence indicates that lipid droplets also play important and diverse roles in the cellular handling of lipids and proteins that may not be directly related to energy homeostasis. Lipid handling roles of droplets include the storage of hydrophobic vitamin and signaling precursors, and the management of endoplasmic reticulum and oxidative stress. Roles of lipid droplets in protein handling encompass functions in the maturation, storage, and turnover of cellular and viral polypeptides. Other potential roles of lipid droplets may be connected with their intracellular motility and, in some cases, their nuclear localization. This diversity highlights that lipid droplets are very adaptable organelles, performing different functions in different biological contexts. This article is part of a Special Issue entitled: Recent Advances in Lipid Droplet Biology edited by Rosalind Coleman and Matthijs Hesselink.
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Affiliation(s)
- Michael A Welte
- Department of Biology, University of Rochester, Rochester, NY, United States.
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Madhvi A, Hingane S, Srivastav R, Joshi N, Subramani C, Muthumohan R, Khasa R, Varshney S, Kalia M, Vrati S, Surjit M, Ranjith-Kumar CT. A screen for novel hepatitis C virus RdRp inhibitor identifies a broad-spectrum antiviral compound. Sci Rep 2017; 7:5816. [PMID: 28725041 PMCID: PMC5517564 DOI: 10.1038/s41598-017-04449-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/16/2017] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) is a global pathogen and infects more than 185 million individuals worldwide. Although recent development of direct acting antivirals (DAA) has shown promise in HCV therapy, there is an urgent need for the development of more affordable treatment options. We initiated this study to identify novel inhibitors of HCV through screening of compounds from the National Cancer Institute (NCI) diversity dataset. Using cell-based assays, we identified NSC-320218 as a potent inhibitor against HCV with an EC50 of 2.5 μM and CC50 of 75 μM. The compound inhibited RNA dependent RNA polymerase (RdRp) activity of all six major HCV genotypes indicating a pan-genotypic effect. Limited structure-function analysis suggested that the entire molecule is necessary for the observed antiviral activity. However, the compound failed to inhibit HCV NS5B activity in vitro, suggesting that it may not be directly acting on the NS5B protein but could be interacting with a host protein. Importantly, the antiviral compound also inhibited dengue virus and hepatitis E virus replication in hepatocytes. Thus, our study has identified a broad-spectrum antiviral therapeutic agent against multiple viral infections.
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Affiliation(s)
- Abhilasha Madhvi
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Smita Hingane
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Rajpal Srivastav
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Nishant Joshi
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
- Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Chandru Subramani
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Rajagopalan Muthumohan
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Renu Khasa
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Shweta Varshney
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Manjula Kalia
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Sudhanshu Vrati
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Milan Surjit
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - C T Ranjith-Kumar
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India.
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Vidotto A, Morais ATS, Ribeiro MR, Pacca CC, Terzian ACB, Gil LHVG, Mohana-Borges R, Gallay P, Nogueira ML. Systems Biology Reveals NS4B-Cyclophilin A Interaction: A New Target to Inhibit YFV Replication. J Proteome Res 2017; 16:1542-1555. [PMID: 28317380 DOI: 10.1021/acs.jproteome.6b00933] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Yellow fever virus (YFV) replication is highly dependent on host cell factors. YFV NS4B is reported to be involved in viral replication and immune evasion. Here interactions between NS4B and human proteins were determined using a GST pull-down assay and analyzed using 1-DE and LC-MS/MS. We present a total of 207 proteins confirmed using Scaffold 3 Software. Cyclophilin A (CypA), a protein that has been shown to be necessary for the positive regulation of flavivirus replication, was identified as a possible NS4B partner. 59 proteins were found to be significantly increased when compared with a negative control, and CypA exhibited the greatest difference, with a 22-fold change. Fisher's exact test was significant for 58 proteins, and the p value of CypA was the most significant (0.000000019). The Ingenuity Systems software identified 16 pathways, and this analysis indicated sirolimus, an mTOR pathway inhibitor, as a potential inhibitor of CypA. Immunofluorescence and viral plaque assays showed a significant reduction in YFV replication using sirolimus and cyclosporine A (CsA) as inhibitors. Furthermore, YFV replication was strongly inhibited in cells treated with both inhibitors using reporter BHK-21-rep-YFV17D-LucNeoIres cells. Taken together, these data suggest that CypA-NS4B interaction regulates YFV replication. Finally, we present the first evidence that YFV inhibition may depend on NS4B-CypA interaction.
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Affiliation(s)
- Alessandra Vidotto
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Ana T S Morais
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Milene R Ribeiro
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Carolina C Pacca
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Ana C B Terzian
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Laura H V G Gil
- Departamento de Virologia, Centro de Pesquisa Aggeu Magalhães , Fundação Oswaldo Cruz (FIOCRUZ) - Recife, Pernambuco 50740-465, Brazil
| | - Ronaldo Mohana-Borges
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro - UFRJ , Rio de Janeiro RJ 21941-902, Brazil
| | - Philippe Gallay
- Department of Immunology & Microbial Science, The Scripps Research Institute - La Jolla , San Diego, California 92037, United States
| | - Mauricio L Nogueira
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
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Boson B, Denolly S, Turlure F, Chamot C, Dreux M, Cosset FL. Daclatasvir Prevents Hepatitis C Virus Infectivity by Blocking Transfer of the Viral Genome to Assembly Sites. Gastroenterology 2017; 152:895-907.e14. [PMID: 27932311 DOI: 10.1053/j.gastro.2016.11.047] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/15/2016] [Accepted: 11/28/2016] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Daclatasvir is a direct-acting antiviral agent and potent inhibitor of NS5A, which is involved in replication of the hepatitis C virus (HCV) genome, presumably via membranous web shaping, and assembly of new virions, likely via transfer of the HCV RNA genome to viral particle assembly sites. Daclatasvir inhibits the formation of new membranous web structures and, ultimately, of replication complex vesicles, but also inhibits an early assembly step. We investigated the relationship between daclatasvir-induced clustering of HCV proteins, intracellular localization of viral RNAs, and inhibition of viral particle assembly. METHODS Cell-culture-derived HCV particles were produced from Huh7.5 hepatocarcinoma cells in presence of daclatasvir for short time periods. Infectivity and production of physical particles were quantified and producer cells were subjected to subcellular fractionation. Intracellular colocalization between core, E2, NS5A, NS4B proteins, and viral RNAs was quantitatively analyzed by confocal microscopy and by structured illumination microscopy. RESULTS Short exposure of HCV-infected cells to daclatasvir reduced viral assembly and induced clustering of structural proteins with non-structural HCV proteins, including core, E2, NS4B, and NS5A. These clustered structures appeared to be inactive assembly platforms, likely owing to loss of functional connection with replication complexes. Daclatasvir greatly reduced delivery of viral genomes to these core clusters without altering HCV RNA colocalization with NS5A. In contrast, daclatasvir neither induced clustered structures nor inhibited HCV assembly in cells infected with a daclatasvir-resistant mutant (NS5A-Y93H), indicating that daclatasvir targets a mutual, specific function of NS5A inhibiting both processes. CONCLUSIONS In addition to inhibiting replication complex biogenesis, daclatasvir prevents viral assembly by blocking transfer of the viral genome to assembly sites. This leads to clustering of HCV proteins because viral particles and replication complex vesicles cannot form or egress. This dual mode of action of daclatasvir could explain its efficacy in blocking HCV replication in cultured cells and in treatment of patients with HCV infection.
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Affiliation(s)
- Bertrand Boson
- CIRI - International Center for Infectiology Research, Team EVIR, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France
| | - Solène Denolly
- CIRI - International Center for Infectiology Research, Team EVIR, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France
| | - Fanny Turlure
- CIRI - International Center for Infectiology Research, Team EVIR, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France
| | - Christophe Chamot
- Plateau Technique Imagerie/Microcopie, Lyon Bio Image, SFR-BioSciences, ENS de Lyon, Inserm US8, CNRS UMS3444, UCBL, France
| | - Marlène Dreux
- CIRI - International Center for Infectiology Research, Team EVIR, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France
| | - François-Loïc Cosset
- CIRI - International Center for Infectiology Research, Team EVIR, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France.
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Saleem A, Akhtar MF, Mushtaq MF, Saleem M, Muhammad ST, Akhtar B, Sharif A, Peerzada S. Current trends in the treatment of hepatitis C: interventions to avoid adverse effects and increase effectiveness of anti-HCV drugs. EXCLI JOURNAL 2016; 15:578-588. [PMID: 28096788 PMCID: PMC5225681 DOI: 10.17179/excli2016-582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 09/26/2016] [Indexed: 12/14/2022]
Abstract
Viral hepatitis, an inflammatory liver disease, is caused by various genotypes of hepatitis C viruses (HCV). Hepatitis C slowly sprouts into fibrosis, which progresses to cirrhosis. Over a prolonged period of time compensated cirrhosis can advance to decompensated cirrhosis culminating in hepatic failure and death. Conventional treatment of HCV involves the administration of interferons. However, association of interferon with the adverse drug reactions led to the development of novel anti-HCV drugs given as monotherapy or in combination with the other drugs. Advances in drug delivery systems (DDS) improved the pharmacokinetic profile and stability of drugs, ameliorated tissue damages on extravasation and increased the targeting of affected sites. Liposomes and lipid based vehicles have been employed with polyethylene glycol (PEG) so as to stabilize the formulations as PEG drug complex. Sofosbuvir, a novel anti-HCV drug, is administered as monotherapy or in combination with daclatasvir, ledipasivir, protease inhibitors, ribavirin and interferon for the treatment of HCV genotypes 1, 2 and 3. These drug combinations are highly effective in eradicating the interferon resistance, recurrent HCV infection in liver transplant, concurrent HIV infection and preventing interferon related adverse effects. Further investigations to improve drug targeting and identification of new drug targets are highly warranted due to the rapid emergence of drug resistance in HCV.
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Affiliation(s)
- Ammara Saleem
- Faculty of Pharmaceutical Sciences, GC University, Faisalabad, Pakistan
| | | | | | - Muhammad Saleem
- Faculty of Pharmaceutical Sciences, GC University, Faisalabad, Pakistan
| | | | - Bushra Akhtar
- Institute of Pharmacy, Physiology and Pharmacology, University of Agriculture, Faisalabad, Pakistan
| | - Ali Sharif
- Faculty of Pharmacy, The University of Lahore, Lahore, Pakistan
| | - Sohaib Peerzada
- Faculty of Pharmacy, The University of Lahore, Lahore, Pakistan
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Abstract
Autophagy is a catabolic process by which cells remove protein aggregates and damaged organelles for recycling. It can also be used by cells to remove intracellular microbial pathogens, including viruses, in a process known as xenophagy. However, many viruses have developed mechanisms to subvert this intracellular antiviral response and even use this pathway to support their own replications. Hepatitis C virus (HCV) is one such virus and is an important human pathogen that can cause severe liver diseases. Recent studies indicated that HCV could activate the autophagic pathway to support its replication. This review summarizes the current knowledge on the interplay between HCV and autophagy and how this interplay affects HCV replication and host innate immune responses.
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Cyclophilin Inhibitors Remodel the Endoplasmic Reticulum of HCV-Infected Cells in a Unique Pattern Rendering Cells Impervious to a Reinfection. PLoS One 2016; 11:e0159511. [PMID: 27442520 PMCID: PMC4956074 DOI: 10.1371/journal.pone.0159511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/05/2016] [Indexed: 12/15/2022] Open
Abstract
The mechanisms of action by which cyclophilin inhibitors (CypI) interfere with the HCV life cycle remain poorly understood. We reported that CypI and NS5A inhibitors (NS5Ai), but not other classes of anti-HCV agents, prevent assembly of double membrane vesicles (DMVs), which protect replication complexes. We demonstrated that both NS5A and the isomerase cyclophilin A (CypA) are required for DMV formation. Here, we examined whether CypI mediate an additional antiviral effect that could further explain the high efficacy of CypI. We identified a unique action of CypI. CypI remodel the organization of the endoplasmic reticulum (ER) of HCV-infected cells, but not of uninfected cells. This effect is specific since it was not observed for other classes of anti-HCV agents including NS5Ai, and has no effect on the viability of CypI-treated cells. Since ER serves as platform for the establishment of HCV replication complexes, we asked whether the ER reorganization by CypI would prevent cells from being newly infected. Remarkably, CypI-treated HCV-pre-infected cells remain totally impervious to a reinfection, suggesting that the CypI-mediated ER reorganization prevents a reinfection. This block is not due to residual CypI since CypI-resistant HCV variants also fail to infect these cells. The ER reorganization by CypI is rapid and reversible. This study provides the first evidence that CypI trigger a unique ER reorganization of infected cells, rendering cells transiently impervious to a reinfection. This study further suggests that the HCV-induced ER rearrangement represents a key target for the development of new therapies.
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Culley S, Towers GJ, Selwood DL, Henriques R, Grove J. Infection Counter: Automated Quantification of in Vitro Virus Replication by Fluorescence Microscopy. Viruses 2016; 8:v8070201. [PMID: 27455304 PMCID: PMC4974536 DOI: 10.3390/v8070201] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/01/2016] [Accepted: 07/05/2016] [Indexed: 01/24/2023] Open
Abstract
The ability to accurately and reliably quantify viral infection is essential to basic and translational virology research. Here, we describe a simple and robust automated method for using fluorescence microscopy to estimate the proportion of virally infected cells in a monolayer. We provide details of the automated analysis workflow along with a freely available open-source ImageJ plugin, Infection Counter, for performing image quantification. Using hepatitis C virus (HCV) as an example, we have experimentally verified our method, demonstrating that it is equivalent, if not better, than the established focus-forming assay. Finally, we used Infection Counter to assess the anti-HCV activity of SMBz-CsA, a non-immunosuppressive cyclosporine analogue.
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Affiliation(s)
- Siân Culley
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK.
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK.
| | - David L Selwood
- Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK.
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK.
| | - Joe Grove
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK.
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Meyers NL, Fontaine KA, Kumar GR, Ott M. Entangled in a membranous web: ER and lipid droplet reorganization during hepatitis C virus infection. Curr Opin Cell Biol 2016; 41:117-24. [PMID: 27240021 DOI: 10.1016/j.ceb.2016.05.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 05/04/2016] [Accepted: 05/05/2016] [Indexed: 12/19/2022]
Abstract
Hepatitis C virus (HCV) is a major cause of liver disease worldwide. To establish and maintain chronic infection, HCV extensively rearranges cellular organelles to generate distinct compartments for viral RNA replication and virion assembly. Here, we review our current knowledge of how HCV proliferates and remodels ER-derived membranes while preserving and expanding associated lipid droplets during viral infection. Unraveling the molecular mechanisms responsible for HCV-induced membrane reorganization will enhance our understanding of the HCV life-cycle, the associated liver pathology, and the biology of the ER:lipid droplet interface in general.
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Affiliation(s)
- Nathan L Meyers
- Gladstone Institutes, University of California San Francisco, 1650 Owens Street, San Francisco, CA 94941, United States
| | - Krystal A Fontaine
- Gladstone Institutes, University of California San Francisco, 1650 Owens Street, San Francisco, CA 94941, United States
| | - G Renuka Kumar
- Gladstone Institutes, University of California San Francisco, 1650 Owens Street, San Francisco, CA 94941, United States
| | - Melanie Ott
- Gladstone Institutes, University of California San Francisco, 1650 Owens Street, San Francisco, CA 94941, United States.
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Characterization of the Anti-HCV Activities of the New Cyclophilin Inhibitor STG-175. PLoS One 2016; 11:e0152036. [PMID: 27104614 PMCID: PMC4841536 DOI: 10.1371/journal.pone.0152036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/08/2016] [Indexed: 12/18/2022] Open
Abstract
Shortened current direct-acting antiviral (DAA) therapies while less expensive, have not provided satisfactory efficacy in naïve cirrhotics, treatment experienced non-cirrhotics or even genotype-3 (GT3)-infected patients. Since DAA regimens consist of the same classes of inhibitors—NS5A (NS5Ai) and NS5B (NS5Bi) +/- NS3 (NS3i) inhibitors—it is likely that their costs will be high and will provide similar degrees of protection. Integrating drugs with distinct mechanisms of action (MoA) into DAA regimens could provide the solution for shortening the period of treatment. One such class of agents is the cyclophilin inhibitors (CypI), which has shown efficacy in patients. Resistance-associated variants persist for years post-treatment in patients exposed to NS5Ai or NS5Bi who fail to achieve a sustained virologic response, impairing their chance for cure on retreatment with existing DAA combinations. Because of their high barrier to resistance, CypI may be particularly useful as a rescue therapy for patients who have relapsed with DAA resistance-associated variants. In this study, we analyzed the anti-HCV properties of the novel cyclosporine A (CsA) derivate—STG-175. The non-immunosuppressive STG-175 possesses a high (EC50 11.5–38.9 nM) multi-genotypic (GT1a to 4a) anti-HCV activity. STG-175 clears cells from HCV since no viral replication rebound was observed after cessation of drug treatment. It presents a higher barrier to resistance than other CypI or selected DAAs. HCV variants, which emerged under STG-175 pressure, are only ~2-fold resistant to the drug. No cross-resistance was observed with DAAs STG-175 was efficacious against DAA-resistant HCV variants. Drug combination studies revealed that STG-175 provides additive and synergistic effects against GT1a to 4a. STG-175 inhibits the infection of HCV, HIV-1 and HBV in mono-, dual- and triple-infection settings. Altogether these results suggest that the new CypI STG-175 represents an attractive drug partner for IFN-free DAA regimens for the treatment of HCV and co-infections.
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de Armas-Rillo L, Valera MS, Marrero-Hernández S, Valenzuela-Fernández A. Membrane dynamics associated with viral infection. Rev Med Virol 2016; 26:146-60. [PMID: 26817660 PMCID: PMC5066672 DOI: 10.1002/rmv.1872] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/14/2015] [Accepted: 12/16/2015] [Indexed: 12/15/2022]
Abstract
Viral replication and spreading are fundamental events in the viral life cycle, accounting for the assembly and egression of nascent virions, events that are directly associated with viral pathogenesis in target hosts. These processes occur in cellular compartments that are modified by specialized viral proteins, causing a rearrangement of different cell membranes in infected cells and affecting the ER, mitochondria, Golgi apparatus, vesicles and endosomes, as well as processes such as autophagic membrane flux. In fact, the activation or inhibition of membrane trafficking and other related activities are fundamental to ensure the adequate replication and spreading of certain viruses. In this review, data will be presented that support the key role of membrane dynamics in the viral cycle, especially in terms of the assembly, egression and infection processes. By defining how viruses orchestrate these events it will be possible to understand how they successfully complete their route of infection, establishing viral pathogenesis and provoking disease. © 2015 The Authors Reviews in Medical Virology Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Laura de Armas-Rillo
- Laboratorio de Inmunología Celular y Viral, Unidad de Virología IUETSPC, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), Tenerife, Spain
| | - María-Soledad Valera
- Laboratorio de Inmunología Celular y Viral, Unidad de Virología IUETSPC, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), Tenerife, Spain
| | - Sara Marrero-Hernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Virología IUETSPC, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), Tenerife, Spain
| | - Agustín Valenzuela-Fernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Virología IUETSPC, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), Tenerife, Spain
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Khachatoorian R, French SW. Chaperones in hepatitis C virus infection. World J Hepatol 2016; 8:9-35. [PMID: 26783419 PMCID: PMC4705456 DOI: 10.4254/wjh.v8.i1.9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 10/01/2015] [Accepted: 12/18/2015] [Indexed: 02/06/2023] Open
Abstract
The hepatitis C virus (HCV) infects approximately 3% of the world population or more than 185 million people worldwide. Each year, an estimated 350000-500000 deaths occur worldwide due to HCV-associated diseases including cirrhosis and hepatocellular carcinoma. HCV is the most common indication for liver transplantation in patients with cirrhosis worldwide. HCV is an enveloped RNA virus classified in the genus Hepacivirus in the Flaviviridae family. The HCV viral life cycle in a cell can be divided into six phases: (1) binding and internalization; (2) cytoplasmic release and uncoating; (3) viral polyprotein translation and processing; (4) RNA genome replication; (5) encapsidation (packaging) and assembly; and (6) virus morphogenesis (maturation) and secretion. Many host factors are involved in the HCV life cycle. Chaperones are an important group of host cytoprotective molecules that coordinate numerous cellular processes including protein folding, multimeric protein assembly, protein trafficking, and protein degradation. All phases of the viral life cycle require chaperone activity and the interaction of viral proteins with chaperones. This review will present our current knowledge and understanding of the role of chaperones in the HCV life cycle. Analysis of chaperones in HCV infection will provide further insights into viral/host interactions and potential therapeutic targets for both HCV and other viruses.
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Resistance-Associated NS5A Variants of Hepatitis C Virus Are Susceptible to Interferon-Based Therapy. PLoS One 2015; 10:e0138060. [PMID: 26368554 PMCID: PMC4569333 DOI: 10.1371/journal.pone.0138060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 08/25/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND & AIMS The presence of resistance-associated variants (RAVs) of hepatitis C virus (HCV) attenuates the efficacy of direct acting antivirals (DAAs). The objective of this study was to characterize the susceptibility of RAVs to interferon-based therapy. METHODS Direct and deep sequencing were performed to detect Y93H RAV in the NS5A region. Twenty nine genotype 1b patients with detectable RAV at baseline were treated by a combination of simeprevir, pegylated interferon and ribavirin. The longitudinal changes in the proportion of Y93H RAV during therapy and at breakthrough or relapse were determined. RESULTS By direct sequencing, Y93H RAV became undetectable or decreased in proportion at an early time point during therapy (within 7 days) in 57% of patients with both the Y93H variant and wild type virus at baseline when HCV RNA was still detectable. By deep sequencing, the proportion of Y93H RAV against Y93 wild type was 52.7% (5.8%- 97.4%) at baseline which significantly decreased to 29.7% (0.16%- 98.3%) within 7 days of initiation of treatment (p = 0.023). The proportion of Y93H RAV was reduced in 21 of 29 cases (72.4%) and a marked reduction of more than 10% was observed in 14 cases (48.7%). HCV RNA reduction was significantly greater for Y93H RAV (-3.65±1.3 logIU/mL/day) than the Y93 wild type (-3.35±1.0 logIU/mL/day) (p<0.001). CONCLUSION Y93H RAV is more susceptible to interferon-based therapy than the Y93 wild type.
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Gallay PA, Bobardt MD, Chatterji U, Trepanier DJ, Ure D, Ordonez C, Foster R. The Novel Cyclophilin Inhibitor CPI-431-32 Concurrently Blocks HCV and HIV-1 Infections via a Similar Mechanism of Action. PLoS One 2015; 10:e0134707. [PMID: 26263487 PMCID: PMC4532424 DOI: 10.1371/journal.pone.0134707] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/13/2015] [Indexed: 12/17/2022] Open
Abstract
HCV-related liver disease is the main cause of morbidity and mortality of HCV/HIV-1 co-infected patients. Despite the recent advent of anti-HCV direct acting antivirals (DAAs), the treatment of HCV/HIV-1 co-infected patients remains a challenge, as these patients are refractory to most therapies and develop liver fibrosis, cirrhosis and liver cancer more often than HCV mono-infected patients. Until the present study, there was no suitable in vitro assay to test the inhibitory activity of drugs on HCV/HIV-1 co-infection. Here we developed a novel in vitro "co-infection" model where HCV and HIV-1 concurrently replicate in their respective main host target cells--human hepatocytes and CD4+ T-lymphocytes. Using this co-culture model, we demonstrate that cyclophilin inhibitors (CypI), including a novel cyclosporin A (CsA) analog, CPI-431-32, simultaneously inhibits replication of both HCV and HIV-1 when added pre- and post-infection. In contrast, the HIV-1 protease inhibitor nelfinavir or the HCV NS5A inhibitor daclatasvir only blocks the replication of a single virus in the "co-infection" system. CPI-431-32 efficiently inhibits HCV and HIV-1 variants, which are normally resistant to DAAs. CPI-431-32 is slightly, but consistently more efficacious than the most advanced clinically tested CypI--alisporivir (ALV)--at interrupting an established HCV/HIV-1 co-infection. The superior antiviral efficacy of CPI-431-32 over ALV correlates with its higher potency inhibition of cyclophilin A (CypA) isomerase activity and at preventing HCV NS5A-CypA and HIV-1 capsid-CypA interactions known to be vital for replication of the respective viruses. Moreover, we obtained evidence that CPI-431-32 prevents the cloaking of both the HIV-1 and HCV genomes from cellular sensors. Based on these results, CPI-431-32 has the potential, as a single agent or in combination with DAAs, to inhibit both HCV and HIV-1 infections.
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Affiliation(s)
- Philippe A. Gallay
- Department of Immunology & Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Michael D. Bobardt
- Department of Immunology & Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Udayan Chatterji
- Department of Immunology & Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Daniel J. Trepanier
- Ciclofilin Pharmaceuticals Inc., San Diego, California, United States of America
| | - Daren Ure
- Ciclofilin Pharmaceuticals Inc., San Diego, California, United States of America
| | - Cosme Ordonez
- Ciclofilin Pharmaceuticals Inc., San Diego, California, United States of America
| | - Robert Foster
- Ciclofilin Pharmaceuticals Inc., San Diego, California, United States of America
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Ploen D, Hildt E. Hepatitis C virus comes for dinner: How the hepatitis C virus interferes with autophagy. World J Gastroenterol 2015; 21:8492-8507. [PMID: 26229393 PMCID: PMC4515832 DOI: 10.3748/wjg.v21.i28.8492] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/10/2015] [Accepted: 06/16/2015] [Indexed: 02/06/2023] Open
Abstract
Autophagy is a highly-regulated, conserved cellular process for the degradation of intracellular components in lysosomes to maintain the energetic balance of the cell. It is a pro-survival mechanism that plays an important role during development, differentiation, apoptosis, ageing and innate and adaptive immune response. Besides, autophagy has been described to be involved in the development of various human diseases, e.g., chronic liver diseases and the development of hepatocellular carcinoma. The hepatitis C virus (HCV) is a major cause of chronic liver diseases. It has recently been described that HCV, like other RNA viruses, hijacks the autophagic machinery to improve its replication. However, the mechanisms underlying its activation are conflicting. HCV replication and assembly occurs at the so-called membranous web that consists of lipid droplets and rearranged endoplasmic reticulum-derived membranes including single-, double- and multi-membrane vesicles. The double-membrane vesicles have been identified to contain NS3, NS5A, viral RNA and the autophagosomal marker microtubule-associated protein 1 light chain 3, corroborating the involvement of the autophagic pathway in the HCV life-cycle. In this review, we will highlight the crosstalk of the autophagosomal compartment with different steps of the HCV life-cycle and address its implications on favoring the survival of infected hepatocytes.
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