1
|
Barik S. Suppression of Innate Immunity by the Hepatitis C Virus (HCV): Revisiting the Specificity of Host-Virus Interactive Pathways. Int J Mol Sci 2023; 24:16100. [PMID: 38003289 PMCID: PMC10671098 DOI: 10.3390/ijms242216100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
The hepatitis C virus (HCV) is a major causative agent of hepatitis that may also lead to liver cancer and lymphomas. Chronic hepatitis C affects an estimated 2.4 million people in the USA alone. As the sole member of the genus Hepacivirus within the Flaviviridae family, HCV encodes a single-stranded positive-sense RNA genome that is translated into a single large polypeptide, which is then proteolytically processed to yield the individual viral proteins, all of which are necessary for optimal viral infection. However, cellular innate immunity, such as type-I interferon (IFN), promptly thwarts the replication of viruses and other pathogens, which forms the basis of the use of conjugated IFN-alpha in chronic hepatitis C management. As a countermeasure, HCV suppresses this form of immunity by enlisting diverse gene products, such as HCV protease(s), whose primary role is to process the large viral polyprotein into individual proteins of specific function. The exact number of HCV immune suppressors and the specificity and molecular mechanism of their action have remained unclear. Nonetheless, the evasion of host immunity promotes HCV pathogenesis, chronic infection, and carcinogenesis. Here, the known and putative HCV-encoded suppressors of innate immunity have been reviewed and analyzed, with a predominant emphasis on the molecular mechanisms. Clinically, the knowledge should aid in rational interventions and the management of HCV infection, particularly in chronic hepatitis.
Collapse
Affiliation(s)
- Sailen Barik
- EonBio, 3780 Pelham Drive, Mobile, AL 36619, USA
| |
Collapse
|
2
|
Hazra M, Dubey RC. Interdisciplinary in silico studies to understand in-depth molecular level mechanism of drug resistance involving NS3-4A protease of HCV. J Biomol Struct Dyn 2022:1-20. [PMID: 35993498 DOI: 10.1080/07391102.2022.2113823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Hepatitis C virus (HCV) causes hepatitis, a life-threatening disease responsible for liver cirrhosis. Urgent measures have been taken to develop therapeutics against this deadly pathogen. NS3/4A protease is an extremely important target. A series of inhibitors have been developed against this viral protease including Faldaprevir. Unfortunately, the error-prone viral RNA polymerase causes the emergence of resistance, thereby causing reduced effectiveness of those peptidomimetic inhibitors. Among the drug resistant variants, three single amino acid residues (R155, A156 and D168) are notable for their presence in clinical isolates and also their effectivity against most of the known inhibitors in clinical development. Therefore, it is crucial to understand the mechanistic role of those drug resistant variants while designing potent novel inhibitors. In this communication, we have deeply analyzed through using in silico studies to understand the molecular mechanism of alteration of inhibitor binding between wild type and its R155K, A156V and D168V variants. Principal component analysis was carried to identify the backbone fluctuations of important residues in HCV NS3/4A responsible for the inhibitor binding and maintaining drug resistance. Free energy landscape as a function of the principal components has been used to identify the stability and conformation of the key residues that regulate inhibitor binding and their impact in developing drug resistance. Our findings are consistent with the trend of experimental results. The observations are also true in case of other Faldaprevir-like peptidomimetic inhibitors. Understanding this binding mechanism would be significant for the development of novel inhibitors with less susceptibility towards drug resistance.
Collapse
Affiliation(s)
- Mousumi Hazra
- Department of Botany and Microbiology, Gurukula Kangri (Deemed to be University), Haridwar, Uttarakhand, India
| | - Ramesh Chandra Dubey
- Department of Botany and Microbiology, Gurukula Kangri (Deemed to be University), Haridwar, Uttarakhand, India
| |
Collapse
|
3
|
Yang J, Ding S. Chimeric RNA-binding protein-based killing switch targeting hepatocellular carcinoma cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:683-695. [PMID: 34589286 PMCID: PMC8463442 DOI: 10.1016/j.omtn.2021.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 08/13/2021] [Indexed: 11/09/2022]
Abstract
Cancer cell-specific killing switches are synthetic circuits developed as an intelligent weapon to specifically eliminate malignant cells. RNA-delivered synthetic circuits provide safer means to control oncolytic functions, in which proteolysis-responding capsid-cNOT7 is developed to enable logic computation and modular design. Unfortunately, although circuits containing these capsid-cNOT7s exhibited good performance when introduced as replicons, in modified mRNA (modRNA) delivery, the performance was not quite as good. To improve this situation, alternative modules suitable for modRNA delivery need to be developed. An attractive option is RNA-binding protein (RBP)/riboswitches. In this study, RBPs were engineered by fusing with degron and cleavage sites. The compatibility of these chimeric RBPs with proteolysis-based sensing units were tested. Eight two-input logic gates and four three-input logic gates were implemented. After building this chimeric RBP-based system, we constructed a hepatocellular carcinoma (HCC) cell-specific killing circuit using two proteolysis-based sensing units, a two-input logic OR gate, and a leakproof apoptosis-inducing actuator, which distinguished HCC cells and induced apoptosis in a mixed IMR90-PLC/PRF/5 population.
Collapse
Affiliation(s)
- Jiong Yang
- Department of Gastroenterology, Peking University Third Hospital, Beijing 100191, China.,Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases, Beijing 100191, China
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing 100191, China.,Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases, Beijing 100191, China
| |
Collapse
|
4
|
Abstract
Activation and viral control of the innate immune response are hallmarks of hepatitis C virus (HCV) infection and are major determinants of spontaneous clearance or progression to chronic infection and liver disease. In this review, we provide a contemporary overview of how HCV is sensed by the host cell to trigger innate immune activation and the mechanisms deployed by the virus to evade this response. Type I and III interferons (IFNs) are crucial mediators of antiviral innate immunity against HCV, and we specifically highlight the importance of IFN-λ host genetics for the outcome of HCV infection. Last, we focus on the proinflammatory responses elicited by HCV infection and describe our current understanding of how interleukin (IL)-1β signaling and cross talk between the IL-1β and IFN signaling pathways lead to sustained inflammation and increased risk of liver pathology.
Collapse
Affiliation(s)
- Johannes Schwerk
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109, USA
| | - Amina Negash
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109, USA
| | - Ram Savan
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109, USA
| |
Collapse
|
5
|
Gao XJ, Chong LS, Kim MS, Elowitz MB. Programmable protein circuits in living cells. Science 2018; 361:1252-1258. [PMID: 30237357 DOI: 10.1126/science.aat5062] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022]
Abstract
Synthetic protein-level circuits could enable engineering of powerful new cellular behaviors. Rational protein circuit design would be facilitated by a composable protein-protein regulation system in which individual protein components can regulate one another to create a variety of different circuit architectures. In this study, we show that engineered viral proteases can function as composable protein components, which can together implement a broad variety of circuit-level functions in mammalian cells. In this system, termed CHOMP (circuits of hacked orthogonal modular proteases), input proteases dock with and cleave target proteases to inhibit their function. These components can be connected to generate regulatory cascades, binary logic gates, and dynamic analog signal-processing functions. To demonstrate the utility of this system, we rationally designed a circuit that induces cell death in response to upstream activators of the Ras oncogene. Because CHOMP circuits can perform complex functions yet be encoded as single transcripts and delivered without genomic integration, they offer a scalable platform to facilitate protein circuit engineering for biotechnological applications.
Collapse
Affiliation(s)
- Xiaojing J Gao
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Lucy S Chong
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Matthew S Kim
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
| |
Collapse
|
6
|
Hepacivirus NS3/4A Proteases Interfere with MAVS Signaling in both Their Cognate Animal Hosts and Humans: Implications for Zoonotic Transmission. J Virol 2016; 90:10670-10681. [PMID: 27654291 DOI: 10.1128/jvi.01634-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022] Open
Abstract
Multiple novel members of the genus Hepacivirus have recently been discovered in diverse mammalian species. However, to date, their replication mechanisms and zoonotic potential have not been explored in detail. The NS3/4A serine protease of hepatitis C virus (HCV) is critical for cleavage of the viral polyprotein. It also cleaves the cellular innate immune adaptor MAVS, thus decreasing interferon (IFN) production and contributing to HCV persistence in the human host. To investigate the conservation of fundamental aspects of the hepaciviral life cycle, we explored if MAVS cleavage and suppression of innate immune signaling represent a common mechanism employed across different clades of the genus Hepacivirus to enhance viral replication. To estimate the zoonotic potential of these nonhuman hepaciviruses, we assessed if their NS3/4A proteases were capable of cleaving human MAVS. NS3/4A proteases of viruses infecting colobus monkeys, rodents, horses, and cows cleaved the MAVS proteins of their cognate hosts and interfered with the ability of MAVS to induce the IFN-β promoter. All NS3/4A proteases from nonhuman viruses readily cleaved human MAVS. Thus, NS3/4A-dependent cleavage of MAVS is a conserved replication strategy across multiple clades within the genus Hepacivirus Human MAVS is susceptible to cleavage by these nonhuman viral proteases, indicating that it does not pose a barrier for zoonotic transmission of these viruses to humans. IMPORTANCE Virus infection is recognized by cellular sensor proteins triggering innate immune signaling and antiviral defenses. While viruses have evolved strategies to thwart these antiviral programs in their cognate host species, these evasion mechanisms are often ineffective in a novel host, thus limiting viral transmission across species. HCV, the best-characterized member of the genus Hepacivirus within the family Flaviviridae, uses its NS3/4A protease to disrupt innate immune signaling by cleaving the cellular adaptor protein MAVS. Recently, a large number of HCV-related viruses have been discovered in various animal species, including wild, livestock, and companion animals. We show that the NS3/4A proteases of these hepaciviruses from different animals and representing various clades of the genus cleave their cognate host MAVS proteins in addition to human MAVS. Therefore, cleavage of MAVS is a common strategy of hepaciviruses, and human MAVS is likely unable to limit replication of these nonhuman viruses upon zoonotic exposure.
Collapse
|
7
|
Kuznetsova SS, Kolesanova EF, Talanova AV, Veselovsky AV. [Prospects for the design of new therapeutically significant protease inhibitors based on knottins and sunflower seed trypsin inhibitor (SFTI 1)]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2016; 62:353-68. [PMID: 27562989 DOI: 10.18097/pbmc20166204353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Plant seed knottins, mainly from the Cucurbitacea family, and sunflower seed trypsin inhibitor (SFTI 1) are the most low-molecular canonical peptide inhibitors of serine proteases. High efficiency of inhibition of various serine proteases, structure rigidity together with the possibility of limited variations of amino acid sequences, high chemical stability, lack of toxic properties, opportunity of production by either chemical synthesis or use of heterologous expression systems make these inhibitors attractive templates for design of new compounds for regulation of therapeutically significant serine protease activities. Hence the design of such compounds represents a prospective research field. The review considers structural characteristics of these inhibitors, their properties, methods of preparation and design of new analogs. Examples of successful employment of natural serine protease inhibitors belonging to knottin family and SFTI 1 as templates for the design of highly specific inhibitors of certain proteases are given.
Collapse
Affiliation(s)
| | | | - A V Talanova
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | | |
Collapse
|
8
|
Guo Z, Prongay A, Tong X, Fischmann T, Bogen S, Velazquez F, Venkatraman S, Njoroge FG, Madison V. Computational Study of the Effects of Mutations A156T, D168V, and D168Q on the Binding of HCV Protease Inhibitors. J Chem Theory Comput 2015; 2:1657-63. [PMID: 26627036 DOI: 10.1021/ct600151y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The effect of the resistance mutations A156T, D168V, and D168Q in HCV protease on the binding of SCH 6, SCH 503034, VX-950, BILN-2061, and compound 1 was evaluated using the free energy perturbation (FEP) approach. All the inhibitors are highly potent against the wild-type enzyme, but their activity was affected differently by the mutants. A156T reduced the activity of SCH 503034, BILN-2061, and VX950 drastically (200-1000-fold) but that of SCH 6 only moderately (27-fold). SCH 503034, SCH 6, and VX-950 were not affected by either mutation D168V or D168Q, but these mutations conferred a high level of resistance to BILN-2061. Comparison of BILN-2061 with its acyclic analogue compound 1 emphasized the importance of inhibitor flexibility in overcoming drug resistance arising from the D168Q mutation. The results from FEP calculations compared well with experimental binding potencies within an error of <1 kcal/mol. Structural analysis was carried out to relate the resistance profiles to the atomic changes in the mutants.
Collapse
Affiliation(s)
- Zhuyan Guo
- Departments of Structural Chemistry, Medicinal Chemistry, and Antiviral Therapy, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Andrew Prongay
- Departments of Structural Chemistry, Medicinal Chemistry, and Antiviral Therapy, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Xiao Tong
- Departments of Structural Chemistry, Medicinal Chemistry, and Antiviral Therapy, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Thierry Fischmann
- Departments of Structural Chemistry, Medicinal Chemistry, and Antiviral Therapy, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Stephane Bogen
- Departments of Structural Chemistry, Medicinal Chemistry, and Antiviral Therapy, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Francisco Velazquez
- Departments of Structural Chemistry, Medicinal Chemistry, and Antiviral Therapy, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Srikanth Venkatraman
- Departments of Structural Chemistry, Medicinal Chemistry, and Antiviral Therapy, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - F George Njoroge
- Departments of Structural Chemistry, Medicinal Chemistry, and Antiviral Therapy, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| | - Vincent Madison
- Departments of Structural Chemistry, Medicinal Chemistry, and Antiviral Therapy, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033
| |
Collapse
|
9
|
Nagpal N, Goyal S, Wahi D, Jain R, Jamal S, Singh A, Rana P, Grover A. Molecular principles behind Boceprevir resistance due to mutations in hepatitis C NS3/4A protease. Gene 2015; 570:115-21. [PMID: 26055089 DOI: 10.1016/j.gene.2015.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 05/28/2015] [Accepted: 06/03/2015] [Indexed: 02/05/2023]
Abstract
The hepatitis C virus (HCV) infection is a primary cause of chronic hepatitis which eventually progresses to cirrhosis and in some instances might advance to hepatocellular carcinoma. According to the WHO report, HCV infects 130-150 million people globally and every year 350,000 to 500,000 people die from hepatitis C virus infection. Great achievement has been made in viral treatment evolution, after the development of HCV NS3/4A protease inhibitor (Boceprevir). However, efficacy of Boceprevir is compromised by the emergence of drug resistant variants. The molecular principle behind drug resistance of the protease mutants such as (V36M, T54S and R155K) is still poorly understood. Therefore in this study, we employed a series of computational strategies to analyze the binding of antiviral drug, Boceprevir to HCV NS3/4A protease mutants. Our results clearly demonstrate that the point mutations (V36M, T54S and R155K) in protease are associated with lowering of its binding affinity with Boceprevir. Exhaustive analysis of the simulated Boceprevir-bound wild and mutant complexes revealed variations in hydrophobic interactions, hydrogen bond occupancy and salt bridge interactions. Also, substrate envelope analysis scrutinized that the studied mutations reside outside the substrate envelope which may affect the Boceprevir affinity towards HCV protease but not the protease enzymatic activity. Furthermore, structural analyses of the binding site volume and flexibility show impairment in flexibility and stability of the binding site residues in mutant structures. In order to combat Boceprevir resistance, renovation of binding interactions between the drug and protease may be valuable. The structural insight from this study reveals the mechanism of the Boceprevir resistance and the results can be valuable for the design of new PIs with improved efficiency.
Collapse
Affiliation(s)
- Neha Nagpal
- Department of Biotechnology, Delhi Technological University, Delhi 110042, India
| | - Sukriti Goyal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan 304022, India
| | - Divya Wahi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ritu Jain
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Salma Jamal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan 304022, India
| | - Aditi Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Preeti Rana
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
| |
Collapse
|
10
|
Grammatikos G, Jabara CB, Ahmad MQ, Herrmann E, Zeuzem S, Welsch C. Genetic background for development of resistance mutations within the HCV NS3 protease-helicase in direct acting antiviral naive patients. Antivir Ther 2013; 19:455-61. [PMID: 24457994 DOI: 10.3851/imp2734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2013] [Indexed: 10/25/2022]
Abstract
BACKGROUND Subtype-specific response to ketoamide NS3 protease inhibitors is observed in patients with genotype 1 HCV infection. Whether the genetic diversity in the molecular target site of ketoamide compounds prior to treatment plays a role for resistance development and lower treatment response in subtype 1a is poorly understood. METHODS Using a public database, we retrieved worldwide NS3-sequence information of 581 dominant HCV variants from patients chronically infected with genotype 1 that were naive to direct-acting antivirals. We applied measures from phylogeny to study the pretreatment genetic diversity and complexity in NS3 full-length as well as the protease-helicase interface for subtype 1a and 1b, respectively. RESULTS We found polymorphic sites more frequently in variants of subtype 1b than subtype 1a. Moreover, a significantly higher number of synonymous and non-synonymous substitutions were found in subtype 1b (P<0.001). Transitions were more frequent than transversions, most notably in subtype 1a, whereas the higher average number of nucleotide differences per site was found in subtype 1b. A comparison of NS3 full-length versus domain interface residues for both subtypes revealed a significant difference only for synonymous substitutions (P<0.001). CONCLUSIONS Our study suggests that the nature of a mismatch nucleotide exchange in NS3 may constitute an important viral genetic factor for response to ketoamide protease inhibitors. Our analysis further suggests that the subtype-specific pace of resistance development seen in clinical trials is not primarily related to differences in genetic diversity in the direct acting antiviral naive population, but rather appears to correlate with the natural frequency of transition mutations characteristic of each subtype.
Collapse
Affiliation(s)
- Georgios Grammatikos
- Department of Internal Medicine I, Frankfurt University Hospital, Goethe University, Frankfurt am Main, Germany
| | | | | | | | | | | |
Collapse
|
11
|
Abstract
Advances in the field of boron chemistry have expanded the application of boron from material use to medicine. Boron-based drugs represent a new class of molecules that possess several biomedical applications including use as imaging agents for both optical and nuclear imaging as well as therapeutic agents with anticancer, antiviral, antibacterial, antifungal and other disease-specific activities. For example, bortezomib (Velcade(®)), the only drug in clinical use with boron as an active element, was approved in 2003 as a proteasome inhibitor for the treatment of multiple myeloma and non-Hodgkin's lymphoma. Several other boron-based compounds are in various phases of clinical trials, which illustrates the promise of this approach for medicinal chemists working in the area of boron chemistry. It is expected that in the near future, several boron-containing drugs should become available in the market with better efficacy and potency than existing drugs. This article discusses the current status of the development of boron-based compounds as diagnostic and therapeutic agents in humans.
Collapse
|
12
|
Xue W, Ban Y, Liu H, Yao X. Computational study on the drug resistance mechanism against HCV NS3/4A protease inhibitors vaniprevir and MK-5172 by the combination use of molecular dynamics simulation, residue interaction network, and substrate envelope analysis. J Chem Inf Model 2013; 54:621-33. [PMID: 23745769 DOI: 10.1021/ci400060j] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hepatitis C virus (HCV) NS3/4A protease is an important and attractive target for anti-HCV drug development and discovery. Vaniprevir (phase III clinical trials) and MK-5172 (phase II clinical trials) are two potent antiviral compounds that target NS3/4A protease. However, the emergence of resistance to these two inhibitors reduced the effectiveness of vaniprevir and MK-5172 against viral replication. Among the drug resistance mutations, three single-site mutations at residues Arg155, Ala156, and Asp168 in NS3/4A protease are especially important due to their resistance to nearly all inhibitors in clinical development. A detailed understanding of drug resistance mechanism to vaniprevir and MK-5172 is therefore very crucial for the design of novel potent agents targeting viral variants. In this work, molecular dynamics (MD) simulation, binding free energy calculation, free energy decomposition, residue interaction network (RIN), and substrate envelope analysis were used to study the detailed drug resistance mechanism of the three mutants R155K, A156T, and D168A to vaniprevir and MK-5172. MD simulation was used to investigate the binding mode for these two inhibitors to wild-type and resistant mutants of HCV NS3/4A protease. Binding free energy calculation and free energy decomposition analysis reveal that drug resistance mutations reduced the interactions between the active site residues and substituent in the P2 to P4 linker of vaniprevir and MK-5172. Furthermore, RIN and substrate envelope analysis indicate that the studied mutations of the residues are located outside the substrate (4B5A) binding site and selectively decrease the affinity of inhibitors but not the activity of the enzyme and consequently help NS3/4A protease escape from the effect of the inhibitors without influencing the affinity of substrate binding. These findings can provide useful information for understanding the drug resistance mechanism against vaniprevir and MK-5172. The results can also provide some potential clues for further design of novel inhibitors that are less susceptible to drug resistance.
Collapse
Affiliation(s)
- Weiwei Xue
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University , Lanzhou 730000, China
| | | | | | | |
Collapse
|
13
|
Olaby RA, Azzazy HM, Harris R, Chromy B, Vielmetter J, Balhorn R. Identification of ligands that target the HCV-E2 binding site on CD81. J Comput Aided Mol Des 2013; 27:337-46. [DOI: 10.1007/s10822-013-9649-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 04/15/2013] [Indexed: 11/29/2022]
|
14
|
Venkatraman S, Velazquez F, Gavalas S, Wu W, Chen KX, Nair AG, Bennett F, Huang Y, Pinto P, Jiang Y, Selyutin O, Vibulbhan B, Zeng Q, Lesburg C, Duca J, Huang HC, Agrawal S, Jiang CK, Ferrari E, Li C, Kozlowski J, Rosenblum S, Shih NY, Njoroge FG. Discovery of novel tricyclic indole derived inhibitors of HCV NS5B RNA dependent RNA polymerase. Bioorg Med Chem 2013; 21:2007-17. [DOI: 10.1016/j.bmc.2013.01.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 01/03/2013] [Accepted: 01/11/2013] [Indexed: 10/27/2022]
|
15
|
Preclinical Profile and Characterization of the Hepatitis C Virus NS3 Protease Inhibitor Asunaprevir (BMS-650032). Antimicrob Agents Chemother 2012; 56:5387-96. [PMID: 22869577 DOI: 10.1128/aac.01186-12] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Asunaprevir (ASV; BMS-650032) is a hepatitis C virus (HCV) NS3 protease inhibitor that has demonstrated efficacy in patients chronically infected with HCV genotype 1 when combined with alfa interferon and/or the NS5A replication complex inhibitor daclatasvir. ASV competitively binds to the NS3/4A protease complex, with K(i) values of 0.4 and 0.24 nM against recombinant enzymes representing genotypes 1a (H77) and 1b (J4L6S), respectively. Selectivity was demonstrated by the absence of any significant activity against the closely related GB virus-B NS3 protease and a panel of human serine or cysteine proteases. In cell culture, ASV inhibited replication of HCV replicons representing genotypes 1 and 4, with 50% effective concentrations (EC(50)s) ranging from 1 to 4 nM, and had weaker activity against genotypes 2 and 3 (EC(50), 67 to 1,162 nM). Selectivity was again demonstrated by the absence of activity (EC(50), >12 μM) against a panel of other RNA viruses. ASV exhibited additive or synergistic activity in combination studies with alfa interferon, ribavirin, and/or inhibitors specifically targeting NS5A or NS5B. Plasma and tissue exposures in vivo in several animal species indicated that ASV displayed a hepatotropic disposition (liver-to-plasma ratios ranging from 40- to 359-fold across species). Twenty-four hours postdose, liver exposures across all species tested were ≥110-fold above the inhibitor EC(50)s observed with HCV genotype-1 replicons. Based on these virologic and exposure properties, ASV holds promise for future utility in a combination with other anti-HCV agents in the treatment of HCV-infected patients.
Collapse
|
16
|
Discovery of boceprevir, a direct-acting NS3/4A protease inhibitor for treatment of chronic hepatitis C infections. Trends Pharmacol Sci 2012; 33:289-94. [DOI: 10.1016/j.tips.2012.03.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 03/16/2012] [Accepted: 03/16/2012] [Indexed: 12/22/2022]
|
17
|
Shiryaev SA, Thomsen ER, Cieplak P, Chudin E, Cheltsov AV, Chee MS, Kozlov IA, Strongin AY. New details of HCV NS3/4A proteinase functionality revealed by a high-throughput cleavage assay. PLoS One 2012; 7:e35759. [PMID: 22558217 PMCID: PMC3338790 DOI: 10.1371/journal.pone.0035759] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 03/20/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The hepatitis C virus (HCV) genome encodes a long polyprotein, which is processed by host cell and viral proteases to the individual structural and non-structural (NS) proteins. HCV NS3/4A serine proteinase (NS3/4A) is a non-covalent heterodimer of the N-terminal, ∼180-residue portion of the 631-residue NS3 protein with the NS4A co-factor. NS3/4A cleaves the polyprotein sequence at four specific regions. NS3/4A is essential for viral replication and has been considered an attractive drug target. METHODOLOGY/PRINCIPAL FINDINGS Using a novel multiplex cleavage assay and over 2,660 peptide sequences derived from the polyprotein and from introducing mutations into the known NS3/4A cleavage sites, we obtained the first detailed fingerprint of NS3/4A cleavage preferences. Our data identified structural requirements illuminating the importance of both the short-range (P1-P1') and long-range (P6-P5) interactions in defining the NS3/4A substrate cleavage specificity. A newly observed feature of NS3/4A was a high frequency of either Asp or Glu at both P5 and P6 positions in a subset of the most efficient NS3/4A substrates. In turn, aberrations of this negatively charged sequence such as an insertion of a positively charged or hydrophobic residue between the negatively charged residues resulted in inefficient substrates. Because NS5B misincorporates bases at a high rate, HCV constantly mutates as it replicates. Our analysis revealed that mutations do not interfere with polyprotein processing in over 5,000 HCV isolates indicating a pivotal role of NS3/4A proteolysis in the virus life cycle. CONCLUSIONS/SIGNIFICANCE Our multiplex assay technology in light of the growing appreciation of the role of proteolytic processes in human health and disease will likely have widespread applications in the proteolysis research field and provide new therapeutic opportunities.
Collapse
Affiliation(s)
- Sergey A. Shiryaev
- Inflammatory and Infectious Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Elliot R. Thomsen
- R&D Department, Prognosys Biosciences Inc., La Jolla, California, United States of America
| | - Piotr Cieplak
- Inflammatory and Infectious Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Eugene Chudin
- R&D Department, Prognosys Biosciences Inc., La Jolla, California, United States of America
| | - Anton V. Cheltsov
- Inflammatory and Infectious Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Mark S. Chee
- R&D Department, Prognosys Biosciences Inc., La Jolla, California, United States of America
| | - Igor A. Kozlov
- R&D Department, Prognosys Biosciences Inc., La Jolla, California, United States of America
| | - Alex Y. Strongin
- Inflammatory and Infectious Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| |
Collapse
|
18
|
Smoum R, Rubinstein A, Dembitsky VM, Srebnik M. Boron containing compounds as protease inhibitors. Chem Rev 2012; 112:4156-220. [PMID: 22519511 DOI: 10.1021/cr608202m] [Citation(s) in RCA: 300] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Reem Smoum
- The School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel.
| | | | | | | |
Collapse
|
19
|
Shapira A, Shapira S, Gal-Tanamy M, Zemel R, Tur-Kaspa R, Benhar I. Removal of hepatitis C virus-infected cells by a zymogenized bacterial toxin. PLoS One 2012; 7:e32320. [PMID: 22359682 PMCID: PMC3281143 DOI: 10.1371/journal.pone.0032320] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 01/26/2012] [Indexed: 11/19/2022] Open
Abstract
Hepatitis C virus (HCV) infection is a major cause of chronic liver disease and has become a global health threat. No HCV vaccine is currently available and treatment with antiviral therapy is associated with adverse side effects. Moreover, there is no preventive therapy for recurrent hepatitis C post liver transplantation. The NS3 serine protease is necessary for HCV replication and represents a prime target for developing anti HCV therapies. Recently we described a therapeutic approach for eradication of HCV infected cells that is based on protein delivery of two NS3 protease-activatable recombinant toxins we named "zymoxins". These toxins were inactivated by fusion to rationally designed inhibitory peptides via NS3-cleavable linkers. Once delivered to cells where NS3 protease is present, the inhibitory peptide is removed resulting in re-activation of cytotoxic activity. The zymoxins we described suffered from two limitations: they required high levels of protease for activation and had basal activities in the un-activated form that resulted in a narrow potential therapeutic window. Here, we present a solution that overcame the major limitations of the "first generation zymoxins" by converting MazF ribonuclease, the toxic component of the E. coli chromosomal MazEF toxin-antitoxin system, into an NS3-activated zymoxin that is introduced to cells by means of gene delivery. We constructed an expression cassette that encodes for a single polypeptide that incorporates both the toxin and a fragment of its potent natural antidote, MazE, linked via an NS3-cleavable linker. While covalently paired to its inhibitor, the ribonuclease is well tolerated when expressed in naïve, healthy cells. In contrast, activating proteolysis that is induced by even low levels of NS3, results in an eradication of NS3 expressing model cells and HCV infected cells. Zymoxins may thus become a valuable tool in eradicating cells infected by intracellular pathogens that express intracellular proteases.
Collapse
Affiliation(s)
- Assaf Shapira
- Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel
- Molecular Hepatology Research Laboratory, Sackler School of Medicine, Felsenstein Medical Research Center, Tel-Aviv University, Petah Tikva, Israel
| | - Shiran Shapira
- The Integrated Cancer Prevention Center, Tel Aviv Medical Center, Tel-Aviv, Israel
- Sackler School of Medicine, Tel-Aviv University, Ramat Aviv, Israel
| | - Meital Gal-Tanamy
- Molecular Hepatology Research Laboratory, Sackler School of Medicine, Felsenstein Medical Research Center, Tel-Aviv University, Petah Tikva, Israel
| | - Romy Zemel
- Molecular Hepatology Research Laboratory, Sackler School of Medicine, Felsenstein Medical Research Center, Tel-Aviv University, Petah Tikva, Israel
| | - Ran Tur-Kaspa
- Molecular Hepatology Research Laboratory, Sackler School of Medicine, Felsenstein Medical Research Center, Tel-Aviv University, Petah Tikva, Israel
- Department of Medicine D and Liver Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Itai Benhar
- Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel
- * E-mail:
| |
Collapse
|
20
|
Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V and D168A to TMC435. Antiviral Res 2011; 93:126-37. [PMID: 22127068 DOI: 10.1016/j.antiviral.2011.11.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 11/05/2011] [Accepted: 11/14/2011] [Indexed: 12/15/2022]
Abstract
Hepatitis C virus (HCV) NS3/4A protease represents an attractive drug target for antiviral therapy. However, drug resistance often occurs, making many protease inhibitors ineffective and allowing viral replication to occur. Herein, based on the recently determined structure of NS3/4A-TMC435 complex, atomic-level models of the key residue mutated (R155K, A156V and D168A) NS3/4A-TMC435 complexes were constructed. Subsequently, by using molecular dynamics simulations, binding free energy calculation and substrate envelope analysis, the structural and energetic changes responsible for drug resistance were investigated. The values of the calculated binding free energy follow consistently the order of the experimental activities. More importantly, the computational results demonstrate that R155K and D168A mutations break the intermolecular salt bridges network at the extended S2 subsite and affect the TMC435 binding, while A156V mutation leads to a significant steric clash with TMC435 and further disrupts the two canonical substrate-like intermolecular hydrogen bond interactions (TMC435(N1-H46)⋯Arg155(O) and Ala157(N-H)⋯TMC435(O2)). In addition, by structural analysis, all the three key residue mutations occur outside the substrate envelope and selectively weaken TMC435's binding affinity without effect on its natural substrate peptide (4B5A). These findings could provide some insights into the resistance mechanism of NS3/4A protease mutants to TMC435 and would be critical for the development of novel inhibitors that are less susceptible to drug resistance.
Collapse
|
21
|
Sistigu A, Bracci L, Valentini M, Proietti E, Bona R, Negri DRM, Ciccaglione AR, Tritarelli E, Nisini R, Equestre M, Costantino A, Marcantonio C, Santini SM, Lapenta C, Donati S, Tataseo P, Miceli M, Cara A, Federico M. Strong CD8+ T cell antigenicity and immunogenicity of large foreign proteins incorporated in HIV-1 VLPs able to induce a Nef-dependent activation/maturation of dendritic cells. Vaccine 2011; 29:3465-75. [PMID: 21382480 DOI: 10.1016/j.vaccine.2011.02.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 02/15/2011] [Accepted: 02/16/2011] [Indexed: 12/21/2022]
Abstract
Virus-like particles (VLPs) are excellent tools for vaccines against pathogens and tumors. They can accommodate foreign polypeptides whose incorporation efficiency and immunogenicity however decrease strongly with the increase of their size. We recently described the CD8(+) T cell immune response against a small foreign antigen (i.e., the 98 amino acid long human papilloma virus E7 protein) incorporated in human immunodeficiency virus (HIV)-1 based VLPs as product of fusion with an HIV-1 Nef mutant (Nef(mut)). Here, we extended our previous investigations by testing the antigenic/immunogenic properties of Nef(mut)-based VLPs incorporating much larger heterologous products, i.e., human hepatitis C virus (HCV) NS3 and influenza virus NP proteins, which are composed of 630 and 498 amino acids, respectively. We observed a remarkable cross-presentation of HCV NS3 in dendritic cells challenged with Nef(mut)-NS3 VLPs, as detected using a NS3 specific CD8(+) T cell clone as well as PBMCs from HCV infected patients. On the other hand, when injected in mice, Nef(mut)-NP VLPs elicited strong anti-NP CD8(+) T cell and CTL immune responses. In addition, we revealed the ability of Nef(mut) incorporated in VLPs to activate and mature primary human immature dendritic cells (iDCs). This phenomenon correlated with the activation of Src tyrosine kinase-related intracellular signaling, and can be transmitted from VLP-challenged to bystander iDCs. Overall, these results prove that Nef(mut)-based VLPs represent a rather flexible platform for the design of innovative CD8(+) T cell vaccines.
Collapse
Affiliation(s)
- A Sistigu
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Shapira A, Gal-Tanamy M, Nahary L, Litvak-Greenfeld D, Zemel R, Tur-Kaspa R, Benhar I. Engineered toxins "zymoxins" are activated by the HCV NS3 protease by removal of an inhibitory protein domain. PLoS One 2011; 6:e15916. [PMID: 21264238 PMCID: PMC3021518 DOI: 10.1371/journal.pone.0015916] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2010] [Accepted: 11/29/2010] [Indexed: 12/28/2022] Open
Abstract
The synthesis of inactive enzyme precursors, also known as "zymogens," serves as a mechanism for regulating the execution of selected catalytic activities in a desirable time and/or site. Zymogens are usually activated by proteolytic cleavage. Many viruses encode proteases that execute key proteolytic steps of the viral life cycle. Here, we describe a proof of concept for a therapeutic approach to fighting viral infections through eradication of virally infected cells exclusively, thus limiting virus production and spread. Using the hepatitis C virus (HCV) as a model, we designed two HCV NS3 protease-activated "zymogenized" chimeric toxins (which we denote "zymoxins"). In these recombinant constructs, the bacterial and plant toxins diphtheria toxin A (DTA) and Ricin A chain (RTA), respectively, were fused to rationally designed inhibitor peptides/domains via an HCV NS3 protease-cleavable linker. The above toxins were then fused to the binding and translocation domains of Pseudomonas exotoxin A in order to enable translocation into the mammalian cells cytoplasm. We show that these toxins exhibit NS3 cleavage dependent increase in enzymatic activity upon NS3 protease cleavage in vitro. Moreover, a higher level of cytotoxicity was observed when zymoxins were applied to NS3 expressing cells or to HCV infected cells, demonstrating a potential therapeutic window. The increase in toxin activity correlated with NS3 protease activity in the treated cells, thus the therapeutic window was larger in cells expressing recombinant NS3 than in HCV infected cells. This suggests that the "zymoxin" approach may be most appropriate for application to life-threatening acute infections where much higher levels of the activating protease would be expected.
Collapse
Affiliation(s)
- Assaf Shapira
- Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel
| | - Meital Gal-Tanamy
- Molecular Hepatology Research Laboratory, Felsenstein Medical Research Center, Sackler School of Medicine, Tel-Aviv University, Petah Tikva, Israel
| | - Limor Nahary
- Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel
| | - Dana Litvak-Greenfeld
- Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel
| | - Romy Zemel
- Molecular Hepatology Research Laboratory, Felsenstein Medical Research Center, Sackler School of Medicine, Tel-Aviv University, Petah Tikva, Israel
| | - Ran Tur-Kaspa
- Molecular Hepatology Research Laboratory, Felsenstein Medical Research Center, Sackler School of Medicine, Tel-Aviv University, Petah Tikva, Israel
- Department of Medicine D and Liver Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Itai Benhar
- Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel
| |
Collapse
|
23
|
Hepatitis C virus NS2 protein serves as a scaffold for virus assembly by interacting with both structural and nonstructural proteins. J Virol 2010; 85:86-97. [PMID: 20962101 DOI: 10.1128/jvi.01070-10] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many aspects of the assembly of hepatitis C virus (HCV) remain incompletely understood. To characterize the role of NS2 in the production of infectious virus, we determined NS2 interaction partners among other HCV proteins during productive infection. Pulldown assays showed that NS2 forms complexes with both structural and nonstructural proteins, including E1, E2, p7, NS3, and NS5A. Confocal microscopy also demonstrated that NS2 colocalizes with E1, E2, and NS5A in dot-like structures near lipid droplets. However, NS5A did not coprecipitate with E2 and interacted only weakly with NS3 in pulldown assays. Also, there was no demonstrable interaction between p7 and E2 or NS3 in such assays. Therefore, NS2 is uniquely capable of interacting with both structural and nonstructural proteins. Among mutations in p7, NS2, and NS3 that prevent production of infectious virus, only p7 mutations significantly reduced NS2-mediated protein interactions. These p7 mutations altered the intracellular distribution of NS2 and E2 and appeared to modulate the membrane topology of the C-terminal domain of NS2. These results suggest that NS2 acts to coordinate virus assembly by mediating interactions between envelope proteins and NS3 and NS5A within replication complexes adjacent to lipid droplets, where virus particle assembly is thought to occur. p7 may play an accessory role by regulating NS2 membrane topology, which is important for NS2-mediated protein interactions and therefore NS2 function.
Collapse
|
24
|
Tews BA, Popescu CI, Dubuisson J. Last stop before exit - hepatitis C assembly and release as antiviral drug targets. Viruses 2010; 2:1782-1803. [PMID: 21994707 PMCID: PMC3185729 DOI: 10.3390/v2081782] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 07/16/2010] [Accepted: 08/04/2010] [Indexed: 12/15/2022] Open
Abstract
Chronic Hepatitis C infection is a global health problem. While primary infection is often inapparent, it becomes chronic in most cases. Chronic infection with Hepatitis C virus (HCV) frequently leads to liver cirrhosis or liver cancer. Consequently, HCV infection is one of the leading causes for liver transplantation in industrialized countries. Current treatment is not HCV specific and is only effective in about half of the infected patients. This situation underlines the need for new antivirals against HCV. To develop new and more efficient drugs, it is essential to specifically target the different steps of the viral life cycle. Of those steps, the targeting of HCV assembly has the potential to abolish virus production. This review summarizes the advances in our understanding of HCV particle assembly and the identification of new antiviral targets of potential interest in this late step of the HCV life cycle.
Collapse
Affiliation(s)
- Birke Andrea Tews
- Hepatitis C Laboratory, Center of Infection and Immunity of Lille, University Lille Nord de France, CNRS UMR8204, INSERM U1019, Pasteur Institute of Lille, 1, rue du professeur Calmette, BP447, 59021 Lille, France; E-Mails: (C.-I.P.); (J.D.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-320-87-1162; Fax: +33-320-87-1201
| | - Costin-Ioan Popescu
- Hepatitis C Laboratory, Center of Infection and Immunity of Lille, University Lille Nord de France, CNRS UMR8204, INSERM U1019, Pasteur Institute of Lille, 1, rue du professeur Calmette, BP447, 59021 Lille, France; E-Mails: (C.-I.P.); (J.D.)
- Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031, Bucharest, Romania
| | - Jean Dubuisson
- Hepatitis C Laboratory, Center of Infection and Immunity of Lille, University Lille Nord de France, CNRS UMR8204, INSERM U1019, Pasteur Institute of Lille, 1, rue du professeur Calmette, BP447, 59021 Lille, France; E-Mails: (C.-I.P.); (J.D.)
| |
Collapse
|
25
|
Epstein JH, Quan PL, Briese T, Street C, Jabado O, Conlan S, Ali Khan S, Verdugo D, Hossain MJ, Hutchison SK, Egholm M, Luby SP, Daszak P, Lipkin WI. Identification of GBV-D, a novel GB-like flavivirus from old world frugivorous bats (Pteropus giganteus) in Bangladesh. PLoS Pathog 2010; 6:e1000972. [PMID: 20617167 PMCID: PMC2895649 DOI: 10.1371/journal.ppat.1000972] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 05/27/2010] [Indexed: 11/19/2022] Open
Abstract
Bats are reservoirs for a wide range of zoonotic agents including lyssa-, henipah-, SARS-like corona-, Marburg-, Ebola-, and astroviruses. In an effort to survey for the presence of other infectious agents, known and unknown, we screened sera from 16 Pteropus giganteus bats from Faridpur, Bangladesh, using high-throughput pyrosequencing. Sequence analyses indicated the presence of a previously undescribed virus that has approximately 50% identity at the amino acid level to GB virus A and C (GBV-A and -C). Viral nucleic acid was present in 5 of 98 sera (5%) from a single colony of free-ranging bats. Infection was not associated with evidence of hepatitis or hepatic dysfunction. Phylogenetic analysis indicates that this first GBV-like flavivirus reported in bats constitutes a distinct species within the Flaviviridae family and is ancestral to the GBV-A and -C virus clades.
Collapse
Affiliation(s)
- Jonathan H. Epstein
- Conservation Medicine Program, Wildlife Trust, New York, New York, United States of America
| | - Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Craig Street
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Omar Jabado
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Sean Conlan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Shahneaz Ali Khan
- Conservation Medicine Program, Wildlife Trust, New York, New York, United States of America
- Chittagong Veterinary & Animal Sciences University, Chittagong, Bangladesh
| | - Dawn Verdugo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - M. Jahangir Hossain
- Programme on Infectious Disease and Vaccine Sciences, International Centre for Diarrheal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | | | - Michael Egholm
- 454 Life Sciences, Branford, Connecticut, United States of America
| | - Stephen P. Luby
- Programme on Infectious Disease and Vaccine Sciences, International Centre for Diarrheal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Peter Daszak
- Conservation Medicine Program, Wildlife Trust, New York, New York, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| |
Collapse
|
26
|
Rajagopal V, Gurjar M, Levin MK, Patel SS. The protease domain increases the translocation stepping efficiency of the hepatitis C virus NS3-4A helicase. J Biol Chem 2010; 285:17821-32. [PMID: 20363755 PMCID: PMC2878546 DOI: 10.1074/jbc.m110.114785] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 04/01/2010] [Indexed: 01/24/2023] Open
Abstract
Hepatitis C virus (HCV) NS3 protein has two enzymatic activities of helicase and protease that are essential for viral replication. The helicase separates the strands of DNA and RNA duplexes using the energy from ATP hydrolysis. To understand how ATP hydrolysis is coupled to helicase movement, we measured the single turnover helicase translocation-dissociation kinetics and the pre-steady-state P(i) release kinetics on single-stranded RNA and DNA substrates of different lengths. The parameters of stepping were determined from global fitting of the two types of kinetic measurements into a computational model that describes translocation as a sequence of coupled hydrolysis-stepping reactions. Our results show that the HCV helicase moves with a faster rate on single stranded RNA than on DNA. The HCV helicase steps on the RNA or DNA one nucleotide at a time, and due to imperfect coupling, not every ATP hydrolysis event produces a successful step. Comparison of the helicase domain (NS3h) with the protease-helicase (NS3-4A) shows that the most significant contribution of the protease domain is to improve the translocation stepping efficiency of the helicase. Whereas for NS3h, only 20% of the hydrolysis events result in translocation, the coupling for NS3-4A is near-perfect 93%. The presence of the protease domain also significantly reduces the stepping rate, but it doubles the processivity. These effects of the protease domain on the helicase can be explained by an improved allosteric cross-talk between the ATP- and nucleic acid-binding sites achieved by the overall stabilization of the helicase domain structure.
Collapse
Affiliation(s)
- Vaishnavi Rajagopal
- From the
Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854 and
| | - Madhura Gurjar
- From the
Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854 and
| | - Mikhail K. Levin
- the
Department of Biostatistics & Bioinformatics, Duke University Medical Center, Durham, North Carolina 27710
| | - Smita S. Patel
- From the
Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854 and
| |
Collapse
|
27
|
Venkatraman S, Velazquez F, Wu W, Blackman M, Madison V, Njoroge FG. Potent ketoamide inhibitors of HCV NS3 protease derived from quaternized P1 groups. Bioorg Med Chem Lett 2010; 20:2151-5. [DOI: 10.1016/j.bmcl.2010.02.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 02/10/2010] [Accepted: 02/10/2010] [Indexed: 10/19/2022]
|
28
|
Liefhebber JMP, Hensbergen PJ, Deelder AM, Spaan WJM, van Leeuwen HC. Characterization of hepatitis C virus NS3 modifications in the context of replication. J Gen Virol 2009; 91:1013-8. [PMID: 19923258 DOI: 10.1099/vir.0.016881-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Post-translational modifications (PTMs) of viral proteins regulate various stages of infection. With only 10 proteins, hepatitis C virus (HCV) can orchestrate its complete viral life cycle. HCV non-structural protein 3 (NS3) has many functions. It has protease and helicase activities, interacts with several host-cell proteins and plays a role in translation, replication and virus-particle formation. Organization of all these functions is necessary and could be regulated by PTMs. We therefore searched for modifications of the NS3 protein in the subgenomic HCV replicon. When performing a tag-capture approach coupled with two-dimensional gel electrophoresis analyses, we observed that isolated His6-NS3 yielded multiple spots. Individual protein spots were digested in gel and analysed by mass spectrometry. Differences observed between the individual peptide mass fingerprints suggested the presence of modified peptides and allowed us to identify N-terminal acetylation and an adaptive mutation of NS3 (Q1067R). Further analysis of other NS3 variants revealed phosphorylation of NS3.
Collapse
Affiliation(s)
- Jolanda M P Liefhebber
- Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | | | | | | | | |
Collapse
|
29
|
Potent aza-peptide derived inhibitors of HCV NS3 protease. Bioorg Med Chem Lett 2009; 19:4760-3. [DOI: 10.1016/j.bmcl.2009.06.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 06/08/2009] [Accepted: 06/15/2009] [Indexed: 12/24/2022]
|
30
|
Venkatraman S, Blackman M, Wu W, Nair L, Arasappan A, Padilla A, Bogen S, Bennett F, Chen K, Pichardo J, Tong X, Prongay A, Cheng KC, Girijavallabhan V, George Njoroge F. Discovery of novel P3 sulfonamide-capped inhibitors of HCV NS3 protease. Inhibitors with improved cellular potencies. Bioorg Med Chem 2009; 17:4486-95. [DOI: 10.1016/j.bmc.2009.05.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 05/01/2009] [Accepted: 05/05/2009] [Indexed: 12/30/2022]
|
31
|
|
32
|
Rögnvaldsson T, Etchells TA, You L, Garwicz D, Jarman I, Lisboa PJG. How to find simple and accurate rules for viral protease cleavage specificities. BMC Bioinformatics 2009; 10:149. [PMID: 19445713 PMCID: PMC2698905 DOI: 10.1186/1471-2105-10-149] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 05/16/2009] [Indexed: 01/02/2023] Open
Abstract
Background Proteases of human pathogens are becoming increasingly important drug targets, hence it is necessary to understand their substrate specificity and to interpret this knowledge in practically useful ways. New methods are being developed that produce large amounts of cleavage information for individual proteases and some have been applied to extract cleavage rules from data. However, the hitherto proposed methods for extracting rules have been neither easy to understand nor very accurate. To be practically useful, cleavage rules should be accurate, compact, and expressed in an easily understandable way. Results A new method is presented for producing cleavage rules for viral proteases with seemingly complex cleavage profiles. The method is based on orthogonal search-based rule extraction (OSRE) combined with spectral clustering. It is demonstrated on substrate data sets for human immunodeficiency virus type 1 (HIV-1) protease and hepatitis C (HCV) NS3/4A protease, showing excellent prediction performance for both HIV-1 cleavage and HCV NS3/4A cleavage, agreeing with observed HCV genotype differences. New cleavage rules (consensus sequences) are suggested for HIV-1 and HCV NS3/4A cleavages. The practical usability of the method is also demonstrated by using it to predict the location of an internal cleavage site in the HCV NS3 protease and to correct the location of a previously reported internal cleavage site in the HCV NS3 protease. The method is fast to converge and yields accurate rules, on par with previous results for HIV-1 protease and better than previous state-of-the-art for HCV NS3/4A protease. Moreover, the rules are fewer and simpler than previously obtained with rule extraction methods. Conclusion A rule extraction methodology by searching for multivariate low-order predicates yields results that significantly outperform existing rule bases on out-of-sample data, but are more transparent to expert users. The approach yields rules that are easy to use and useful for interpreting experimental data.
Collapse
|
33
|
Critical role of cyclophilin A and its prolyl-peptidyl isomerase activity in the structure and function of the hepatitis C virus replication complex. J Virol 2009; 83:6554-65. [PMID: 19386705 DOI: 10.1128/jvi.02550-08] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Replication of hepatitis C virus (HCV) RNA occurs on intracellular membranes, and the replication complex (RC) contains viral RNA, nonstructural proteins, and cellular cofactors. We previously demonstrated that cyclophilin A (CyPA) is an essential cofactor for HCV infection and the intracellular target of cyclosporine's anti-HCV effect. Here we investigate the mechanism by which CyPA facilitates HCV replication. Cyclosporine treatment specifically blocked the incorporation of NS5B into the RC without affecting either the total protein level or the membrane association of the protein. Other nonstructural proteins or viral RNAs in the RC were not affected. NS5B from the cyclosporine-resistant replicon was resistant to this disruption of RC incorporation. We also isolated membrane fractions from both naïve and HCV-positive cells and found that CyPA is recruited into membrane fractions in HCV-replicating cells via an interaction with RC-associated NS5B, which is sensitive to cyclosporine treatment. Finally, we introduced point mutations in the prolyl-peptidyl isomerase (PPIase) motif of CyPA and demonstrated a critical role of this motif in HCV replication in cDNA rescue experiments. We propose a model in which the incorporation of the HCV polymerase into the RC depends on its interaction with a cellular chaperone protein and in which cyclosporine inhibits HCV replication by blocking this critical interaction and the PPIase activity of CyPA. Our results provide a mechanism of action for the cyclosporine-mediated inhibition of HCV and identify a critical role of CyPA's PPIase activity in the proper assembly and function of the HCV RC.
Collapse
|
34
|
Abstract
HCV is a small RNA virus belonging to the genus Hepacivirus within the virus family Flaviviridae. Infection with HCV often leads to chronic liver diseases including chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Current therapy, based on the use of interferon-alpha (IFN-alpha) in combination with ribavirin, results in limited success, especially in patients infected with the most prevalent genotype 1 viruses. Better therapies are needed, but the inability to propagate HCV in cell culture hampers antiviral drug-discovery efforts. Recently, fully permissive cell-culture systems have been developed that use viral RNA derived from the genotype 2a JFH-1 strain of HCV. Although these systems mark a significant breakthrough for HCV research, the parallel development of a tractable genotype 1a infection system (H77S virus) has provided significant advantages in assessing genotype 1-specific interventions, given the highly heterogeneous nature of HCV. H77S RNA contains five cell culture-adaptive mutations that are placed throughout the nonstructural protein-coding segment of the genome and render the RNA capable of robust replication in human hepatoma (Huh-7) cells. Although significantly less efficient than JFH-1 RNA, H77S RNA produces moderate titers of cell culture-infectious virus when transfected into Huh-7 cells.
Collapse
Affiliation(s)
- Minkyung Yi
- Center for Hepatitis Research, Institute for Human Infections and the Department of Microbiology & Immunology, University of Texas Galveston, TX, USA
| | | |
Collapse
|
35
|
Venkatraman S, Velazquez F, Wu W, Blackman M, Chen KX, Bogen S, Nair L, Tong X, Chase R, Hart A, Agrawal S, Pichardo J, Prongay A, Cheng KC, Girijavallabhan V, Piwinski J, Shih NY, Njoroge FG. Discovery and structure-activity relationship of P1-P3 ketoamide derived macrocyclic inhibitors of hepatitis C virus NS3 protease. J Med Chem 2009; 52:336-46. [PMID: 19102654 DOI: 10.1021/jm800940u] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hepatitis C virus (HCV) infection is the major cause of chronic liver disease, leading to cirrhosis and hepatocellular carcinoma, and affects more than 200 million people worldwide. Although combination therapy of interferon-alpha and ribavirin is reasonably successful in treating majority of genotypes, its efficacy against the predominant genotype (genotype 1) is moderate at best, with only about 40% of the patients showing sustained virological response. Herein, the SAR leading to the discovery of a series of ketoamide derived P(1)-P(3) macrocyclic inhibitors that are more potent than the first generation clinical candidate, boceprevir (1, Sch 503034), is discussed. The optimization of these macrocyclic inhibitors identified a P(3) imide capped analogue 52 that was 20 times more potent than 1 and demonstrated good oral pharmacokinetics in rats. X-ray structure of 52 bound to NS3 protease and biological data are also discussed.
Collapse
Affiliation(s)
- Srikanth Venkatraman
- Schering Plough Research Institute, K-15, MS-3545, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
This review provides an overview of the development of viral protease inhibitors as antiviral drugs. We concentrate on HIV-1 protease inhibitors, as these have made the most significant advances in the recent past. Thus, we discuss the biochemistry of HIV-1 protease, inhibitor development, clinical use of inhibitors, and evolution of resistance. Since many different viruses encode essential proteases, it is possible to envision the development of a potent protease inhibitor for other viruses if the processing site sequence and the catalytic mechanism are known. At this time, interest in developing inhibitors is limited to viruses that cause chronic disease, viruses that have the potential to cause large-scale epidemics, or viruses that are sufficiently ubiquitous that treating an acute infection would be beneficial even if the infection was ultimately self-limiting. Protease inhibitor development is most advanced for hepatitis C virus (HCV), and we also provide a review of HCV NS3/4A serine protease inhibitor development, including combination therapy and resistance. Finally, we discuss other viral proteases as potential drug targets, including those from Dengue virus, cytomegalovirus, rhinovirus, and coronavirus.
Collapse
Affiliation(s)
- Hans-Georg Kräusslich
- Hygiene Institute Department of Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, Heidelberg, 69120 Germany
| | - Ralf Bartenschlager
- Hygiene Institute Department of Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, Heidelberg, 69120 Germany
| |
Collapse
|
37
|
Bermúdez-Aguirre AD, Padilla-Noriega L, Zenteno E, Reyes-Leyva J. Identification of Amino Acid Variants in the Hepatitis C Virus Non-Structural Protein 4A. TOHOKU J EXP MED 2009; 218:165-75. [DOI: 10.1620/tjem.218.165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Alejandro Daniel Bermúdez-Aguirre
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México
- Laboratorio de Virología, Centro de Investigaciones Biomédicas de Oriente, Instituto Mexicano del Seguro Social, Hospital General de Zona No. 5
| | - Luis Padilla-Noriega
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México
| | - Edgar Zenteno
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México
- Facultad de Medicina Humana, Universidad Ricardo Palma
| | - Julio Reyes-Leyva
- Laboratorio de Virología, Centro de Investigaciones Biomédicas de Oriente, Instituto Mexicano del Seguro Social, Hospital General de Zona No. 5
| |
Collapse
|
38
|
Abstract
Hepatitis C virus (HCV) infection is one of the most serious public health problems in the world. HCV leads patients to develop hepatic cirrhosis and precipitates hepatocellular carcinoma. HCV establishes persistent infection by impairing host innate and adaptive immune responses. HCV infected hepatocytes sense the infection through Pathogen Associated Molecular Patterns (PAMPs). The sensor molecules, Pattern Recognition Receptors (PRRs) contain two distinct categories, toll like receptors (TLR) and cytoplasmic Retinoic Acid inducible Gene I (RIG-I) like helicases (RLHs). In the hepatocyte, the cytoplasmic PRR, Retinoic Acid inducible Gene I (RIG-I) plays the central role of HCV viral genome recognition, resulting in activation of signaling to induce type I interferon and proinflammatory cytokines. Type I IFN induces more than 300 effector molecules known as interferon stimulated genes (ISGs) that establish an antiviral state in infected cells and neighboring cells. The activation of innate immunity is also critical for the mounting of innate and adaptive immunity. However, a variety of viral strategies of HCV disrupt host innate immune signaling and ISG function, resulting in a dysfunctional immune response against HCV and poor responses to the current type I IFN based therapy. Many studies have reported immune dysfunction during HCV infection in cell culture, animal models and patients. This review article focuses on understanding how the hepatic innate immunity sensor, PRR, associates with HCV PAMPs, and how HCV escapes from host immunity.
Collapse
Affiliation(s)
- Takeshi Saito
- Department of Immunology, University of Washington School of Medicine, H578 HSB 1959 N.E. Pacific St, Seattle, WA 98195-7650, USA.
| | | |
Collapse
|
39
|
van der Poorten D, George J. Disease-specific mechanisms of fibrosis: hepatitis C virus and nonalcoholic steatohepatitis. Clin Liver Dis 2008; 12:805-24, ix. [PMID: 18984468 DOI: 10.1016/j.cld.2008.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Our mechanistic understanding of liver fibrosis has increased dramatically in recent years for all liver diseases and for hepatitis C and nonalcoholic steatohepatitis (NASH) in particular. Hepatitis C causes liver injury and fibrosis through direct cytopathic means, direct and indirect interactions with hepatic stellate cells, and activation of the immune system. Steatosis and insulin resistance, which are intrinsic deficits in NASH, are also of great importance in hepatitis C and may be induced by viral or host metabolic factors. For NASH, the key mediators of damage include oxidative stress, fat compartmentalization, visceral fat, apoptosis, and adipokine derangement. This article explores in depth the disease-specific mechanisms of fibrosis in hepatitis C and NASH, with a focus on recent developments.
Collapse
|
40
|
A drug-controllable tag for visualizing newly synthesized proteins in cells and whole animals. Proc Natl Acad Sci U S A 2008; 105:7744-9. [PMID: 18511556 DOI: 10.1073/pnas.0803060105] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Research on basic cellular processes involving local production or delivery of proteins, such as activity-dependent synaptic modification in neurons, would benefit greatly from a robust, nontoxic method to visualize selectively newly synthesized copies of proteins of interest within cells, tissues, or animals. We report a technique for covalent labeling of newly synthesized proteins of interest based on drug-dependent preservation of epitope tags. Epitope tags are removed from proteins of interest immediately after translation by the activity of a sequence-specific protease until the time a protease inhibitor is added, after which newly synthesized protein copies retain their tags. This method, which we call TimeSTAMP for time-specific tagging for the age measurement of proteins, allows sensitive and nonperturbative visualization and quantification of newly synthesized proteins of interest with exceptionally tight temporal control. We demonstrate applications of TimeSTAMP in retrospectively identifying growing synapses in cultured neurons and in visualizing the distribution of recently synthesized proteins in intact fly brains.
Collapse
|
41
|
NS3 helicase domains involved in infectious intracellular hepatitis C virus particle assembly. J Virol 2008; 82:7624-39. [PMID: 18508894 DOI: 10.1128/jvi.00724-08] [Citation(s) in RCA: 172] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A mutation within subdomain 1 of the hepatitis C virus (HCV) NS3 helicase (NS3-Q221L) (M. Yi, Y. Ma, J. Yates, and S. M. Lemon, J. Virol. 81:629-638, 2007) rescues a defect in production of infectious virus by an intergenotypic chimeric RNA (HJ3). Although NS3-Gln-221 is highly conserved across HCV genotypes, the Leu-221 substitution had no effect on RNA replication or NS3-associated enzymatic activities. However, while transfection of unmodified HJ3 RNA failed to produce either extracellular or intracellular infectious virus, transfection of HJ3 RNA containing the Q221L substitution (HJ3/QL) resulted in rapid accumulation of intracellular infectious particles with release into extracellular fluids. In the absence of the Q221L mutation, both NS5A and NS3 were recruited to core protein on the surface of lipid droplets, but there was no assembly of core into high-density, rapidly sedimenting particles. Further analysis demonstrated that a Q221N mutation minimally rescued virus production and led to a second-site I399V mutation in subdomain 2 of the helicase. Similarly, I399V alone allowed only low-level virus production and led to selection of an I286V mutation in subdomain 1 of the helicase which fully restored virus production, confirming the involvement of both major helicase subdomains in the assembly process. Thus, multiple mutations in the helicase rescue a defect in an early-intermediate step in virus assembly that follows the recruitment of NS5A to lipid droplets and precedes the formation of dense intracellular viral particles. These data reveal a previously unsuspected role for the NS3 helicase in early virion morphogenesis and provide a new perspective on HCV assembly.
Collapse
|
42
|
Teixeira R, Marcos LA, Friedman SL. Immunopathogenesis of hepatitis C virus infection and hepatic fibrosis: New insights into antifibrotic therapy in chronic hepatitis C. Hepatol Res 2007; 37:579-95. [PMID: 17517074 DOI: 10.1111/j.1872-034x.2007.00085.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Fibrosis and cirrhosis represent the consequences of a sustained wound-healing response to chronic liver injury of any cause. Chronic hepatitis C virus (HCV) has emerged as a leading cause of cirrhosis in the USA and throughout the world. HCV may induce fibrogenesis directly by hepatic stellate cell activation or indirectly by promoting oxidative stress and apoptosis of infected cells. The ultimate result of chronic HCV injury is the accumulation of extracellular matrix with high density type I collagen within the subendothelial space of Disse, culminating in cirrhosis with hepatocellular dysfunction. The treatment of hepatitis C with the combination of pegylated interferon and ribavirin is still both problematic and costly, has suboptimal efficacy, serious side effects and a high level of intolerance, and is contraindicated in many patients. Hence, new approaches have assumed greater importance, for which there is an urgent need. The sustained progress in understanding the pathophysiology of hepatic fibrosis in the past two decades has increased the possibility of developing drugs specifically targeting the fibrogenic process. Future efforts should identify genetic markers associated with fibrosis risk in order to tailor the treatment of HCV infection based on genetically regulated pathways of injury and/or fibrosis. Such advances will expand the arsenal to overcome liver fibrosis, particularly in patients with hepatic diseases who have limited treatment options, such as those patients with chronic hepatitis C who have a high risk of fibrosis progression and recurrent HCV disease after liver transplantation.
Collapse
Affiliation(s)
- Rosângela Teixeira
- School of Medicine, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | |
Collapse
|
43
|
Abstract
Since the discovery of the hepatitis C virus (HCV) as the major cause of non-A, non-B hepatitis in 1989, the search for specific targeted antiviral therapy for HCV (STAT-C) has been underway. Recently, major advances in the understanding of HCV biology and the development of an in vitro system of HCV replication have contributed to the selection of multiple candidate drugs for the treatment of hepatitis C. In 2006, five such candidate drugs have entered phase II clinical trials in patients chronically infected with hepatitis C, including small molecule inhibitors of the HCV NS3 serine protease and NS5B RNA-dependent RNA polymerase. This review focuses on hepatitis C protease and polymerase inhibitors that have progressed to phase II clinical development, foreshadowing the era of STAT-Cs.
Collapse
Affiliation(s)
- Mark S Sulkowski
- Johns Hopkins University School of Medicine, 600 North Wolfe Street, 1830 Building, Room 448, Baltimore, MD 21287, USA.
| |
Collapse
|
44
|
Abstract
The innate immune response is triggered by a variety of pathogens, including viruses, and requires rapid induction of type I interferons (IFN), such as IFNβ and IFNα. IFN induction occurs when specific pathogen motifs bind to specific cellular receptors. In non-professional immune, virally-infected cells, IFN induction is essentially initiated after the binding of dsRNA structures to TLR3 receptors or to intracytosolic RNA helicases, such as RIG-I /MDA5. This leads to the recruitment of specific adaptors, such as TRIF for TLR3 and the mitochondrial-associated IPS-1/VISA/MAVS/CARDIF adapter protein for the RNA helicases, and the ultimate recruitment of kinases, such as MAPKs, the canonical IKK complex and the TBK1/IKKε kinases, which activate the transcription factors ATF-2/c-jun, NF-κB and IRF3, respectively. The coordinated action of these transcription factors leads to induction of IFN and of pro-inflammatory cytokines and to the establishment of the innate immune response. HCV can cleave both the adapters TRIF and IPS-1/VISA/MAVS/CARDIF through the action of its NS3/4A protease. This provokes abrogation of the induction of the IFN and cytokine pathways and favours viral propagation and presumably HCV chronic infection.
Collapse
Affiliation(s)
- Eliane F Meurs
- Hepacivirus Unit, Department of Virology, Pasteur Institute, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.
| | | |
Collapse
|
45
|
Le Guillou-Guillemette H, Vallet S, Gaudy-Graffin C, Payan C, Pivert A, Goudeau A, Lunel-Fabiani F. Genetic diversity of the hepatitis C virus: Impact and issues in the antiviral therapy. World J Gastroenterol 2007; 13:2416-26. [PMID: 17552024 PMCID: PMC4146759 DOI: 10.3748/wjg.v13.i17.2416] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The hepatitis C Virus (HCV) presents a high degree of genetic variability which is explained by the combination of a lack of proof reading by the RNA dependant RNA polymerase and a high level of viral replication. The resulting genetic polymorphism defines a classification in clades, genotypes, subtypes, isolates and quasispecies. This diversity is known to reflect the range of responses to Interferon therapy. The genotype is one of the predictive parameters currently used to define the antiviral treatment strategy and the chance of therapeutic success. Studies have also reported the potential impact of the viral genetic polymorphism in the outcome of antiviral therapy in patients infected by the same HCV genotype. Both structural and non structural genomic regions of HCV have been suggested to be involved in the Interferon pathway and the resistance to antiviral therapy. In this review, we first detail the viral basis of HCV diversity. Then, the HCV genetic regions that may be implicated in resistance to therapy are described, with a focus on the structural region encoded by the E2 gene and the non-structural genes NS3, NS5A and NS5B. Both mechanisms of the Interferon resistance and of the new antiviral drugs are described in this review.
Collapse
Affiliation(s)
- H Le Guillou-Guillemette
- Laboratory of Virology, Department of Infectious Agents, University Hospital of Angers, 4 rue Larrey, 49933 Angers Cedex 9, France
| | | | | | | | | | | | | |
Collapse
|
46
|
Johnson CL, Owen DM, Gale M. Functional and therapeutic analysis of hepatitis C virus NS3.4A protease control of antiviral immune defense. J Biol Chem 2007; 282:10792-803. [PMID: 17289677 DOI: 10.1074/jbc.m610361200] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chronic hepatitis C virus (HCV) infection is a major global public health problem. HCV infection is supported by viral strategies to evade the innate antiviral response wherein the viral NS3.4A protease complex targets and cleaves the interferon promoter stimulator-1 (IPS-1) adaptor protein to ablate signaling of interferon alpha/beta immune defenses. Here we examined the structural requirements of NS3.4A and the therapeutic potential of NS3.4A inhibitors to control the innate immune response against virus infection. The structural composition of NS3 includes an amino-terminal serine protease domain and a carboxyl-terminal RNA helicase domain. NS3 mutants lacking the helicase domain retained the ability to control virus signaling initiated by retinoic acid-inducible gene-I (RIG-I) or melanoma differentiation antigen 5 and suppressed the downstream activation of interferon regulatory factor-3 (IRF-3) and nuclear factor kappaB (NF-kappaB) through the targeted proteolysis of IPS-1. This regulation was abrogated by truncation of the NS3 protease domain or by point mutations that ablated protease activity. NS3.4A protease control of antiviral immune signaling was due to targeted proteolysis of IPS-1 by the NS3 protease domain and minimal NS4A cofactor. Treatment of HCV-infected cells with an NS3 protease inhibitor prevented IPS-1 proteolysis by the HCV protease and restored RIG-I immune defense signaling during infection. Thus, the NS3.4A protease domain can target IPS-1 for cleavage and is essential for blocking RIG-I signaling to IRF-3 and NF-kappaB, whereas the helicase domain is dispensable for this action. Our results indicate that NS3.4A protease inhibitors have immunomodulatory potential to restore innate immune defenses to HCV infection.
Collapse
Affiliation(s)
- Cynthia L Johnson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | | | | |
Collapse
|
47
|
Vallet S, Gouriou S, Nkontchou G, Hotta H, Vilerio M, Legrand-Quillien MC, Beaugrand M, Trinchet JC, Nousbaum JB, Dény P, Gaudy C, Goudeau A, Picard B, Payan C. Is hepatitis C virus NS3 protease quasispecies heterogeneity predictive of progression from cirrhosis to hepatocellular carcinoma? J Viral Hepat 2007; 14:96-106. [PMID: 17244249 DOI: 10.1111/j.1365-2893.2006.00773.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We investigated whether an HCV NS3 protease quasispecies heterogeneity was associated with progression from viral cirrhosis to hepatocellular carcinoma (HCC). The NS3 protease quasispecies structure of 10 HCV-1b cirrhotic patients (controls) was compared with that of 10 paired HCV-1b cirrhotic patients who displayed progression to HCC (cases). NS3 protease genetic complexity and diversity did not differ significantly between cases and controls. Amino acid substitutions were detected at 20 (11%) and 25 (14%) sites in at least two variants of the NS3 protease in cases and controls, respectively. Significant differences in the percentage of substituted clones were observed for 10 NS3 sites. Mutations Y56F, I71V, T72I, Q86P, P89S, S101G/D, R117H, S122G/T/N, V132I and V170I were more frequently observed in the NS3 protease sequences of controls than in those of cases. Residue V107 was substituted in NS3 cases but not in controls. However, these differences did not allow the definition of a specific NS3 profile related to HCC occurrence. The NS3 secondary structure B1-1 previously identified as potentially predictive of HCC was identified with a higher frequency in cases quasispecies (84.2%) than in controls (55.9%; P < 0.05). Our results suggest that there may be a relationship to fibrosis progression when diversity parameters are considered together with secondary structure profiles. Further investigations are required to determine the cellular interactions of HCV NS3 protease in the context of carcinogenesis.
Collapse
Affiliation(s)
- S Vallet
- Microbiologie, CHU Morvan, Brest, France.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Bilodeau M, Lamarre D. New treatment strategies against hepatitis C viral infection. CANADIAN JOURNAL OF GASTROENTEROLOGY = JOURNAL CANADIEN DE GASTROENTEROLOGIE 2007; 20:735-9. [PMID: 17111056 PMCID: PMC2660829 DOI: 10.1155/2006/863509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Treatment of hepatitis C virus infection is currently based on a combination of pegylated interferon and ribavirin. Because efficacy of this therapy remains suboptimal and side effects sometimes problematic, major efforts have been put forward by scientists and the pharmaceutical industry to develop alternative treatments for this chronic infection. Over the past few years, clinical studies performed with some of these new agents have been presented at major international meetings. The present paper aims to review the rationale underlying the development of these new forms of treatment as well as the current available data concerning their clinical efficacy.
Collapse
Affiliation(s)
- Marc Bilodeau
- Service d'hepatologie, Hopital Saint-Luc du CHUM, Montreal, Canada.
| | | |
Collapse
|
49
|
Breiman A, Vitour D, Vilasco M, Ottone C, Molina S, Pichard L, Fournier C, Delgrange D, Charneau P, Duverlie G, Wychowski C, Maurel P, Meurs EF. A hepatitis C virus (HCV) NS3/4A protease-dependent strategy for the identification and purification of HCV-infected cells. J Gen Virol 2006; 87:3587-3598. [PMID: 17098974 DOI: 10.1099/vir.0.82214-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
As a tool for the identification and/or purification of hepatitis C virus (HCV)-infected cells, a chimeric form of the Gal4VP16 transcription factor was engineered to be activated only in the presence of the HCV NS3/4A protease and to induce different reporter genes [choramphenical acetyltransferase (CAT), green fluorescent protein (GFP) and the cell-surface marker H-2K(k)] through the (Gal4)(5)-E1b promoter. For this, the NS5A/5B trans-cleavage motif of HCV of genotype 1a was inserted between Gal4VP16 and the N terminus of the endoplasmic reticulum (ER)-resident protein PERK, and it was demonstrated that it could be cleaved specifically by NS3/4A. Accordingly, transient transfection in tetracycline-inducible UHCV-11 cells expressing the HCV polyprotein of genotype 1a revealed the migration of the Gal4VP16 moiety of the chimera from the ER to the nucleus upon HCV expression. Activation of the chimera provoked specific gene induction, as shown by CAT assay, first in UHCV-11 cells and then in Huh-7 cells expressing an HCV replicon of genotype 1b (Huh-7 Rep). In addition, the GFP reporter gene allowed rapid fluorescence monitoring of HCV expression in the Huh-7 Rep cells. Finally, the chimera was introduced into Huh-7.5 cells infected with cell culture-generated HCV JFH1 (genotype 2a), allowing the purification of the HCV-infected cells by immunomagnetic cell sorting using H-2K(k) as gene reporter. In conclusion, the Gal4VP16 chimera activation system can be used for the rapid identification and purification of HCV-infected cells.
Collapse
Affiliation(s)
- Adrien Breiman
- Unité Hépacivirus, Département de Virologie, Institut Pasteur, 28 rue du Dr Roux, F-75724 Paris Cedex 15, France
| | - Damien Vitour
- Unité Hépacivirus, Département de Virologie, Institut Pasteur, 28 rue du Dr Roux, F-75724 Paris Cedex 15, France
| | - Myriam Vilasco
- Unité Hépacivirus, Département de Virologie, Institut Pasteur, 28 rue du Dr Roux, F-75724 Paris Cedex 15, France
| | - Catherine Ottone
- Unité Hépacivirus, Département de Virologie, Institut Pasteur, 28 rue du Dr Roux, F-75724 Paris Cedex 15, France
| | | | | | - Chantal Fournier
- Etablissement Français du Sang (EFS) Pyrénées-Méditerranée, F-34094 Montpellier, France
| | - David Delgrange
- Institut Pasteur de Lille, Groupe Hépatite C, Institut de Biologie de Lille, F-59021 Lille, France
| | - Pierre Charneau
- Laboratoire Virologie Moléculaire et Vectorologie, Institut Pasteur, 28 rue du Dr Roux, F-75724 Paris Cedex 15, France
| | | | - Czeslaw Wychowski
- Institut Pasteur de Lille, Groupe Hépatite C, Institut de Biologie de Lille, F-59021 Lille, France
| | | | - Eliane F Meurs
- Unité Hépacivirus, Département de Virologie, Institut Pasteur, 28 rue du Dr Roux, F-75724 Paris Cedex 15, France
| |
Collapse
|
50
|
Venkatraman S, Bogen SL, Arasappan A, Bennett F, Chen K, Jao E, Liu YT, Lovey R, Hendrata S, Huang Y, Pan W, Parekh T, Pinto P, Popov V, Pike R, Ruan S, Santhanam B, Vibulbhan B, Wu W, Yang W, Kong J, Liang X, Wong J, Liu R, Butkiewicz N, Chase R, Hart A, Agrawal S, Ingravallo P, Pichardo J, Kong R, Baroudy B, Malcolm B, Guo Z, Prongay A, Madison V, Broske L, Cui X, Cheng KC, Hsieh Y, Brisson JM, Prelusky D, Korfmacher W, White R, Bogdanowich-Knipp S, Pavlovsky A, Bradley P, Saksena AK, Ganguly A, Piwinski J, Girijavallabhan V, Njoroge FG. Discovery of (1R,5S)-N-[3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]- 3-[2(S)-[[[(1,1-dimethylethyl)amino]carbonyl]amino]-3,3-dimethyl-1-oxobutyl]- 6,6-dimethyl-3-azabicyclo[3.1.0]hexan-2(S)-carboxamide (SCH 503034), a selective, potent, orally bioavailable hepatitis C virus NS3 protease inhibitor: a potential therapeutic agent for the treatment of hepatitis C infection. J Med Chem 2006; 49:6074-86. [PMID: 17004721 DOI: 10.1021/jm060325b] [Citation(s) in RCA: 196] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hepatitis C virus (HCV) infection is the major cause of chronic liver disease, leading to cirrhosis and hepatocellular carcinoma, which affects more than 170 million people worldwide. Currently the only therapeutic regimens are subcutaneous interferon-alpha or polyethylene glycol (PEG)-interferon-alpha alone or in combination with oral ribavirin. Although combination therapy is reasonably successful with the majority of genotypes, its efficacy against the predominant genotype (genotype 1) is moderate at best, with only about 40% of the patients showing sustained virological response. Herein, the SAR leading to the discovery of 70 (SCH 503034), a novel, potent, selective, orally bioavailable NS3 protease inhibitor that has been advanced to clinical trials in human beings for the treatment of hepatitis C viral infections is described. X-ray structure of inhibitor 70 complexed with the NS3 protease and biological data are also discussed.
Collapse
Affiliation(s)
- Srikanth Venkatraman
- Schering Plough Research Institute, K-15, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|