1
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Knodel MM, Wittum G, Vollmer J. Efficient Estimates of Surface Diffusion Parameters for Spatio-Temporally Resolved Virus Replication Dynamics. Int J Mol Sci 2024; 25:2993. [PMID: 38474240 DOI: 10.3390/ijms25052993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Advanced methods of treatment are needed to fight the threats of virus-transmitted diseases and pandemics. Often, they are based on an improved biophysical understanding of virus replication strategies and processes in their host cells. For instance, an essential component of the replication of the hepatitis C virus (HCV) proceeds under the influence of nonstructural HCV proteins (NSPs) that are anchored to the endoplasmatic reticulum (ER), such as the NS5A protein. The diffusion of NSPs has been studied by in vitro fluorescence recovery after photobleaching (FRAP) experiments. The diffusive evolution of the concentration field of NSPs on the ER can be described by means of surface partial differential equations (sufPDEs). Previous work estimated the diffusion coefficient of the NS5A protein by minimizing the discrepancy between an extended set of sufPDE simulations and experimental FRAP time-series data. Here, we provide a scaling analysis of the sufPDEs that describe the diffusive evolution of the concentration field of NSPs on the ER. This analysis provides an estimate of the diffusion coefficient that is based only on the ratio of the membrane surface area in the FRAP region to its contour length. The quality of this estimate is explored by a comparison to numerical solutions of the sufPDE for a flat geometry and for ten different 3D embedded 2D ER grids that are derived from fluorescence z-stack data of the ER. Finally, we apply the new data analysis to the experimental FRAP time-series data analyzed in our previous paper, and we discuss the opportunities of the new approach.
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Affiliation(s)
- Markus M Knodel
- Simulation in Technology, TechSim, 75248 Ölbronn-Dürrn, Germany
| | - Gabriel Wittum
- Modelling and Simulation (MaS), Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Jürgen Vollmer
- Institute for Theoretical Physics, Leipzig University, 04081 Leipzig, Germany
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2
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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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3
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Bulankina AV, Richter RM, Welsch C. Regulatory Role of Phospholipids in Hepatitis C Virus Replication and Protein Function. Pathogens 2022; 11:102. [PMID: 35056049 PMCID: PMC8779051 DOI: 10.3390/pathogens11010102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/16/2022] Open
Abstract
Positive-strand RNA viruses such as hepatitis C virus (HCV) hijack key factors of lipid metabolism of infected cells and extensively modify intracellular membranes to support the viral lifecycle. While lipid metabolism plays key roles in viral particle assembly and maturation, viral RNA synthesis is closely linked to the remodeling of intracellular membranes. The formation of viral replication factories requires a number of interactions between virus proteins and host factors including lipids. The structure-function relationship of those proteins is influenced by their lipid environments and lipids that selectively modulate protein function. Here, we review our current understanding on the roles of phospholipids in HCV replication and of lipid-protein interactions in the structure-function relationship of the NS5A protein. NS5A is a key factor in membrane remodeling in HCV-infected cells and is known to recruit phosphatidylinositol 4-kinase III alpha to generate phosphatidylinositol 4-phosphate at the sites of replication. The dynamic interplay between lipids and viral proteins within intracellular membranes is likely key towards understanding basic mechanisms in the pathobiology of virus diseases, the mode of action of specific antiviral agents and related drug resistance mechanisms.
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Affiliation(s)
- Anna V. Bulankina
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, 60590 Frankfurt, Germany; (A.V.B.); (R.M.R.)
- Research Group “Molecular Evolution & Adaptation”, 60590 Frankfurt, Germany
| | - Rebecca M. Richter
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, 60590 Frankfurt, Germany; (A.V.B.); (R.M.R.)
- Research Group “Molecular Evolution & Adaptation”, 60590 Frankfurt, Germany
| | - Christoph Welsch
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, 60590 Frankfurt, Germany; (A.V.B.); (R.M.R.)
- Research Group “Molecular Evolution & Adaptation”, 60590 Frankfurt, Germany
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4
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Feng S, Luan X, Wang Y, Wang H, Zhang Z, Wang Y, Tian Z, Liu M, Xiao Y, Zhao Y, Zhou R, Zhang S. Eltrombopag is a potential target for drug intervention in SARS-CoV-2 spike protein. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104419. [PMID: 32540428 PMCID: PMC7290210 DOI: 10.1016/j.meegid.2020.104419] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/27/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is a current global threat for which there is an urgent need to search for an effective therapy. The transmembrane spike (S) glycoprotein of SARS-CoV-2 directly binds to the host angiotensin-converting enzyme 2 (ACE2) and mediates viral entrance, which is therefore considered as a promising drug target. Considering that new drug development is a time-consuming process, drug repositioning may facilitate rapid drug discovery dealing with sudden infectious diseases. Here, we compared the differences between the virtual structural proteins of SARS-CoV-2 and SARS-CoV, and selected a pocket mainly localizing in the fusion cores of S2 domain for drug screening. A virtual drug design algorithm screened the Food and Drug Administration-approved drug library of 1234 compounds, and 13 top scored compounds were obtained through manual screening. Through in vitro molecular interaction experiments, eltrombopag was further verified to possess a high binding affinity to S protein plus human ACE2 and could potentially affect the stability of the ACE2-S protein complex. Hence, it is worth further exploring eltrombopag as a potential drug for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Siqin Feng
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaodong Luan
- School of Medicine, Tsinghua University, Haidian District, Beijing, China,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yifei Wang
- School of Medicine, Tsinghua University, Haidian District, Beijing, China
| | - Hui Wang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhiyu Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yiyang Wang
- School of Medicine, Tsinghua University, Haidian District, Beijing, China
| | - Zhuang Tian
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Meixi Liu
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Xiao
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yong Zhao
- Beijing Beike Deyuan Bio-Pharm Technology Co. Ltd, Beijing, China
| | - Ruilin Zhou
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; School of Medicine, Tsinghua University, Haidian District, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.
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5
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Liu D, Ndongwe TP, Puray-Chavez M, Casey MC, Izumi T, Pathak VK, Tedbury PR, Sarafianos SG. Effect of P-body component Mov10 on HCV virus production and infectivity. FASEB J 2020; 34:9433-9449. [PMID: 32496609 DOI: 10.1096/fj.201800641r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 03/28/2020] [Accepted: 05/04/2020] [Indexed: 12/11/2022]
Abstract
Mov10 is a processing body (P-body) protein and an interferon-stimulated gene that can affect replication of retroviruses, hepatitis B virus, and hepatitis C virus (HCV). The mechanism of HCV inhibition by Mov10 is unknown. Here, we investigate the effect of Mov10 on HCV infection and determine the virus life cycle steps affected by changes in Mov10 overexpression. Mov10 overexpression suppresses HCV RNA in both infectious virus and subgenomic replicon systems. Additionally, Mov10 overexpression decreases the infectivity of released virus, unlike control P-body protein DCP1a that has no effect on HCV RNA production or infectivity of progeny virus. Confocal imaging of uninfected cells shows endogenous Mov10 localized at P-bodies. However, in HCV-infected cells, Mov10 localizes in circular structures surrounding cytoplasmic lipid droplets with NS5A and core protein. Mutagenesis experiments show that the RNA binding activity of Mov10 is required for HCV inhibition, while its P-body localization, helicase, and ATP-binding functions are not required. Unexpectedly, endogenous Mov10 promotes HCV replication, as CRISPR-Cas9-based Mov10 depletion decreases HCV replication and infection levels. Our data reveal an important and complex role for Mov10 in HCV replication, which can be perturbed by excess or insufficient Mov10.
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Affiliation(s)
- Dandan Liu
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Tanyaradzwa P Ndongwe
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Maritza Puray-Chavez
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Mary C Casey
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Taisuke Izumi
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, MD, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, MD, USA
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
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6
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Kostic M, Jones LH. Critical Assessment of Targeted Protein Degradation as a Research Tool and Pharmacological Modality. Trends Pharmacol Sci 2020; 41:305-317. [PMID: 32222318 PMCID: PMC7202367 DOI: 10.1016/j.tips.2020.02.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 02/08/2023]
Abstract
Small molecules continue to dominate drug discovery because of their ease of use, lower cost of manufacturing, and access to intracellular targets. However, despite these advantages, small molecules are more likely to fail in clinical trials compared with biologicals and their development remains limited to a small subset of disease-relevant 'druggable' targets. Targeted protein degradation has recently emerged as a novel pharmacological modality that promises to overcome small molecule limitations whilst retaining their key advantages. Here, we use a Strengths-Weaknesses-Opportunities-Threats (SWOT) framework to critically assess the current status of this rapidly evolving field. We expect that degrader molecules are only the beginning of a range of novel targeting modalities that hijack existing endogenous cellular machineries to chemically redirect biological targets and pathways. Therefore, this piece may offer a roadmap for enhancing development of both degraders and related modalities.
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Affiliation(s)
- Milka Kostic
- Department of Cancer Biology and Chemical Biology Program, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215, USA.
| | - Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute, 360 Longwood Ave, Boston, MA 02215, USA.
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7
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Rageh AH, Abdel-Aal FAM, Pyell U. Optimization of a sensitive and robust strategy for micellar electrokinetic chromatographic analysis of sofosbuvir in combination with its co-formulated hepatitis C antiviral drugs. J Chromatogr A 2019; 1616:460795. [PMID: 31918849 DOI: 10.1016/j.chroma.2019.460795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/27/2019] [Accepted: 12/14/2019] [Indexed: 02/06/2023]
Abstract
Based on our previous work with "pseudostationary-ion exchanger sweeping", we use this strategy to develop a sensitive, reliable and robust method for the analysis of the newly-FDA approved hepatitis C antiviral drugs namely; sofosbuvir (SOV), daclatasvir (DAC), ledipasvir (LED) and velpatasvir (VEP) in their pure forms and co-formulated pharmaceutical dosage forms using micellar electrokinetic chromatography (MEKC) as a separation method. For the first time, a successful separation of all the investigated compounds was achieved in less than 8 min using a basic background electrolyte (BGE) composed of 25 mmol L-1 SDS + 20% (v/v) ACN (acetonitrile) in 10 mmol L-1 disodium tetraborate buffer (final apparent pH is 9.90). A special focus was given to optimize the composition of the sample matrix to maintain the solubility of the analytes within the sample zone while gaining additional benefits regarding analyte zone focusing. It was found that replacing phosphoric acid (as a sample matrix) with a zwitterionic/isoelectric buffering compound (L-glutamic acid) has a substantial positive impact on the obtained enrichment efficiency. The interplay of other enrichment principles such as the retention factor gradient effect (RFGE) is also discussed. A full validation study is performed based on the pharmacopeial and ICH guidelines. The obtained limits of detection and quantitation are as low as 0.63 and 1.3 μg mL-1; respectively for SOV and DAC and 1.3 and 2.5 μg mL-1; respectively for LED and VEP using UV-DAD as a detection method. The selectivity of the developed method for determination of the studied compounds in their pharmaceutical dosage forms or in the presence of ribavirin (RIB) or elbasvir (ELB), which are other prescribed medications in the treatment regimen of patients with hepatitis C virus infection, is demonstrated. It is shown that with acidic sample matrix and basic BGE, an efficient and precise approach was designed in which analyte adsorption on the capillary wall was minimized while keeping repeatable peak height, peak area and migration time together with the highest possible enrichment efficiency.
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Affiliation(s)
- Azza H Rageh
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Assiut University, 71526 Assiut, Egypt; Department of Chemistry, University of Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany.
| | - Fatma A M Abdel-Aal
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Assiut University, 71526 Assiut, Egypt
| | - Ute Pyell
- Department of Chemistry, University of Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
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8
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Kuchay S, Saeed M, Giorgi C, Li J, Hoffmann HH, Pinton P, Rice CM, Pagano M. NS5A Promotes Constitutive Degradation of IP3R3 to Counteract Apoptosis Induced by Hepatitis C Virus. Cell Rep 2019; 25:833-840.e3. [PMID: 30355490 DOI: 10.1016/j.celrep.2018.09.088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/17/2018] [Accepted: 09/26/2018] [Indexed: 01/28/2023] Open
Abstract
FBXL2 targets IP3R3 for ubiquitin-mediated degradation to limit Ca2+ flux to mitochondria and, consequently, apoptosis. Efficient replication of hepatitis C virus (HCV) requires geranylgeranylation of FBXL2. Here, we show that the viral protein NS5A forms a trimeric complex with IP3R3 and FBXL2, unmasking IP3R3's degron in the absence of inositol 1,4,5-trisphosphate (IP3) stimulation. FBXL2 knockdown or expression of a stable IP3R3 mutant causes persistent Ca2+ flux and sensitizes cells to apoptosis, resulting in the inhibition of viral replication. Importantly, the effect of FBXL2 silencing is rescued by depleting IP3R3, but not p85β, another established FBXL2 substrate, indicating that the anti-HCV effect of FBXL2 knockdown is largely due to IP3R3 stabilization. Finally, disruption of the FBXL2-NS5A-IP3R3 complex using somatic cell genetics or pharmacologic inhibition results in IP3R3 stabilization and suppression of HCV replication. This study reveals an IP3-independent molecular mechanism through which HCV promotes IP3R3 degradation, thereby inhibiting virus-induced apoptosis and establishing chronic infection.
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Affiliation(s)
- Shafi Kuchay
- Department of Biochemistry and Molecular Pharmacology, Laura and Isaac Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Howard Hughes Medical Institute, 522 First Avenue, SRB 1107, New York, NY 10016, USA.
| | - Mohsan Saeed
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065, USA
| | - Carlotta Giorgi
- Department of Biochemistry and Molecular Pharmacology, Laura and Isaac Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Ferrara, Italy
| | - Jie Li
- Department of Biochemistry and Molecular Pharmacology, Laura and Isaac Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065, USA
| | - Paolo Pinton
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Ferrara, Italy
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065, USA.
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, Laura and Isaac Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Howard Hughes Medical Institute, 522 First Avenue, SRB 1107, New York, NY 10016, USA.
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9
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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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10
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Martin S, Blankenship C, Rausch JW, Sztuba-Solinska J. Using SHAPE-MaP to probe small molecule-RNA interactions. Methods 2019; 167:105-116. [DOI: 10.1016/j.ymeth.2019.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/20/2019] [Accepted: 04/16/2019] [Indexed: 01/14/2023] Open
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11
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Knodel MM, Targett-Adams P, Grillo A, Herrmann E, Wittum G. Advanced Hepatitis C Virus Replication PDE Models within a Realistic Intracellular Geometric Environment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E513. [PMID: 30759770 PMCID: PMC6388173 DOI: 10.3390/ijerph16030513] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/08/2019] [Accepted: 01/16/2019] [Indexed: 02/06/2023]
Abstract
The hepatitis C virus (HCV) RNA replication cycle is a dynamic intracellular process occurring in three-dimensional space (3D), which is difficult both to capture experimentally and to visualize conceptually. HCV-generated replication factories are housed within virus-induced intracellular structures termed membranous webs (MW), which are derived from the Endoplasmatic Reticulum (ER). Recently, we published 3D spatiotemporal resolved diffusion⁻reaction models of the HCV RNA replication cycle by means of surface partial differential equation (sPDE) descriptions. We distinguished between the basic components of the HCV RNA replication cycle, namely HCV RNA, non-structural viral proteins (NSPs), and a host factor. In particular, we evaluated the sPDE models upon realistic reconstructed intracellular compartments (ER/MW). In this paper, we propose a significant extension of the model based upon two additional parameters: different aggregate states of HCV RNA and NSPs, and population dynamics inspired diffusion and reaction coefficients instead of multilinear ones. The combination of both aspects enables realistic modeling of viral replication at all scales. Specifically, we describe a replication complex state consisting of HCV RNA together with a defined amount of NSPs. As a result of the combination of spatial resolution and different aggregate states, the new model mimics a cis requirement for HCV RNA replication. We used heuristic parameters for our simulations, which were run only on a subsection of the ER. Nevertheless, this was sufficient to allow the fitting of core aspects of virus reproduction, at least qualitatively. Our findings should help stimulate new model approaches and experimental directions for virology.
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Affiliation(s)
- Markus M Knodel
- Department of Mathematics, Chair of Applied Mathematics 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 11, 91058 Erlangen, Germany.
| | | | - Alfio Grillo
- Dipartimento di Scienze Matematiche (DISMA) "G.L. Lagrange", Politecnico di Torino, Corso Duca degli Abruzzi, 24, 10129 Torino (TO), Italy.
| | - Eva Herrmann
- Department of Medicine, Institute for Biostatistics and Mathematic Modeling, Goethe Universität Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Gabriel Wittum
- Goethe Center for Scientific Computing (G-CSC), Goethe Universität Frankfurt, Kettenhofweg 139, 60325 Frankfurt am Main, Germany.
- Applied Mathematics and Computational Science, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia.
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12
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Zhang Y, Zou J, Zhao X, Yuan Z, Yi Z. Hepatitis C virus NS5A inhibitor daclatasvir allosterically impairs NS4B-involved protein-protein interactions within the viral replicase and disrupts the replicase quaternary structure in a replicase assembly surrogate system. J Gen Virol 2018; 100:69-83. [PMID: 30516462 DOI: 10.1099/jgv.0.001180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Daclatasvir (DCV) is a highly potent direct-acting antiviral that targets the non-structural protein 5A (NS5A) of hepatitis C virus (HCV) and has been used with great clinical success. Previous studies have demonstrated its impact on viral replication complex assembly. However, the precise mechanisms by which DCV impairs the replication complex assembly remains elusive. In this study, by using HCV subgenomic replicons and a viral replicase assembly surrogate system in which the HCV NS3-5B polyprotein is expressed to mimic the viral replicase assembly, we assessed the impact of DCV on the aggregation and tertiary structure of NS5A, the protein-protein interactions within the viral replicase and the quaternary structure of the viral replicase. We found that DCV did not affect aggregation and tertiary structure of NS5A. DCV induced a quaternary structural change of the viral replicase, as evidenced by selective increase of NS4B's sensitivity to proteinase K digestion. Mechanically, DCV impaired the NS4B-involved protein-protein interactions within the viral replicase. These phenotypes were consistent with the phenotypes of several reported NS4B mutants that abolish the viral replicase assembly. The DCV-resistant mutant Y93H was refractory to the DCV-induced reduction of the NS4B-involved protein interactions and the quaternary structural change of the viral replicase. In addition, Y93H reduced NS4B-involved protein-protein interactions within the viral replicase and attenuated viral replication. We propose that DCV may induce a positional change of NS5A, which allosterically affects protein interactions within the replicase components and disrupts replicase assembly.
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Affiliation(s)
- Yang Zhang
- 1Key Laboratory of Medical Molecular Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Jingyi Zou
- 1Key Laboratory of Medical Molecular Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Xiaomin Zhao
- 1Key Laboratory of Medical Molecular Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Zhenghong Yuan
- 1Key Laboratory of Medical Molecular Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Zhigang Yi
- 2Department of Pathogen Diagnosis and Biosafety, Shanghai Public Health Clinical Center, Fudan University, Shanghai, PR China.,1Key Laboratory of Medical Molecular Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, PR China
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13
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A novel molecularly imprinted sensing platform based on MWCNTs/AuNPs decorated 3D starfish like hollow nickel skeleton as a highly conductive nanocomposite for selective and ultrasensitive analysis of a novel pan-genotypic inhibitor velpatasvir in body fluids. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.08.105] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Ahmed M. Era of direct acting anti-viral agents for the treatment of hepatitis C. World J Hepatol 2018; 10:670-684. [PMID: 30386460 PMCID: PMC6206157 DOI: 10.4254/wjh.v10.i10.670] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/10/2018] [Accepted: 05/24/2018] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C infection is universal and the most common indication of liver transplantation in the United States. The period of less effective interferon therapy with intolerable side effects has gone. Now we have stepped into the era of direct acting anti-viral agents (DAAs) against hepatitis C virus. Treatment of hepatitis C is now extremely effective, tolerable and requires a short duration of intake of oral agents. Less monitoring is required with the current therapy and drug-drug interactions are less than the previous regimen. The current treatment options of chronic hepatitis C with various DAAs are discussed in this article.
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Affiliation(s)
- Monjur Ahmed
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Thomas Jefferson University, Philadelphia, PA 19107, United States
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15
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You Y, Kim HS, Park JW, Keum G, Jang SK, Kim BM. Sulfur(vi) fluoride exchange as a key reaction for synthesizing biaryl sulfate core derivatives as potent hepatitis C virus NS5A inhibitors and their structure-activity relationship studies. RSC Adv 2018; 8:31803-31821. [PMID: 35548241 PMCID: PMC9085918 DOI: 10.1039/c8ra05471a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/28/2018] [Indexed: 12/25/2022] Open
Abstract
Extremely potent, new hepatitis C virus (HCV) nonstructural 5A (NS5A) featuring substituted biaryl sulfate core structures was designed and synthesized. Based on the previously reported novel HCV NS5A inhibitors featuring biaryl sulfate core structures which exhibit two-digit picomolar half-maximal effective concentration (EC50) values against HCV genotype 1b and 2a, the new inhibitors equipped with the sulfate core structures containing diversely substituted aryl groups were explored. In this study, highly efficient, chemoselective coupling reactions between an arylsulfonyl fluoride and an aryl silyl ether, known as the sulfur(vi) fluoride exchange (SuFEx) reaction, were utilized. Among the inhibitors prepared based on the SuFEx chemistry, compounds 14, 15 and 29 exhibited two-digit picomolar EC50 values against GT-1b and single digit or sub nanomolar activities against the HCV GT-2a strain. Nonsymmetrical inhibitors containing an imidazole and amide moieties on each side of the sulfate core structures were also synthesized. In addition, a biotinylated probe targeting NS5A protein was prepared for labeling using the same synthetic methodology.
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Affiliation(s)
- Youngsu You
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 South Korea
| | - Hee Sun Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology Pohang 37673 South Korea
| | - Jung Woo Park
- Supercomputing Modeling & Simulation Center, Division of Data Analysis, Korea Institute of Science and Technology Information (KISTI) 245 Daehak-ro, Yuseong-gu Daejeon 34141 South Korea
| | - Gyochang Keum
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST) Hwarangno 14-gil 5, Seongbuk-gu Seoul 02455 South Korea
| | - Sung Key Jang
- Department of Life Sciences, Pohang University of Science and Technology Pohang 37673 South Korea
| | - B Moon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 South Korea
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16
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Knops E, Sierra S, Kalaghatgi P, Heger E, Kaiser R, Kalinina OV. Epistatic Interactions in NS5A of Hepatitis C Virus Suggest Drug Resistance Mechanisms. Genes (Basel) 2018; 9:E343. [PMID: 29986475 PMCID: PMC6071292 DOI: 10.3390/genes9070343] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/29/2018] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) causes a major health burden and can be effectively treated by direct-acting antivirals (DAAs). The non-structural protein 5A (NS5A), which plays a role in the viral genome replication, is one of the DAAs’ targets. Resistance-associated viruses (RAVs) harbouring NS5A resistance-associated mutations (RAMs) have been described at baseline and after therapy failure. A mutation from glutamine to arginine at position 30 (Q30R) is a characteristic RAM for the HCV sub/genotype (GT) 1a, but arginine corresponds to the wild type in the GT-1b; still, GT-1b strains are susceptible to NS5A-inhibitors. In this study, we show that GT-1b strains with R30Q often display other specific NS5A substitutions, particularly in positions 24 and 34. We demonstrate that in GT-1b secondary substitutions usually happen after initial R30Q development in the phylogeny, and that the chemical properties of the corresponding amino acids serve to restore the positive charge in this region, acting as compensatory mutations. These findings may have implications for RAVs treatment.
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Affiliation(s)
- Elena Knops
- Institute of Virology, University of Cologne, 50935 Cologne, Germany.
| | - Saleta Sierra
- Institute of Virology, University of Cologne, 50935 Cologne, Germany.
- German Center for Infection Research (DZIF)-Cologne-Bonn Partner Site, 50935 Cologne, Germany.
| | - Prabhav Kalaghatgi
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF)-Saarbrücken Partner Site, 66123 Saarbrücken, Germany.
| | - Eva Heger
- Institute of Virology, University of Cologne, 50935 Cologne, Germany.
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, 50935 Cologne, Germany.
- German Center for Infection Research (DZIF)-Cologne-Bonn Partner Site, 50935 Cologne, Germany.
| | - Olga V Kalinina
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.
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17
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Yokota H. Applications of proteomics in pharmaceutical research and development. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:17-21. [PMID: 29753086 DOI: 10.1016/j.bbapap.2018.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/10/2018] [Accepted: 05/08/2018] [Indexed: 01/13/2023]
Abstract
The significance of proteomics in the pharmaceutical industry has increased since overcoming initial difficulties. This review discusses recent proteomics publications from pharmaceutical companies to identify new trends in proteomics applications to research and development. Applications of proteomics such as chemical proteomics, protein expression profiling, targeted protein quantitation, analysis of protein-protein interactions and post-translational modification are widely used by various sections of the industry. Technological advancements in proteomics will further accelerate pharmaceutical research and development.
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Affiliation(s)
- Hiroyuki Yokota
- Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba-shi 305-8585, Japan.
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18
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Quantitative Analysis of Hepatitis C NS5A Viral Protein Dynamics on the ER Surface. Viruses 2018; 10:v10010028. [PMID: 29316722 PMCID: PMC5795441 DOI: 10.3390/v10010028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/02/2018] [Accepted: 01/04/2018] [Indexed: 02/06/2023] Open
Abstract
Exploring biophysical properties of virus-encoded components and their requirement for virus replication is an exciting new area of interdisciplinary virological research. To date, spatial resolution has only rarely been analyzed in computational/biophysical descriptions of virus replication dynamics. However, it is widely acknowledged that intracellular spatial dependence is a crucial component of virus life cycles. The hepatitis C virus-encoded NS5A protein is an endoplasmatic reticulum (ER)-anchored viral protein and an essential component of the virus replication machinery. Therefore, we simulate NS5A dynamics on realistic reconstructed, curved ER surfaces by means of surface partial differential equations (sPDE) upon unstructured grids. We match the in silico NS5A diffusion constant such that the NS5A sPDE simulation data reproduce experimental NS5A fluorescence recovery after photobleaching (FRAP) time series data. This parameter estimation yields the NS5A diffusion constant. Such parameters are needed for spatial models of HCV dynamics, which we are developing in parallel but remain qualitative at this stage. Thus, our present study likely provides the first quantitative biophysical description of the movement of a viral component. Our spatio-temporal resolved ansatz paves new ways for understanding intricate spatial-defined processes central to specfic aspects of virus life cycles.
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19
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Masalova OV, Lesnova EI, Solyev PN, Zakirova NF, Prassolov VS, Kochetkov SN, Ivanov AV, Kushch AA. Modulation of Cell Death Pathways by Hepatitis C Virus Proteins in Huh7.5 Hepatoma Cells. Int J Mol Sci 2017; 18:E2346. [PMID: 29113144 PMCID: PMC5713315 DOI: 10.3390/ijms18112346] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/27/2017] [Accepted: 11/03/2017] [Indexed: 12/20/2022] Open
Abstract
The hepatitis C virus (HCV) causes chronic liver disease leading to fibrosis, cirrhosis, and hepatocellular carcinoma. HCV infection triggers various types of cell death which contribute to hepatitis C pathogenesis. However, much is still unknown about the impact of viral proteins on them. Here we present the results of simultaneous immunocytochemical analysis of markers of apoptosis, autophagy, and necrosis in Huh7.5 cells expressing individual HCV proteins or their combinations, or harboring the virus replicon. Stable replication of the full-length HCV genome or transient expression of its core, Е1/Е2, NS3 and NS5B led to the death of 20-47% cells, 72 h posttransfection, whereas the expression of the NS4A/B, NS5A or NS3-NS5B polyprotein did not affect cell viability. HCV proteins caused different impacts on the activation of caspases-3, -8 and -9 and on DNA fragmentation. The structural core and E1/E2 proteins promoted apoptosis, whereas non-structural NS4A/B, NS5A, NS5B suppressed apoptosis by blocking various members of the caspase cascade. The majority of HCV proteins also enhanced autophagy, while NS5A also induced necrosis. As a result, the death of Huh7.5 cells expressing the HCV core was induced via apoptosis, the cells expressing NS3 and NS5B via autophagy-associated death, and the cells expressing E1/E2 glycoproteins or harboring HCV the replicon via both apoptosis and autophagy.
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Affiliation(s)
- Olga V Masalova
- Ivanovsky Institute of Virology, Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow 123098, Russia.
| | - Ekaterina I Lesnova
- Ivanovsky Institute of Virology, Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow 123098, Russia.
| | - Pavel N Solyev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
| | - Natalia F Zakirova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
| | - Vladimir S Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
| | - Alexander V Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
| | - Alla A Kushch
- Ivanovsky Institute of Virology, Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow 123098, Russia.
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20
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3D Spatially Resolved Models of the Intracellular Dynamics of the Hepatitis C Genome Replication Cycle. Viruses 2017; 9:v9100282. [PMID: 28973992 PMCID: PMC5691296 DOI: 10.3390/v9100282] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/21/2017] [Accepted: 09/29/2017] [Indexed: 02/07/2023] Open
Abstract
Mathematical models of virus dynamics have not previously acknowledged spatial resolution at the intracellular level despite substantial arguments that favor the consideration of intracellular spatial dependence. The replication of the hepatitis C virus (HCV) viral RNA (vRNA) occurs within special replication complexes formed from membranes derived from endoplasmatic reticulum (ER). These regions, termed membranous webs, are generated primarily through specific interactions between nonstructural virus-encoded proteins (NSPs) and host cellular factors. The NSPs are responsible for the replication of the vRNA and their movement is restricted to the ER surface. Therefore, in this study we developed fully spatio-temporal resolved models of the vRNA replication cycle of HCV. Our simulations are performed upon realistic reconstructed cell structures-namely the ER surface and the membranous webs-based on data derived from immunostained cells replicating HCV vRNA. We visualized 3D simulations that reproduced dynamics resulting from interplay of the different components of our models (vRNA, NSPs, and a host factor), and we present an evaluation of the concentrations for the components within different regions of the cell. Thus far, our model is restricted to an internal portion of a hepatocyte and is qualitative more than quantitative. For a quantitative adaption to complete cells, various additional parameters will have to be determined through further in vitro cell biology experiments, which can be stimulated by the results deccribed in the present study.
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21
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Gao M, O'Boyle DR, Roberts S. HCV NS5A replication complex inhibitors. Curr Opin Pharmacol 2017; 30:151-157. [PMID: 27643675 DOI: 10.1016/j.coph.2016.07.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/21/2016] [Accepted: 07/25/2016] [Indexed: 01/29/2023]
Abstract
The development of anti-HCV drugs is one of the most successful stories of antiviral therapy. In fact, for the first time in human history we have the potential to eradicate a chronic viral infection using only orally administered direct antiviral agents (DAAs). HCV NS5A replication complex inhibitors, exemplified by Daclatasvir (DCV, BMS-790052, Daklinza®), are a new class of DAA. The astonishing in vitro potency of DCV (pM to low nM range) translated to remarkable efficacy in clinical trials, and 2nd generation NS5A inhibitors have become essential components of HCV combination therapies. The current cure rate of effective combination therapies exceeds 90% in most clinical trials. The extraordinary potency of NS5A inhibitors promoted significant efforts to understand their mechanism(s) of inhibition.
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Affiliation(s)
- Min Gao
- Bristol-Myers Squibb Company, Wallingford, CT 06492, USA.
| | | | - Susan Roberts
- Bristol-Myers Squibb Company, Wallingford, CT 06492, USA
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22
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Zayed RA, Omran D, Zayed AA, Elmessery LO. Determinants of Infection Outcome in HCV-Genotype 4. Viral Immunol 2017; 30:560-567. [PMID: 28731371 DOI: 10.1089/vim.2017.0071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) infection represents a worldwide health problem and has been for long an attractive point of research due to diversity among different genotypes regarding unique geographical distribution and diverse treatment outcome. HCV is considered a major cause of chronic liver disease and cirrhosis, which leads to liver failure and hepatocellular carcinoma requiring liver transplantation. Of the HCV genotypes identified, HCV genotype 4 (HCV-4) is the least studied. HCV-4 is responsible for ∼10% of HCV infections and is common in the Middle East and Africa; recently it is increasingly prevalent in European Countries. HCV-4 is a continuing epidemic in Egypt, having the highest prevalence of HCV worldwide. "Know your epidemic, know your response" concept necessitates better understanding of HCV-4 characteristics to control disease dissemination and progression, which compromises the life quality of chronic HCV-infected patients. In this review, we discuss the epidemiology, natural history, and treatment options for patients with HCV-4 infection.
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Affiliation(s)
- Rania A Zayed
- 1 Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University , Giza, Cairo, Egypt
| | - Dalia Omran
- 2 Department of Endemic Medicine and Hepato-gastroenterology, Faculty of Medicine, Cairo University , Giza, Cairo, Egypt
| | - Abeer A Zayed
- 3 Department of Forensic Medicine and Clinical Toxicology, Faculty of Medicine, Cairo University , Giza, Cairo, Egypt
| | - Lobna O Elmessery
- 1 Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University , Giza, Cairo, Egypt
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23
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Abstract
Multiple direct-acting antiviral (DAA)-based regimens are currently approved that provide one or more interferon-free treatment options for hepatitis C virus (HCV) genotypes (G) 1-6. The choice of a DAA regimen, duration of therapy, and use of ribavirin depends on multiple viral and host factors, including HCV genotype, the detection of resistance-associated amino acid (aa) substitutions (RASs), prior treatment experience, and presence of cirrhosis. In regard to viral factors that may guide the treatment choice, the most important is the infecting genotype because a number of DAAs are genotype-designed. The potency and the genetic barrier may also impact the choice of treatment. One important and debated possible virologic factor that may negatively influence the response to DAAs is the presence of baseline RASs. Baseline resistance testing is currently not routinely considered or recommended for initiating HCV treatment, due to the overall high response rates (sustained virological response >90%) obtained. Exceptions are patients infected by HCV G1a when initiating treatment with simeprevir and elbasvir/grazoprevir or in those with cirrhosis prior to daclatasvir/sofosbuvir treatment because of natural polymorphisms demonstrated in sites of resistance. On the basis of these observations, first-line strategies should be optimized to overcome treatment failure due to HCV resistance.
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24
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Benzine T, Brandt R, Lovell WC, Yamane D, Neddermann P, De Francesco R, Lemon SM, Perelson AS, Ke R, McGivern DR. NS5A inhibitors unmask differences in functional replicase complex half-life between different hepatitis C virus strains. PLoS Pathog 2017; 13:e1006343. [PMID: 28594932 PMCID: PMC5464671 DOI: 10.1371/journal.ppat.1006343] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/10/2017] [Indexed: 01/06/2023] Open
Abstract
Hepatitis C virus (HCV) RNA is synthesized by the replicase complex (RC), a macromolecular assembly composed of viral non-structural proteins and cellular co-factors. Inhibitors of the HCV NS5A protein block formation of new RCs but do not affect RNA synthesis by pre-formed RCs. Without new RC formation, existing RCs turn over and are eventually lost from the cell. We aimed to use NS5A inhibitors to estimate the half-life of the functional RC of HCV. We compared different cell culture-infectious strains of HCV that may be grouped based on their sensitivity to lipid peroxidation: robustly replicating, lipid peroxidation resistant (LPOR) viruses (e.g. JFH-1 or H77D) and more slowly replicating, lipid peroxidation sensitive (LPOS) viruses (e.g. H77S.3 and N.2). In luciferase assays, LPOS HCV strains declined under NS5A inhibitor therapy with much slower kinetics compared to LPOR HCV strains. This difference in rate of decline was not observed for inhibitors of the NS5B RNA-dependent RNA polymerase suggesting that the difference was not simply a consequence of differences in RNA stability. In further analyses, we compared two isoclonal HCV variants: the LPOS H77S.3 and the LPOR H77D that differ only by 12 amino acids. Differences in rate of decline between H77S.3 and H77D following NS5A inhibitor addition were not due to amino acid sequences in NS5A but rather due to a combination of amino acid differences in the non-structural proteins that make up the HCV RC. Mathematical modeling of intracellular HCV RNA dynamics suggested that differences in RC stability (half-lives of 3.5 and 9.9 hours, for H77D and H77S.3, respectively) are responsible for the different kinetics of antiviral suppression between LPOS and LPOR viruses. In nascent RNA capture assays, the rate of RNA synthesis decline following NS5A inhibitor addition was significantly faster for H77D compared to H77S.3 indicating different half-lives of functional RCs. Inhibitors targeting the HCV NS5A protein are a key component of highly effective interferon-free combination therapies for chronic hepatitis C. Despite their high potency against HCV, the precise details of their mode of action are poorly understood. They are known to block assembly and release of virus particles from infected hepatocytes, resulting in a rapid drop in viral RNA in the blood. Additionally they block formation of intracellular membrane structures that are the site of viral RNA synthesis in infected hepatocytes. By preventing membrane remodeling, NS5A inhibitors effectively block formation of new RCs within the cell. Following addition of NS5A inhibitors to infected cell cultures, the kinetics of antiviral suppression were found to vary between different HCV strains, independent of specific differences in NS5A sequence. Using an integrated experimental and mathematical modeling approach, we provide evidence that the rate of decline of viral RNA abundance in infected cells treated with NS5A inhibitors is determined by the stability or half-life of the functional HCV RC.
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Affiliation(s)
- Tiffany Benzine
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ryan Brandt
- Department of Mathematics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - William C. Lovell
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daisuke Yamane
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Petra Neddermann
- INGM -Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Raffaele De Francesco
- INGM -Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Stanley M. Lemon
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ruian Ke
- Department of Mathematics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - David R. McGivern
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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25
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Gitto S, Gamal N, Andreone P. NS5A inhibitors for the treatment of hepatitis C infection. J Viral Hepat 2017; 24:180-186. [PMID: 27925362 DOI: 10.1111/jvh.12657] [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: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/12/2022]
Abstract
Today, we are witnessing a new era for the treatment of hepatitis C with excellent rates of virologic response and very good safety profiles. Among the many classes of direct-acting antivirals, the inhibitors of nonstructural protein 5A are particularly interesting. NS5A is a phosphorylated protein with a relevant role in viral replication. HCV-NS5A inhibitors show high potency, very good safety profile and high barrier to resistance. The amazing in vitro effectiveness of this class is associated with great efficacy in clinical trials in combination protocols with antivirals of other classes, with sustained virological response (SVR) obtained in more than 90% of patients. Herein, we sought to review the current knowledge regarding the NS5A protease complex inhibitors with special emphasis on clinical efficacy and development of viral resistance.
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Affiliation(s)
- Stefano Gitto
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Nesrine Gamal
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Pietro Andreone
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
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26
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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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Hayes CN, Imamura M, Chayama K. The practical management of chronic hepatitis C infection in Japan - dual therapy of daclatasvir + asunaprevir. Expert Rev Gastroenterol Hepatol 2017; 11:103-113. [PMID: 27936974 DOI: 10.1080/17474124.2017.1270205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Without treatment, many of the 200 million people worldwide with chronic hepatitis C virus (HCV) infection will develop cirrhosis or liver cancer. Japan was the first nation to approve an interferon-free therapy for HCV, and sustained viral response (SVR) rates >90% have been achieved with asunaprevir, a protease inhibitor, plus daclatasvir, an inhibitor of the non-structural 5A (NS5A) protein. Areas covered: This review provides an overview of the results from both clinical trials and real world experience with asunaprevir and daclatasvir therapy focused primarily on Japan. A literature search using the keywords 'asunaprevir,' 'daclatasvir,' 'interferon-free therapy,' and 'direct-acting antiviral drugs' was initially used to select relevant literature for inclusion in the review. Expert commentary: While not approved in the United States, dual therapy with asunaprevir plus daclatasvir has already been successfully used in Japan and throughout East Asia to treat many thousands of patients. Pre-existing or treatment-emergent NS5A-Y93 or -L31 resistance-associated variants (RAVs) may lead to viral breakthrough, and alternative therapies should be considered for these patients, but patients who harbor NS5A RAVs only at low frequency are likely to achieve SVR. The therapy has also been shown to be safe and effective with renal dysfunction or liver cirrhosis.
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Affiliation(s)
- C Nelson Hayes
- a Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical and Health Sciences , Hiroshima University , Minami-ku , Hiroshima , Japan.,b Liver Research Project Center , Hiroshima University , Hiroshima , Japan
| | - Michio Imamura
- a Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical and Health Sciences , Hiroshima University , Minami-ku , Hiroshima , Japan.,b Liver Research Project Center , Hiroshima University , Hiroshima , Japan
| | - Kazuaki Chayama
- a Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical and Health Sciences , Hiroshima University , Minami-ku , Hiroshima , Japan.,b Liver Research Project Center , Hiroshima University , Hiroshima , Japan.,c Laboratory for Digestive Diseases , Center for Genomic Medicine, RIKEN , Hiroshima , Japan
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Abstract
The allure of phenotypic screening, combined with the industry preference for target-based approaches, has prompted the development of innovative chemical biology technologies that facilitate the identification of new therapeutic targets for accelerated drug discovery. A chemogenomic library is a collection of selective small-molecule pharmacological agents, and a hit from such a set in a phenotypic screen suggests that the annotated target or targets of that pharmacological agent may be involved in perturbing the observable phenotype. In this Review, we describe opportunities for chemogenomic screening to considerably expedite the conversion of phenotypic screening projects into target-based drug discovery approaches. Other applications are explored, including drug repositioning, predictive toxicology and the discovery of novel pharmacological modalities.
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Wang H, Tai AW. Continuous de novo generation of spatially segregated hepatitis C virus replication organelles revealed by pulse-chase imaging. J Hepatol 2017; 66:55-66. [PMID: 27599826 PMCID: PMC5167665 DOI: 10.1016/j.jhep.2016.08.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 08/22/2016] [Accepted: 08/26/2016] [Indexed: 01/22/2023]
Abstract
BACKGROUND & AIMS Like all positive-sense RNA viruses, hepatitis C virus (HCV) induces host membrane alterations for its replication. In chronically infected cells, it is not known whether these viral replication organelles are being continually resupplied by newly synthesized viral proteins in situ, or whether they are generated de novo. Here we aimed to study temporal events in replication organelles formation and maturation. METHODS Here we use pulse-chase labeling in combination with confocal microscopy, correlative light electron microscopy and biochemical methods to identify temporally distinct populations of replication organelles in living cells and study the formation, morphogenesis as well as compositional and functional changes of replication organelles over time. RESULTS We found that HCV replication organelles are continuously generated de novo at spatially distinct sites from preformed ones. This process is accompanied by accumulated intracellular membrane alteration, increased cholesterol delivery, NS5A phosphorylation, and positive-strand RNA content, and by eventual association with HCV core protein around lipid droplets. Generation of spatially segregated foci requires viral NS5A and the host factors phosphatidylinositol 4-kinase and oxysterol-binding protein, while association of foci with lipid droplets requires cholesterol. CONCLUSIONS Our results reveal that HCV replication organelles are not static structures, but instead are continuously generated and dynamically change in composition and possibly also in function. LAY SUMMARY Hepatitis C virus replication membrane structures are continuously generated at spatially distinct sites. New replication organelles are different in composition, and possibly also in function, compared to old replication organelles.
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Affiliation(s)
- Hongliang Wang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Andrew W. Tai
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
,Medicine Service, Ann Arbor Veterans Administration Health System, Ann Arbor, Michigan
,Correspondence: Andrew W. Tai, University of Michigan, 6520 MSRB I SPC 5682, 1150 W Medical Center Dr, Ann Arbor, MI 48109-5682, Tel: (734) 764-2804, FAX: (734) 763-2535,
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Human Choline Kinase-α Promotes Hepatitis C Virus RNA Replication through Modulation of Membranous Viral Replication Complex Formation. J Virol 2016; 90:9075-95. [PMID: 27489281 PMCID: PMC5044849 DOI: 10.1128/jvi.00960-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/20/2016] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED Hepatitis C virus (HCV) infection reorganizes cellular membranes to create an active viral replication site named the membranous web (MW). The role that human choline kinase-α (hCKα) plays in HCV replication remains elusive. Here, we first showed that hCKα activity, not the CDP-choline pathway, promoted viral RNA replication. Confocal microscopy and subcellular fractionation of HCV-infected cells revealed that a small fraction of hCKα colocalized with the viral replication complex (RC) on the endoplasmic reticulum (ER) and that HCV infection increased hCKα localization to the ER. In the pTM-NS3-NS5B model, NS3-NS5B expression increased the localization of the wild-type, not the inactive D288A mutant, hCKα on the ER, and hCKα activity was required for effective trafficking of hCKα and NS5A to the ER. Coimmunoprecipitation showed that hCKα was recruited onto the viral RC presumably through its binding to NS5A domain 1 (D1). hCKα silencing or treatment with CK37, an hCKα activity inhibitor, abolished HCV-induced MW formation. In addition, hCKα depletion hindered NS5A localization on the ER, interfered with NS5A and NS5B colocalization, and mitigated NS5A-NS5B interactions but had no apparent effect on NS5A-NS4B and NS4B-NS5B interactions. Nevertheless, hCKα activity was not essential for the binding of NS5A to hCKα or NS5B. These findings demonstrate that hCKα forms a complex with NS5A and that hCKα activity enhances the targeting of the complex to the ER, where hCKα protein, not activity, mediates NS5A binding to NS5B, thereby promoting functional membranous viral RC assembly and viral RNA replication. IMPORTANCE HCV infection reorganizes the cellular membrane to create an active viral replication site named the membranous web (MW). Here, we report that human choline kinase-α (hCKα) acts as an essential host factor for HCV RNA replication. A fraction of hCKα colocalizes with the viral replication complex (RC) on the endoplasmic reticulum (ER) in HCV-infected cells. NS3-NS5B expression increases ER localization of wild-type, but not D288A mutant, hCKα, and hCKα activity facilitates the transport of itself and NS5A to the ER. Silencing or inactivation of hCKα abrogates MW formation. Moreover, hCKα is recruited by NS5A independent of hCKα activity, presumably through binding to NS5A D1. hCKα activity then mediates the ER targeting of the hCKα-NS5A complex. On the ER membrane, hCKα protein, per se, induces NS5A binding to NS5B, thereby promoting membranous RC formation and viral RNA replication. Our study may benefit the development of hCKα-targeted anti-HCV therapeutics.
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Alavian SM, Rezaee-Zavareh MS. Daclatasvir-based Treatment Regimens for Hepatitis C Virus Infection: A Systematic Review and Meta-Analysis. HEPATITIS MONTHLY 2016; 16:e41077. [PMID: 27826322 PMCID: PMC5097339 DOI: 10.5812/hepatmon.41077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/07/2016] [Accepted: 08/14/2016] [Indexed: 12/11/2022]
Abstract
CONTEXT Direct acting antivirals (DAAs) have recently emerged as a promising therapeutic regimen for the treatment of hepatitis C virus (HCV) infection, which is a major public health problem. Among the known DAAs, daclatasvir (DCV), an inhibitor of the non-structural 5A protein, has been used in combination with several drugs for treatment of infection with HCV of different genotypes under different conditions. We conducted a systematic review and meta-analysis of combination therapy with DCV. EVIDENCE ACQUISITION We performed a systematic search in PubMed, Scopus, Science Direct and Web of Science with appropriate keywords for DCV. Studies that evaluated any regimen containing DCV and reported the sustained virological response (SVR) 12 weeks after therapy based on the HCV genotype, treatment duration and use of ribavirin (RBV) were included. The selected studies were considered for meta-analysis using STATA 11.0. RESULTS We found six different regimens containing DCV: DCV/asunaprevir (ASV), DCV/ASV/beclubavir, DCV/pegylated interferon lambda or alpha/RBV with or without ASV, DCV/simeprevir, DCV/VX-135 and DCV/sofosbuvir (SOF). Most of these regimens were used for the treatment of HCV genotype 1 infections, and in most cases, treatment failure was noted in subtype 1a infections. Among all these regimens, DCV/SOF with or without RBV for 12 or 24 weeks was found to be an efficacious approach for treatment of different types of patients with infections with different HCV genotypes. CONCLUSIONS Among the treatment regimens containing DCV, DCV/SOF has the highest SVR rate for the treatment of infection with different HCV genotypes in different patient contexts; thus, this regimen shows promise for the treatment of HCV infections.
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Affiliation(s)
- Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases (BRCGL), Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Middle East Liver Diseases (MELD) Center, Tehran, IR Iran
- Meta-analysis Study Group for Treatment of Hepatitis C, Iran Hepatitis Network, Tehran, IR Iran
| | - Mohammad Saeid Rezaee-Zavareh
- Middle East Liver Diseases (MELD) Center, Tehran, IR Iran
- Meta-analysis Study Group for Treatment of Hepatitis C, Iran Hepatitis Network, Tehran, IR Iran
- Students’ Research Committee, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
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Jensen CM, Holle LM. Ledipasvir-Sofosbuvir: A Once-Daily Oral Treatment Option for Chronic Hepatitis C Virus Genotype 1 Infection. Pharmacotherapy 2016; 36:562-74. [PMID: 27027412 DOI: 10.1002/phar.1748] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chronic hepatitis C virus (HCV) genotype 1 historically has been the most difficult to treat HCV genotype, and patients infected with this genotype had been previously treated with interferon-based therapy. In recent years, however, treatment options for chronic HCV infection have rapidly changed to an all-oral regimen. Ledipasvir-sofosbuvir is an oral fixed-dose (ledipasvir 90 mg-sofosbuvir 400 mg) combination of two direct-acting antiviral drugs. Four phase 3 clinical trials (ION-1-4) evaluated ledipasvir-sofosbuvir with and without ribavirin in patients with HCV genotype 1. High rates of sustained virologic response (SVR) occurred with ledipasvir-sofosbuvir alone in treatment-naïve and treatment-experienced patients without cirrhosis as well as in treatment-naïve patients with cirrhosis when administered for 12 weeks. In treatment-experienced patients with cirrhosis, 24 weeks of ledipasvir-sofosbuvir was also highly effective. Furthermore, treatment-naïve patients without cirrhosis (particularly those with HCV RNA serum concentrations < 6 million IU/ml) can achieve a similar SVR with only 8 weeks of therapy. Similarly, in patients coinfected with human immunodeficiency virus and HCV genotype 1 who were treated with ledipasvir-sofosbuvir for 12 weeks, a high SVR was observed in those with and without cirrhosis as well as treatment-naïve and treatment-experienced patients. Ledipasvir-sofosbuvir is well tolerated, with fatigue, headache, nausea, diarrhea, and insomnia being the most common adverse effects, which are typically mild to moderate in nature. This combination antiviral can be taken with or without food. Key factors to consider when prescribing ledipasvir-sofosbuvir are drug interactions including those mediated by the P-glycoprotein transporter and increased pH, cost of the drug or insurance coverage, comorbid conditions, and patient and provider preferences. Postmarketing experience and ongoing clinical trials will further define the safety and role of ledipasvir-sofosbuvir in the treatment of HCV genotype 1.
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Affiliation(s)
| | - Lisa M Holle
- Department of Pharmacy Practice, UConn School of Pharmacy, Storrs, Connecticut
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33
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Synergistic Activity of Combined NS5A Inhibitors. Antimicrob Agents Chemother 2015; 60:1573-83. [PMID: 26711745 DOI: 10.1128/aac.02639-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/13/2015] [Indexed: 12/29/2022] Open
Abstract
Daclatasvir (DCV) is a first-in-class hepatitis C virus (HCV) nonstructural 5A replication complex inhibitor (NS5A RCI) that is clinically effective in interferon-free combinations with direct-acting antivirals (DAAs) targeting alternate HCV proteins. Recently, we reported NS5A RCI combinations that enhance HCV inhibitory potential in vitro, defining a new class of HCV inhibitors termed NS5A synergists (J. Sun, D. R. O'Boyle II, R. A. Fridell, D. R. Langley, C. Wang, S. Roberts, P. Nower, B. M. Johnson F. Moulin, M. J. Nophsker, Y. Wang, M. Liu, K. Rigat, Y. Tu, P. Hewawasam, J. Kadow, N. A. Meanwell, M. Cockett, J. A. Lemm, M. Kramer, M. Belema, and M. Gao, Nature 527:245-248, 2015, doi:10.1038/nature15711). To extend the characterization of NS5A synergists, we tested new combinations of DCV and NS5A synergists against genotype (gt) 1 to 6 replicons and gt 1a, 2a, and 3a viruses. The kinetics of inhibition in HCV-infected cells treated with DCV, an NS5A synergist (NS5A-Syn), or a combination of DCV and NS5A-Syn were distinctive. Similar to activity observed clinically, DCV caused a multilog drop in HCV, followed by rebound due to the emergence of resistance. DCV-NS5A-Syn combinations were highly efficient at clearing cells of viruses, in line with the trend seen in replicon studies. The retreatment of resistant viruses that emerged using DCV monotherapy with DCV-NS5A-Syn resulted in a multilog drop and rebound in HCV similar to the initial decline and rebound observed with DCV alone on wild-type (WT) virus. A triple combination of DCV, NS5A-Syn, and a DAA targeting the NS3 or NS5B protein cleared the cells of viruses that are highly resistant to DCV. Our data support the observation that the cooperative interaction of DCV and NS5A-Syn potentiates both the genotype coverage and resistance barrier of DCV, offering an additional DAA option for combination therapy and tools for explorations of NS5A function.
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34
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Daclatasvir-containing all-oral regimens for the treatment of hepatitis C virus infection. Hepatol Int 2015; 10:258-66. [PMID: 26542068 DOI: 10.1007/s12072-015-9668-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 09/02/2015] [Indexed: 12/21/2022]
Abstract
The treatment of chronic hepatitis C is revolutionizing rapidly. The aim of this study is to review the efficacy and safety of daclatasvir (DCV)-containing all-oral regimens in clinical studies for chronic hepatitis C treatment. Using PubMed and search terms of 'DCV,' 'hepatitis C virus (HCV) treatment,' and 'HCV NS5A inhibitors,' literature on the clinical development of DCV, as well as abstracts presented at the April 2015 annual meeting of the European Association for the Study of the Liver (EASL) and November 2014 annual meeting of the American Association for the Study of Liver Diseases were reviewed. The final search was undertaken on 14 July 2015. With its potent antiviral activity to all HCV genotypes (GT) demonstrated in preclinical, phases 1-3 studies, DCV has been acting as a very competent team player in clinical trials of all-oral regimens. It is generally safe and well tolerated with a low genetic barrier to resistance and low potential for drug-drug interaction. Administered with a non-structural protein 3 (NS3) protease inhibitor (asunaprevir, ASV) with or without a non-nucleoside NS5B polymerase inhibitor (beclabuvir, BCV), or a nucleotide NS5B polymerase inhibitor (sofosbuvir, SOF), DCV is able to achieve greater than a 90-% HCV eradication rate in both treatment-naïve and treatment-experienced patients with GT 1. A triple combination regimen with DCV/ASV/BCV results in 100% sustained virologic response (SVR) rates in HCV GT 4 treatment-naïve subjects. DCV/SOF combination also had demonstrated up to 90-% SVR rates in GT 3-infected non-cirrhotic patients. The efficacy and safety of DCV-containing all-oral regimens highlight a new era of interferon-free therapy for chronic hepatitis C.
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35
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The yin and yang of hepatitis C: synthesis and decay of hepatitis C virus RNA. Nat Rev Microbiol 2015; 13:544-58. [PMID: 26256788 DOI: 10.1038/nrmicro3506] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) is an unusual RNA virus that has a striking capacity to persist for the remaining life of the host in the majority of infected individuals. In order to persist, HCV must balance viral RNA synthesis and decay in infected cells. In this Review, we focus on interactions between the positive-sense RNA genome of HCV and the host RNA-binding proteins and microRNAs, and describe how these interactions influence the competing processes of viral RNA synthesis and decay to achieve stable, long-term persistence of the viral genome. Furthermore, we discuss how these processes affect hepatitis C pathogenesis and therapeutic strategies against HCV.
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36
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Novel benzidine and diaminofluorene prolinamide derivatives as potent hepatitis C virus NS5A inhibitors. Eur J Med Chem 2015; 101:163-78. [PMID: 26134551 DOI: 10.1016/j.ejmech.2015.06.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/14/2015] [Accepted: 06/15/2015] [Indexed: 12/21/2022]
Abstract
Our study describes the discovery of a series of highly potent hepatitis C virus (HCV) NS5A inhibitors based on symmetrical prolinamide derivatives of benzidine and diaminofluorene. Through modification of benzidine, l-proline, and diaminofluorene derivatives, we developed novel inhibitor structures, which allowed us to establish a library of potent HCV NS5A inhibitors. After optimizing the benzidine prolinamide backbone, we identified inhibitors embedding meta-substituted benzidine core structures that exhibited the most potent anti-HCV activities. Furthermore, through a battery of studies including hERG ligand binding assay, CYP450 binding assay, rat plasma stability test, human liver microsomal stability test, and pharmacokinetic studies, the identified compounds 24, 26, 27, 42, and 43 are found to be nontoxic, and are expected to be effective therapeutic anti-HCV agents.
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37
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Hett EC, Xu H, Geoghegan KF, Gopalsamy A, Kyne RE, Menard CA, Narayanan A, Parikh MD, Liu S, Roberts L, Robinson RP, Tones MA, Jones LH. Rational targeting of active-site tyrosine residues using sulfonyl fluoride probes. ACS Chem Biol 2015; 10:1094-8. [PMID: 25571984 DOI: 10.1021/cb5009475] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This work describes the first rational targeting of tyrosine residues in a protein binding site by small-molecule covalent probes. Specific tyrosine residues in the active site of the mRNA-decapping scavenger enzyme DcpS were modified using reactive sulfonyl fluoride covalent inhibitors. Structure-based molecular design was used to create an alkyne-tagged probe bearing the sulfonyl fluoride warhead, thus enabling the efficient capture of the protein from a complex proteome. Use of the probe in competition experiments with a diaminoquinazoline DcpS inhibitor permitted the quantification of intracellular target occupancy. As a result, diaminoquinazoline upregulators of survival motor neuron protein that are used for the treatment of spinal muscular atrophy were confirmed as inhibitors of DcpS in human primary cells. This work illustrates the utility of sulfonyl fluoride probes designed to react with specific tyrosine residues of a protein and augments the chemical biology toolkit by these probes uses in target validation and molecular pharmacology.
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Affiliation(s)
- Erik C. Hett
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Hua Xu
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Kieran F. Geoghegan
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ariamala Gopalsamy
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Robert E. Kyne
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Carol A. Menard
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Arjun Narayanan
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mihir D. Parikh
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Shenping Liu
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Lee Roberts
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ralph P. Robinson
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Michael A. Tones
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Lyn H. Jones
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
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Kwon HJ, Xing W, Chan K, Niedziela-Majka A, Brendza KM, Kirschberg T, Kato D, Link JO, Cheng G, Liu X, Sakowicz R. Direct binding of ledipasvir to HCV NS5A: mechanism of resistance to an HCV antiviral agent. PLoS One 2015; 10:e0122844. [PMID: 25856426 PMCID: PMC4391872 DOI: 10.1371/journal.pone.0122844] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/19/2015] [Indexed: 01/01/2023] Open
Abstract
Ledipasvir, a direct acting antiviral agent (DAA) targeting the Hepatitis C Virus NS5A protein, exhibits picomolar activity in replicon cells. While its mechanism of action is unclear, mutations that confer resistance to ledipasvir in HCV replicon cells are located in NS5A, suggesting that NS5A is the direct target of ledipasvir. To date co-precipitation and cross-linking experiments in replicon or NS5A transfected cells have not conclusively shown a direct, specific interaction between NS5A and ledipasvir. Using recombinant, full length NS5A, we show that ledipasvir binds directly, with high affinity and specificity, to NS5A. Ledipasvir binding to recombinant NS5A is saturable with a dissociation constant in the low nanomolar range. A mutant form of NS5A (Y93H) that confers resistance to ledipasvir shows diminished binding to ledipasvir. The current study shows that ledipasvir inhibits NS5A through direct binding and that resistance to ledipasvir is the result of a reduction in binding affinity to NS5A mutants.
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Affiliation(s)
- Hyock Joo Kwon
- Gilead Sciences, Inc., Foster City, California, United States of America
- * E-mail:
| | - Weimei Xing
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Katie Chan
- Gilead Sciences, Inc., Foster City, California, United States of America
| | | | | | | | - Darryl Kato
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - John O. Link
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Guofeng Cheng
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Xiaohong Liu
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Roman Sakowicz
- Gilead Sciences, Inc., Foster City, California, United States of America
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39
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Fast hepatitis C virus RNA elimination and NS5A redistribution by NS5A inhibitors studied by a multiplex assay approach. Antimicrob Agents Chemother 2015; 59:3482-92. [PMID: 25845863 DOI: 10.1128/aac.00223-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/27/2015] [Indexed: 12/18/2022] Open
Abstract
While earlier therapeutic strategies for the treatment of hepatitis C virus (HCV) infection relied exclusively on interferon (IFN) and ribavirin (RBV), four direct-acting antiviral agents (DAAs) have now been approved, aiming for an interferon-free strategy with a short treatment duration and fewer side effects. To facilitate studies on the mechanism of action (MOA) and efficacy of DAAs, we established a multiplex assay approach, which employs flow cytometry, a Gaussia luciferase reporter system, Western blot analysis, reverse transcription-quantitative PCR (RT-qPCR), a limited dilution assay (50% tissue culture infectious dose [TCID50]), and an image profiling assay that follows the NS5A redistribution in response to drug treatment. We used this approach to compare the relative potency of various DAAs and the kinetics of their antiviral effects as a potential preclinical measure of their potential clinical utility. We evaluated the NS5A inhibitors ledipasvir (LDV) and daclatasvir (DCV), the NS3/4A inhibitor danoprevir (DNV), and the NS5B inhibitor sofosbuvir (SOF). In terms of kinetics, our data demonstrate that the NS5A inhibitor LDV, followed closely by DCV, has the fastest effect on suppression of viral proteins and RNA and on redistribution of NS5A. In terms of MOA, LDV has a more pronounced effect than DCV on the viral replication, assembly, and infectivity of released virus. Our approach can be used to facilitate the study of the biological processes involved in HCV replication and help identify optimal drug combinations.
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Chukkapalli V, Berger KL, Kelly SM, Thomas M, Deiters A, Randall G. Daclatasvir inhibits hepatitis C virus NS5A motility and hyper-accumulation of phosphoinositides. Virology 2014; 476:168-179. [PMID: 25546252 DOI: 10.1016/j.virol.2014.12.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 12/09/2014] [Indexed: 12/18/2022]
Abstract
Combinations of direct-acting antivirals (DAAs) against the hepatitis C virus (HCV) have the potential to revolutionize the HCV therapeutic regime. An integral component of DAA combination therapies is HCV NS5A inhibitors. It has previously been proposed that NS5A DAAs inhibit two functions of NS5A: RNA replication and virion assembly. In this study, we characterize the impact of a prototype NS5A DAA, daclatasvir (DCV), on HCV replication compartment formation. DCV impaired HCV replicase localization and NS5A motility. In order to characterize the mechanism behind altered HCV replicase localization, we examined the impact of DCV on the interaction of NS5A with its essential cellular cofactor, phosphatidylinositol-4-kinase III α (PI4KA). We observed that DCV does not inhibit PI4KA directly, nor does it impair early events of the NS5A-PI4KA interaction that can occur when NS5A is expressed alone. NS5A functions that are unaffected by DCV include PI4KA binding, as determined by co-immunoprecipitation, and a basal accumulation of the PI4KA product, PI4P. However, DCV impairs late steps in PI4KA activation that requires NS5A expressed in the context of the HCV polyprotein. These NS5A functions include hyper-stimulation of PI4P levels and appropriate replication compartment formation. The data are most consistent with a model wherein DCV inhibits conformational changes in the NS5A protein or protein complex formations that occur in the context of HCV polyprotein expression and stimulate PI4P hyper-accumulation and replication compartment formation.
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Affiliation(s)
- Vineela Chukkapalli
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Kristi L Berger
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Sean M Kelly
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Meryl Thomas
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Glenn Randall
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA.
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41
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Hepatitis C virus life cycle and lipid metabolism. BIOLOGY 2014; 3:892-921. [PMID: 25517881 PMCID: PMC4280516 DOI: 10.3390/biology3040892] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/04/2014] [Accepted: 12/08/2014] [Indexed: 12/12/2022]
Abstract
Hepatitis C Virus (HCV) infects over 150 million people worldwide. In most cases HCV infection becomes chronic, causing liver disease ranging from fibrosis to cirrhosis and hepatocellular carcinoma. HCV affects the cholesterol homeostasis and at the molecular level, every step of the virus life cycle is intimately connected to lipid metabolism. In this review, we present an update on the lipids and apolipoproteins that are involved in the HCV infectious cycle steps: entry, replication and assembly. Moreover, the result of the assembly process is a lipoviroparticle, which represents a peculiarity of hepatitis C virion. This review illustrates an example of an intricate virus-host interaction governed by lipid metabolism.
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Kayali Z, Schmidt WN. Finally sofosbuvir: an oral anti-HCV drug with wide performance capability. Pharmgenomics Pers Med 2014; 7:387-98. [PMID: 25540594 PMCID: PMC4270038 DOI: 10.2147/pgpm.s52629] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Chronic Hepatitis C virus (HCV) infection is the leading cause of advanced liver disease worldwide. The virus successfully evades host immune detection and for many years has hampered efforts to find a safe, uncomplicated, and reliable oral antiviral therapy. Initially, interferon and ribavirin therapy was the treatment standard of care, but it offered limited performance across the wide spectrum of HCV disease and was fraught with excessive and often limiting side effects. Sofosbuvir (SOF) is a potent first-in-class nucleoside inhibitor that has recently been approved for treatment of HCV. The drug has low toxicity, a high resistance barrier, and minimal drug interactions with other HCV direct-acting antiviral agents such as protease inhibitors or anti-NS5A agents. SOF is safe and can be used across different viral genotypes, disease stages, and special patient groups, such as those coinfected with human immunodeficiency virus. When used in combination with ribavirin or another direct-acting antiviral agent, SOF has revolutionized the HCV treatment spectrum and set the stage for nearly universal HCV antiviral therapy. More so than any other anti-HCV drug developed to date, SOF offers the widest applicability for all infected patients, and new regimens will be tailored to maximize performance.
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Affiliation(s)
- Zeid Kayali
- Division of Gastroenterology and Hepatology, University of Southern California, Los Angeles, CA, USA
| | - Warren N Schmidt
- Department of Internal Medicine and Research Service, Veterans Affairs Medical Center, Iowa City, IA, USA
- Roy G and Lucille A Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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Nettles JH, Stanton RA, Broyde J, Amblard F, Zhang H, Zhou L, Shi J, McBrayer TR, Whitaker T, Coats SJ, Kohler JJ, Schinazi RF. Asymmetric binding to NS5A by daclatasvir (BMS-790052) and analogs suggests two novel modes of HCV inhibition. J Med Chem 2014; 57:10031-43. [PMID: 25365735 PMCID: PMC4266333 DOI: 10.1021/jm501291c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Symmetric, dimeric daclatasvir (BMS-790052) is the clinical lead for a class of picomolar inhibitors of HCV replication. While specific, resistance-bearing mutations at positions 31 and 93 of domain I strongly suggest the viral NS5A as target, structural mechanism(s) for the drugs' activities and resistance remains unclear. Several previous models suggested symmetric binding modes relative to the homodimeric target; however, none can fully explain SAR details for this class. We present semiautomated workflows to model potential receptor conformations for docking. Surprisingly, ranking docked hits with our library-derived 3D-pharmacophore revealed two distinct asymmetric binding modes, at a conserved poly-proline region between 31 and 93, consistent with SAR. Interfering with protein-protein interactions at this membrane interface can explain potent inhibition of replication-complex formation, resistance, effects on lipid droplet distribution, and virion release. These detailed interaction models and proposed mechanisms of action will allow structure-based design of new NS5A directed compounds with higher barriers to HCV resistance.
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Affiliation(s)
- James H Nettles
- Center for AIDS Research, Department of Pediatrics, Emory University School of Medicine , Atlanta, Georgia 30322, United States
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Berger C, Romero-Brey I, Radujkovic D, Terreux R, Zayas M, Paul D, Harak C, Hoppe S, Gao M, Penin F, Lohmann V, Bartenschlager R. Daclatasvir-like inhibitors of NS5A block early biogenesis of hepatitis C virus-induced membranous replication factories, independent of RNA replication. Gastroenterology 2014; 147:1094-105.e25. [PMID: 25046163 DOI: 10.1053/j.gastro.2014.07.019] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 06/21/2014] [Accepted: 07/15/2014] [Indexed: 12/31/2022]
Abstract
BACKGROUND & AIMS Direct-acting antivirals that target nonstructural protein 5A (NS5A), such as daclatasvir, have high potency against the hepatitis C virus (HCV). They are promising clinical candidates, yet little is known about their antiviral mechanisms. We investigated the mechanisms of daclatasvir derivatives. METHODS We used a combination of biochemical assays, in silico docking models, and high-resolution imaging to investigate inhibitor-induced changes in properties of NS5A, including its interaction with phosphatidylinositol-4 kinase IIIα and induction of the membranous web, which is the site of HCV replication. Analyses were conducted with replicons, infectious virus, and human hepatoma cells that express a HCV polyprotein. Studies included a set of daclatasvir derivatives and HCV variants with the NS5A inhibitor class-defining resistance mutation Y93H. RESULTS NS5A inhibitors did not affect NS5A stability or dimerization. A daclatasvir derivative interacted with NS5A and molecular docking studies revealed a plausible mode by which the inhibitor bound to NS5A dimers. This interaction was impaired in mutant forms of NS5A that are resistant to daclatavir, providing a possible explanation for the reduced sensitivity of the HCV variants to this drug. Potent NS5A inhibitors were found to block HCV replication by preventing formation of the membranous web, which was not linked to an inhibition of phosphatidylinositol-4 kinase IIIα. Correlative light-electron microscopy revealed unequivocally that NS5A inhibitors had no overall effect on the subcellular distribution of NS5A, but completely prevented biogenesis of the membranous web. CONCLUSIONS Highly potent inhibitors of NS5A, such as daclatasvir, block replication of HCV RNA at the stage of membranous web biogenesis-a new paradigm in antiviral therapy.
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Affiliation(s)
- Carola Berger
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Inés Romero-Brey
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Danijela Radujkovic
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Raphael Terreux
- CNRS, UMR5086, Bases Moléculaires et Structurales des Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, Lyon, France; Labex Ecofect (ANR-11-LABX-0042), University of Lyon, Lyon, France; Faculté de Pharmacie (ISPB), Lyon, France
| | - Margarita Zayas
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - David Paul
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Christian Harak
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Simone Hoppe
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Min Gao
- Bristol-Myers Squibb Research and Development, Wallingford, Connecticut
| | - Francois Penin
- CNRS, UMR5086, Bases Moléculaires et Structurales des Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, Lyon, France; Labex Ecofect (ANR-11-LABX-0042), University of Lyon, Lyon, France
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; German Centre for Infection Research, Heidelberg University, Heidelberg, Germany.
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Eyre NS, Helbig KJ, Beard MR. Current and future targets of antiviral therapy in the hepatitis C virus life cycle. Future Virol 2014. [DOI: 10.2217/fvl.14.83] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ABSTRACT Advances in our understanding of the hepatitis C virus (HCV) life cycle have enabled the development of numerous clinically advanced direct-acting antivirals. Indeed, the recent approval of first-generation direct-acting antivirals that target the viral NS3–4A protease and NS5B RNA-dependent RNA polymerase brings closer the possibility of universally efficacious and well-tolerated antiviral therapies for this insidious infection. However, the complexities of comorbidities, unforeseen side effects or drug–drug interactions, viral diversity, the high mutation rate of HCV RNA replication and the elegant and constantly evolving mechanisms employed by HCV to evade host and therapeutically implemented antiviral strategies remain as significant obstacles to this goal. Here, we review advances in our understanding of the HCV life cycle and associated opportunities for antiviral therapy.
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Affiliation(s)
- Nicholas S Eyre
- School of Molecular & Biomedical Science, The University of Adelaide & Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Karla J Helbig
- School of Molecular & Biomedical Science, The University of Adelaide & Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Michael R Beard
- School of Molecular & Biomedical Science, The University of Adelaide & Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
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46
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Eyre NS, Beard MR. HCV NS5A inhibitors disrupt replication factory formation: a novel mechanism of antiviral action. Gastroenterology 2014; 147:959-62. [PMID: 25265576 DOI: 10.1053/j.gastro.2014.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Nicholas S Eyre
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia; Centre for Cancer Biology, Adelaide, Australia
| | - Michael R Beard
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia; Centre for Cancer Biology, Adelaide, Australia.
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Zhong M, Peng E, Huang N, Huang Q, Huq A, Lau M, Colonno R, Li L. Discovery of functionalized bisimidazoles bearing cyclic aliphatic-phenyl motifs as HCV NS5A inhibitors. Bioorg Med Chem Lett 2014; 24:5731-5737. [PMID: 25453810 DOI: 10.1016/j.bmcl.2014.10.057] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/11/2014] [Accepted: 10/17/2014] [Indexed: 02/06/2023]
Abstract
This Letter describes the discovery of a number of functionalized bisimidazoles bearing a cyclohexylphenyl, piperidylphenyl, or bicyclo[2,2,2]octylphenyl motif as HCV NS5A inhibitors. Compounds 2c, 4b and 6 have demonstrated low single-digit nM potency in gt-1a replicon and double-digit pM potency in gt-1b replicon, respectively. Moreover, both 4b and 6 have, respectively, exhibited good oral bioavailability in rats with a favorable liver/plasma ratio of the drug concentration.
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Affiliation(s)
- Min Zhong
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA.
| | - Eric Peng
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA
| | - Ningwu Huang
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA
| | - Qi Huang
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA
| | - Anja Huq
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA
| | - Meiyen Lau
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA
| | - Richard Colonno
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA
| | - Leping Li
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA.
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NS5A inhibitors impair NS5A-phosphatidylinositol 4-kinase IIIα complex formation and cause a decrease of phosphatidylinositol 4-phosphate and cholesterol levels in hepatitis C virus-associated membranes. Antimicrob Agents Chemother 2014; 58:7128-40. [PMID: 25224012 DOI: 10.1128/aac.03293-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The hepatitis C virus (HCV) nonstructural (NS) protein 5A is a multifunctional protein that plays a central role in viral replication and assembly. Antiviral agents directly targeting NS5A are currently in clinical development. Although the elucidation of the mechanism of action (MOA) of NS5A inhibitors has been the focus of intensive research, a detailed understanding of how these agents exert their antiviral effect is still lacking. In this study, we observed that the downregulation of NS5A hyperphosphorylation is associated with the actions of NS5A inhibitors belonging to different chemotypes. NS5A is known to recruit the lipid kinase phosphatidylinositol 4-kinase IIIα (PI4KIIIα) to the HCV-induced membranous web in order to generate phosphatidylinositol 4-phosphate (PI4P) at the sites of replication. We demonstrate that treatment with NS5A inhibitors leads to an impairment in the NS5A-PI4KIIIα complex formation that is paralleled by a significant reduction in PI4P and cholesterol levels within the endomembrane structures of HCV-replicating cells. A similar decrease in PI4P and cholesterol levels was also obtained upon treatment with a PI4KIIIα-targeting inhibitor. In addition, both the NS5A and PI4KIIIα classes of inhibitors induced similar subcellular relocalization of the NS5A protein, causing the formation of large cytoplasmic NS5A-containing clusters previously reported to be one of the hallmarks of inhibition of the action of PI4KIIIα. Because of the similarities between the effects induced by treatment with PI4KIIIα or NS5A inhibitors and the observation that agents targeting NS5A impair NS5A-PI4KIIIα complex formation, we speculate that NS5A inhibitors act by interfering with the function of the NS5A-PI4KIIIα complex.
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Affiliation(s)
- Menashe Elazar
- Department of Medicine, Division of Gastroenterology and Hepatology and Department of Microbiology and Immunology, Stanford University School of Medicine
| | - Jeffrey S Glenn
- Department of Medicine, Division of Gastroenterology and Hepatology and Department of Microbiology and Immunology, Stanford University School of Medicine and Veterans Administration Medical Center, Palo Alto, California.
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50
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McGivern DR, Masaki T, Williford S, Ingravallo P, Feng Z, Lahser F, Asante-Appiah E, Neddermann P, Francesco RD, Howe AY, Lemon SM. Kinetic analyses reveal potent and early blockade of hepatitis C virus assembly by NS5A inhibitors. Gastroenterology 2014; 147:453-62.e7. [PMID: 24768676 PMCID: PMC4107048 DOI: 10.1053/j.gastro.2014.04.021] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/21/2014] [Accepted: 04/09/2014] [Indexed: 01/06/2023]
Abstract
BACKGROUND & AIMS All-oral regimens combining different classes of direct-acting antivirals (DAA) are highly effective for treatment of patients with chronic hepatitis C. NS5A inhibitors will likely form a component of future interferon-sparing treatment regimens. However, despite their potential, the detailed mechanism of action of NS5A inhibitors is unclear. To study their mechanisms, we compared their kinetics of antiviral suppression with those of other classes of DAA, using the hepatitis C virus genotype 1a cell culture-infectious virus H77S.3. METHODS We performed detailed kinetic analyses of specific steps in the hepatitis C virus life cycle using cell cultures incubated with protease inhibitors, polymerase inhibitors, or NS5A inhibitors. Assays were designed to measure active viral RNA synthesis and steady-state RNA abundance, polyprotein synthesis, virion assembly, and infectious virus production. RESULTS Despite their high potency, NS5A inhibitors were slow to inhibit viral RNA synthesis compared with protease or polymerase inhibitors. By 24 hours after addition of an NS5A inhibitor, polyprotein synthesis was reduced <50%, even at micromolar concentrations. In contrast, inhibition of virus release by NS5A inhibitors was potent and rapid, with onset of inhibition as early as 2 hours. Cells incubated with NS5A inhibitors were rapidly depleted of intracellular infectious virus and RNA-containing hepatitis C virus particles, indicating a block in virus assembly. CONCLUSIONS DAAs that target NS5A rapidly inhibit intracellular assembly of genotype 1a virions. They also inhibit formation of functional replicase complexes, but have no activity against preformed replicase, thereby resulting in slow shut-off of viral RNA synthesis.
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Affiliation(s)
- David R. McGivern
- Departments of Medicine and Microbiology & Immunology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA,To whom correspondence should be addressed: David R. McGivern, Ph.D., 8.001A Burnett-Womack CB #7292, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292 USA, Tel: 919-843-9958; Fax: 919-843-7240, , Stanley M. Lemon, M.D., 8.034 Burnett-Womack CB #7292, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292 USA, Tel: 919-843-1848; Fax: 919-843-7240,
| | - Takahiro Masaki
- Departments of Medicine and Microbiology & Immunology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA
| | - Sara Williford
- Departments of Medicine and Microbiology & Immunology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA
| | | | - Zongdi Feng
- Departments of Medicine and Microbiology & Immunology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA
| | | | | | - Petra Neddermann
- Fondazione I.N.G.M., Istituto Nazionale di Genetica Molecolare, 20122 Milan, Italy
| | | | - Anita Y. Howe
- Merck Research Laboratory, Kenilworth, NJ 07033, USA
| | - Stanley M. Lemon
- Departments of Medicine and Microbiology & Immunology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA,To whom correspondence should be addressed: David R. McGivern, Ph.D., 8.001A Burnett-Womack CB #7292, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292 USA, Tel: 919-843-9958; Fax: 919-843-7240, , Stanley M. Lemon, M.D., 8.034 Burnett-Womack CB #7292, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292 USA, Tel: 919-843-1848; Fax: 919-843-7240,
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