1
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Lin CH, Tam HMH, Yang CY, Hsieh FC, Wang JL, Yang CC, Hsu HW, Liu HP, Wu HY. Evolution of the coronavirus spike protein in the full-length genome and defective viral genome under diverse selection pressures. J Gen Virol 2023; 104:001920. [PMID: 37997889 PMCID: PMC10768696 DOI: 10.1099/jgv.0.001920] [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: 06/28/2023] [Accepted: 10/28/2023] [Indexed: 11/25/2023] Open
Abstract
How coronaviruses evolve by altering the structures of their full-length genome and defective viral genome (DVG) under dynamic selection pressures has not been studied. In this study, we aimed to experimentally identify the dynamic evolutionary patterns of the S protein sequence in the full-length genome and DVG under diverse selection pressures, including persistence, innate immunity and antiviral drugs. The evolutionary features of the S protein sequence in the full-length genome and in the DVG under diverse selection pressures are as follows: (i) the number of nucleotide (nt) mutations does not necessarily increase with the number of selection pressures; (ii) certain types of selection pressure(s) can lead to specific nt mutations; (iii) the mutated nt sequence can be reverted to the wild-type nt sequence under the certain type of selection pressure(s); (iv) the DVG can also undergo mutations and evolve independently of the full-length genome; and (v) DVG species are regulated during evolution under diverse selection pressures. The various evolutionary patterns of the S protein sequence in the full-length genome and DVG identified in this study may contribute to coronaviral fitness under diverse selection pressures.
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Affiliation(s)
- Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hon-Man-Herman Tam
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Cheng-Yao Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Feng-Cheng Hsieh
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Jiun-Long Wang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan, ROC
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Chun-Chun Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hsuan-Wei Hsu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hao-Ping Liu
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
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2
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Lin CH, Yang CY, Ou SC, Wang M, Lo CY, Tsai TL, Wu HY. The Impacts of Antivirals on the Coronavirus Genome Structure and Subsequent Pathogenicity, Virus Fitness and Antiviral Design. Biomedicines 2020; 8:E376. [PMID: 32987828 PMCID: PMC7601523 DOI: 10.3390/biomedicines8100376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 01/29/2023] Open
Abstract
With the global threat of SARS-CoV-2, much effort has been focused on treatment and disease control. However, how coronaviruses react to the treatments and whether the surviving viruses have altered their characteristics are also unanswered questions with medical importance. To this end, bovine coronavirus (BCoV), which is in the same genus as SARS-CoV-2, was used as a test model and the findings were as follows. With the treatment of antiviral remdesivir, the selected BCoV variant with an altered genome structure developed resistance, but its pathogenicity was not increased in comparison to that of wild type (wt) BCoV. Under the selection pressure of innate immunity, the genome structure was also altered; however, neither resistance developed nor pathogenicity increased for the selected BCoV variant. Furthermore, both selected BCoV variants showed a better efficiency in adapting to alternative host cells than wt BCoV. In addition, the previously unidentified feature that the spike protein was a common target for mutations under different antiviral treatments might pose a problem for vaccine development because spike protein is a common target for antibody and vaccine designs. The findings derived from this fundamental research may contribute to the disease control and treatments against coronaviruses, including SARS-CoV-2.
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Affiliation(s)
- Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Cheng-Yao Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Shan-Chia Ou
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan;
| | - Meilin Wang
- Department of Microbiology and Immunology, Chung Shan Medical University, Taichung 40201, Taiwan;
| | - Chen-Yu Lo
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Tsung-Lin Tsai
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
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3
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Wagner R, Randolph JT, Patel SV, Nelson L, Matulenko MA, Keddy R, Pratt JK, Liu D, Krueger AC, Donner PL, Hutchinson DK, Flentge C, Betebenner D, Rockway T, Maring CJ, Ng TI, Krishnan P, Pilot-Matias T, Collins C, Panchal N, Reisch T, Dekhtyar T, Mondal R, Stolarik DF, Gao Y, Gao W, Beno DA, Kati WM. Highlights of the Structure-Activity Relationships of Benzimidazole Linked Pyrrolidines Leading to the Discovery of the Hepatitis C Virus NS5A Inhibitor Pibrentasvir (ABT-530). J Med Chem 2018; 61:4052-4066. [PMID: 29653491 DOI: 10.1021/acs.jmedchem.8b00082] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Curative interferon and ribavirin sparing treatments for hepatitis C virus (HCV)-infected patients require a combination of mechanistically orthogonal direct acting antivirals. A shared component of these treatments is usually an HCV NS5A inhibitor. First generation FDA approved treatments, including the component NS5A inhibitors, do not exhibit equivalent efficacy against HCV virus genotypes 1-6. In particular, these first generation NS5A inhibitors tend to select for viral drug resistance. Ombitasvir is a first generation HCV NS5A inhibitor included as a key component of Viekira Pak for the treatment of patients with HCV genotype 1 infection. Since the launch of next generation HCV treatments, functional cure for genotype 1-6 HCV infections has been achieved, as well as shortened treatment duration across a wider spectrum of genotypes. In this paper, we show how we have modified the anchor, linker, and end-cap architecture of our NS5A inhibitor design template to discover a next generation NS5A inhibitor pibrentasvir (ABT-530), which exhibits potent inhibition of the replication of wild-type genotype 1-6 HCV replicons, as well as improved activity against replicon variants demonstrating resistance against first generation NS5A inhibitors.
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Affiliation(s)
- Rolf Wagner
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - John T Randolph
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Sachin V Patel
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Lissa Nelson
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Mark A Matulenko
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Ryan Keddy
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - John K Pratt
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Dachun Liu
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - A Chris Krueger
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Pamela L Donner
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Douglas K Hutchinson
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Charles Flentge
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - David Betebenner
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Todd Rockway
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Clarence J Maring
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Teresa I Ng
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Preethi Krishnan
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Tami Pilot-Matias
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Christine Collins
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Neeta Panchal
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Thomas Reisch
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Tatyana Dekhtyar
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Rubina Mondal
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - DeAnne F Stolarik
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Yi Gao
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Wenqing Gao
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - David A Beno
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Warren M Kati
- Global Pharmaceutical Research and Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
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4
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Hernández-Alonso P, Garijo R, Cuevas JM, Sanjuán R. Experimental evolution of an RNA virus in cells with innate immunity defects. Virus Evol 2015; 1:vev008. [PMID: 27774280 PMCID: PMC5014476 DOI: 10.1093/ve/vev008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Experimental evolution studies have shown that RNA viruses respond rapidly to directional selection and thus can adapt efficiently to changes in host cell tropism, antiviral drugs, or other imposed selective pressures. However, the evolution of RNA viruses under relaxed selection has been less extensively explored. Here, we evolved vesicular stomatitis virus in mouse embryonic fibroblasts knocked-out for PKR, a protein with a central role in antiviral innate immunity. Vesicular stomatitis virus adapted to PKR-negative mouse embryonic fibroblasts in a gene-specific manner, since the evolved viruses exhibited little or no fitness improvement in PKR-positive cells. Full-length sequencing revealed the presence of multiple parallel nucleotide substitutions arising in independent evolution lines. However, site-directed mutagenesis showed that the effects of these substitutions were not PKR dependent. In contrast, we found evidence for sign epistasis, such that a given substitution which was positively selected was strongly deleterious when tested as a single mutation. Our results suggest that virus evolution in cells with specific innate immunity defects may drive viral specialization. However, this process is not deterministic at the molecular level, probably because the fixation of mutations which are tolerated under a relaxed selection regime is governed mainly by random genetic drift.
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Affiliation(s)
- Pablo Hernández-Alonso
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departament de Genètica, Universitat de València, Paterna 46980, Spain
| | - Raquel Garijo
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departament de Genètica, Universitat de València, Paterna 46980, Spain
| | - José M Cuevas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departament de Genètica, Universitat de València, Paterna 46980, Spain
| | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departament de Genètica, Universitat de València, Paterna 46980, Spain
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5
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Upadya MH, Aweya JJ, Tan YJ. Understanding the interaction of hepatitis C virus with host DEAD-box RNA helicases. World J Gastroenterol 2014; 20:2913-2926. [PMID: 24659882 PMCID: PMC3961968 DOI: 10.3748/wjg.v20.i11.2913] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 12/06/2013] [Accepted: 01/20/2014] [Indexed: 02/06/2023] Open
Abstract
The current therapeutic regimen to combat chronic hepatitis C is not optimal due to substantial side effects and the failure of a significant proportion of patients to achieve a sustained virological response. Recently developed direct-acting antivirals targeting hepatitis C virus (HCV) enzymes reportedly increase the virologic response to therapy but may lead to a selection of drug-resistant variants. Besides direct-acting antivirals, another promising class of HCV drugs in development include host targeting agents that are responsible for interfering with the host factors crucial for the viral life cycle. A family of host proteins known as DEAD-box RNA helicases, characterized by nine conserved motifs, is known to play an important role in RNA metabolism. Several members of this family such as DDX3, DDX5 and DDX6 have been shown to play a role in HCV replication and this review will summarize our current knowledge on their interaction with HCV. As chronic hepatitis C is one of the leading causes of hepatocellular carcinoma, the involvement of DEAD-box RNA helicases in the development of HCC will also be highlighted. Continuing research on the interaction of host DEAD-box proteins with HCV and the contribution to viral replication and pathogenesis could be the panacea for the development of novel therapeutics against HCV.
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6
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Lampa AK, Bergman SM, Gustafsson SS, Alogheli H, Åkerblom EB, Lindeberg GG, Svensson RM, Artursson P, Danielson UH, Karlén A, Sandström A. Novel Peptidomimetic Hepatitis C Virus NS3/4A Protease Inhibitors Spanning the P2-P1' Region. ACS Med Chem Lett 2014; 5:249-54. [PMID: 24900813 DOI: 10.1021/ml400217r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/02/2013] [Indexed: 02/06/2023] Open
Abstract
Herein, novel hepatitis C virus NS3/4A protease inhibitors based on a P2 pyrimidinyloxyphenylglycine in combination with various regioisomers of an aryl acyl sulfonamide functionality in P1 are presented. The P1' 4-(trifluoromethyl)phenyl side chain was shown to be particularly beneficial in terms of inhibitory potency. Several inhibitors with K i-values in the nanomolar range were developed and included identification of promising P3-truncated inhibitors spanning from P2-P1'. Of several different P2 capping groups that were evaluated, a preference for the sterically congested Boc group was revealed. The inhibitors were found to retain inhibitory potencies for A156T, D168V, and R155K variants of the protease. Furthermore, in vitro pharmacokinetic profiling showed several beneficial effects on metabolic stability as well as on apparent intestinal permeability from both P3 truncation and the use of the P1' 4-(trifluoromethyl)phenyl side chain.
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Affiliation(s)
- Anna K. Lampa
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Sara M. Bergman
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Sofia S. Gustafsson
- Department of Chemistry−BMC, Uppsala University, BMC, Box 576, SE-751 23 Uppsala,
Sweden
| | - Hiba Alogheli
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Eva B. Åkerblom
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Gunnar G. Lindeberg
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Richard M. Svensson
- Department of Pharmacy, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden
- The Uppsala University Drug
Optimization and Pharmaceutical Profiling Platform, Uppsala University, a Node of the Chemical Biology Consortium
Sweden (CBCS), Box 580, SE-751 23 Uppsala, Sweden
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden
- The Uppsala University Drug
Optimization and Pharmaceutical Profiling Platform, Uppsala University, a Node of the Chemical Biology Consortium
Sweden (CBCS), Box 580, SE-751 23 Uppsala, Sweden
| | - U. Helena Danielson
- Department of Chemistry−BMC, Uppsala University, BMC, Box 576, SE-751 23 Uppsala,
Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Anja Sandström
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
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7
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Macarthur KL, Smolic R, Smolic MV, Wu CH, Wu GY. Update on the Development of Anti-Viral Agents Against Hepatitis C. J Clin Transl Hepatol 2013; 1:9-21. [PMID: 26357602 PMCID: PMC4521270 DOI: 10.14218/jcth.2013.007xx] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/14/2013] [Accepted: 05/14/2013] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) infects nearly 170 million people worldwide and causes chronic hepatitis, cirrhosis, and hepatocellular carcinoma. The search for a drug regimen that maximizes efficacy and minimizes side effects is quickly evolving. This review will discuss a wide range of drug targets currently in all phases of development for the treatment of HCV. Direct data from agents in phase III/IV clinical trials will be presented, along with reported side-effect profiles. The mechanism of action of all treatments and resistance issues are highlighted. Special attention is given to available trial data supporting interferon-free treatment regimens. HCV has become an increasingly important public health concern, and it is important for physicians to stay up to date on the rapidly growing novel therapeutic options.
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Affiliation(s)
| | | | | | - Catherine H. Wu
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, Farmington, CT, USA
| | - George Y. Wu
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, Farmington, CT, USA
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8
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McCauley JA, Rudd MT, Liverton NJ. HCV NS3/4a Protease Inhibitors: Simeprevir (TMC‐435350), Vaniprevir (MK‐7009) and MK‐5172. SUCCESSFUL STRATEGIES FOR THE DISCOVERY OF ANTIVIRAL DRUGS 2013. [DOI: 10.1039/9781849737814-00189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Hepatitis C virus (HCV) infection continues to represent a major health issue, with estimates of 130–170 million people infected worldwide. Recent developments in the HCV NS3/4a protease inhibitor area have significantly improved treatment options for patients. However, a more dramatic paradigm shift in the treatment of HCV infection appears all but certain in coming years, with a move to all oral combination therapy with direct‐acting antivirals (DAAs). HCV protease inhibitors have the potential to play a significant role in these DAA combination therapies. This chapter discusses in detail the design and discovery of three HCV NS3/4a protease inhibitors in clinical development: simeprevir (TMC‐435350), vaniprevir (MK‐7009) and MK‐5172.
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Affiliation(s)
- John A. McCauley
- Department of Medicinal Chemistry Merck Research Laboratories, West Point, PA 19486 USA
| | - Michael T. Rudd
- Department of Medicinal Chemistry Merck Research Laboratories, West Point, PA 19486 USA
| | - Nigel J. Liverton
- Department of Medicinal Chemistry Merck Research Laboratories, West Point, PA 19486 USA
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9
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Asthana S, Shukla S, Vargiu AV, Ceccarelli M, Ruggerone P, Paglietti G, Marongiu ME, Blois S, Giliberti G, La Colla P. Different Molecular Mechanisms of Inhibition of Bovine Viral Diarrhea Virus and Hepatitis C Virus RNA-Dependent RNA Polymerases by a Novel Benzimidazole. Biochemistry 2013; 52:3752-64. [DOI: 10.1021/bi400107h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Shailendra Asthana
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
- Dipartimento di Scienze Fisiche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Saumya Shukla
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | | | - Matteo Ceccarelli
- Dipartimento di Scienze Fisiche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Paolo Ruggerone
- Dipartimento di Scienze Fisiche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Giuseppe Paglietti
- Dipartimento di Scienze del
Farmaco, Università degli Studi di Sassari, Via Muroni 23/a, 07100 Sassari, Italy
| | - Maria E. Marongiu
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Sylvain Blois
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Gabriele Giliberti
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Paolo La Colla
- Dipartimento di Scienze Biomediche,
Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
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10
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Repeated exposure to 5D9, an inhibitor of 3D polymerase, effectively limits the replication of foot-and-mouth disease virus in host cells. Antiviral Res 2013; 98:380-5. [PMID: 23578728 DOI: 10.1016/j.antiviral.2013.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/11/2013] [Accepted: 03/28/2013] [Indexed: 11/21/2022]
Abstract
Foot-and-mouth disease (FMD) is a highly contagious disease of livestock caused by a highly variable RNA virus (FMDV) that has seven serotypes and more than sixty subtypes. Both prophylactic and post-infection means of controlling the disease outbreak, including universally applicable vaccines and emergency response measures such as therapeutic treatments, are on high demand. In this study, we analyzed the long-term exposure outcome to a previously identified inhibitor of 3D polymerase (FMDV 3Dpol) for controlling FMDV infection and for the selection of resistance mutants. The results showed that no escape mutant viruses were isolated from FMDV A24 Cruzeiro infections in cell culture treated with gradually increasing concentrations of the antiviral compound 5D9 (4-chloro-N'-thieno, [2,3-d]pyrimidin-4-ylbenzenesulfonohydrazide) over ten passages. Biochemical and plaque assays revealed that when 5D9 was used at concentrations within a non-toxic range in cells, it drove the virus to undetectable levels at passage eight to ten. This is in contrast with observations made on parallel control (untreated) passages exhibiting fully viable and stable virus progenies. Collectively, the results demonstrated that under the experimental conditions, treatment with 5D9 does not confer a resistant phenotype and the virus is unable to evade the antiviral effect of the inhibitor. Further efforts using quantitative structure-property relationship (QSPR) based modifications of the 5D9 compound may result in the successful development of an effective in vivo antiviral drug targeting FMDV.
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11
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Li G, Li K, Lea AS, Li NL, Abdulla NE, Eltorky MA, Ferguson MR. In situ hybridization for the detection of hepatitis C virus RNA in human liver tissue. J Viral Hepat 2013; 20:183-92. [PMID: 23383657 DOI: 10.1111/j.1365-2893.2012.01642.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 05/01/2012] [Indexed: 12/11/2022]
Abstract
In situ hybridization (ISH) enables visualization of specific nucleic acid in morphologically preserved cells and tissue sections. Detection of the HCV genomes in clinical specimens is useful for differential diagnosis, particularly between recurrent HCV infection and acute cellular rejection in transplant specimens. We optimized an ISH protocol that demonstrated sensitivity and specificity for detecting genomic and replicative form of HCV RNA in tissue biopsies. Digoxigenin (Dig)-labelled sense and anti-sense riboprobes were synthesized using a plasmid containing a fragment of the highly conserved HCV noncoding region as a template. The efficiency of the Dig-labelled riboprobes in detecting genomic and replicative-intermediate HCV RNA was analysed in 30 liver biopsies from patients infected or uninfected with HCV in a blinded study. A Huh7 cell line that stably replicates genome-length HCV RNA was developed to be used as a positive control. Negative control riboprobes were used in parallel to evaluate and control for background staining. The anti-sense probe detected HCV RNA in 20/21 specimens from HCV-infected liver tissues obtained from patients and in 0/9 samples from patients with non-HCV-related liver diseases, resulting in a sensitivity and specificity of 95% and 100%, respectively. HCV genomic RNA was variably distributed in tissue sections and was located primarily in the perinuclear regions in hepatocytes. Detection of HCV RNA by our optimized ISH protocol appears to be a sensitive and specific method when processing clinical specimens. It may also be revealing when exploring the pathophysiology of HCV infection by verifying the presence of viral genetic material within heptocytes and other cellular elements of diseased liver tissue. This methodology might also evaluate the response to antiviral therapies by demonstrating the absence or alteration of genetic material in clinical specimens from successfully treated patients.
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Affiliation(s)
- G Li
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
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12
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TMC647055, a potent nonnucleoside hepatitis C virus NS5B polymerase inhibitor with cross-genotypic coverage. Antimicrob Agents Chemother 2012; 56:4676-84. [PMID: 22710121 DOI: 10.1128/aac.00245-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Hepatitis C virus (HCV) infection is a major global health burden and is associated with an increased risk of liver cirrhosis and hepatocellular carcinoma. There remains an unmet medical need for efficacious and safe direct antivirals with complementary modes of action for combination in treatment regimens to deliver a high cure rate with a short duration of treatment for HCV patients. Here we report the in vitro inhibitory activity, mode of action, binding kinetics, and resistance profile of TMC647055, a novel and potent nonnucleoside inhibitor of the HCV NS5B RNA-dependent RNA polymerase. In vitro combination studies with an HCV NS3/4A protease inhibitor demonstrated potent suppression of HCV RNA replication, confirming the potential for combination of these two classes in the treatment of chronic HCV infection. TMC647055 is a potent nonnucleoside NS5B polymerase inhibitor of HCV replication with a promising in vitro biochemical, kinetic, and virological profile that is currently undergoing clinical evaluation.
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13
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Paulson MS. Generation and quantitation of infectious hepatitis C virus derived from cell culture (HCVcc). CURRENT PROTOCOLS IN PHARMACOLOGY 2011; Chapter 13:Unit 13B.4. [PMID: 21935897 DOI: 10.1002/0471141755.ph13b04s51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The development of robust genotype 1b and genotype 1a hepatitis C virus (HCV) replicon systems has enabled the convenient in vitro study of part of the virus life cycle. This unit describes detailed protocols for generating and measuring infectious HCV, or cell-culture-derived infectious HCV (HCVcc). The HCVcc infectious system has two essential components: (1) cells that are permissive to de novo infection and allow effective replication of the full virus life cycle; and (2) a virus genome that has robust and efficient replication in tissue culture. The assays in this unit are based on protocols designed for Huh-7-derived cell lines that allow robust replication of HCV and are permissive to infection. These protocols are important for the implementation of drug discovery efforts relative to the entire infectious virus life cycle.
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14
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Abstract
The development and approval of direct-acting antiviral agents looks set to transform the treatment of chronic hepatitis C infection. Among the agents in development are novel compounds that inhibit the function of the NS5A protein: a pleiotropic protein with a complex and essential role in viral replication. Preclinical studies have demonstrated the potency of these agents across a broad range of viral genotypes, and in early phase trials, they rapidly suppressed viral replication when administered as monotherapy or in combination with pegylated interferon-α and ribavirin. The discovery and development of NS5A replication complex inhibitors is summarized in this review.
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Affiliation(s)
- Robert G Gish
- Division of Gastroenterology, University of California at San Diego, San Diego, CA 92103-8413, USA.
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15
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Soriano V, Vispo E, Poveda E, Labarga P, Martin-Carbonero L, Fernandez-Montero JV, Barreiro P. Directly acting antivirals against hepatitis C virus. J Antimicrob Chemother 2011; 66:1673-86. [PMID: 21652618 DOI: 10.1093/jac/dkr215] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The approval of directly acting antivirals (DAA) for the treatment of chronic hepatitis C virus (HCV) infection will represent a major breakthrough for the 180 million persons infected worldwide. Paradoxically, hepatitis C is the only human chronic viral disease that can be cured, as all other pathogenic viruses infecting humans either display self-limited courses or establish non-eradicable persistent infections. Until now, treatment of chronic hepatitis C consisted of the combination of peginterferon-α plus ribavirin, which provided limited rates of cure and was associated with frequent side effects. Several DAA have been identified that inhibit the NS3 protease, the NS5B polymerase or the NS5A replication complex, and have entered the final steps of clinical development. These molecules, coupled with significant progress made in the recognition of more potent and safe interferon forms (e.g. interferon-λ) and host protein targets (e.g. alisporivir), are opening a new era in hepatitis C therapeutics. The expectations are so great that, to some extent, it is reminiscent of what happened in 1996 in the HIV field when the introduction of the first protease inhibitors as part of triple combinations revolutionized antiretroviral therapy. To maximize treatment success and reduce the likelihood of drug resistance selection, a proper individualization of hepatitis C therapy will be required, choosing the most convenient drugs and strategies according to distinct viral and host profiles. The complexity of HCV therapeutics has reached a point that presumably will lead to the birth of a new specialist, the HCV doctor.
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Affiliation(s)
- Vincent Soriano
- Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain.
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16
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Preexisting drug-resistance mutations reveal unique barriers to resistance for distinct antivirals. Proc Natl Acad Sci U S A 2011; 108:10290-5. [PMID: 21646519 DOI: 10.1073/pnas.1101515108] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Clinical trials of direct-acting antiviral agents in patients chronically infected with hepatitis C virus (HCV) have demonstrated that viral resistance is detected rapidly during monotherapy. In patients, HCV does not exist as a single, genetically homogenous virus but rather as a population of variants termed "quasispecies." Preexisting variants resistant to specific antiviral drugs, overlooked in traditional hit-to-lead discovery efforts, may be responsible for these poor clinical outcomes. To enable real-time studies of resistance emergence in live cells, we established fluorescent protein-labeled HCV replicon cell lines. We validated these cell lines by demonstrating that antiviral susceptibility and the selection of signature resistance mutations for various drug classes are similar to traditional replicon cell lines. By quantifying the kinetics and uniformity of replication within colonies of drug-resistant fluorescent replicon cells, we showed that resistance emerged from a single cell and preexisted in a treatment-naive replicon population. Within this population, we determined the relative frequency of preexisting replicons capable of establishing foci during treatment with distinct antivirals. By measuring relative frequency as a function of dose, we quantitatively ranked distinct antiviral molecules on the basis of their distinct barriers to resistance. These insights into RNA virus quasispecies structure provide guidance for selecting clinical drug concentrations and selecting antiviral drug combinations most likely to suppress resistance.
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17
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Antiviral activity and mode of action of TMC647078, a novel nucleoside inhibitor of the hepatitis C virus NS5B polymerase. Antimicrob Agents Chemother 2011; 55:3812-20. [PMID: 21576430 DOI: 10.1128/aac.00214-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Chronic infection with hepatitis C virus (HCV) is a major global health burden and is associated with an increased risk of liver cirrhosis and hepatocellular carcinoma. Current therapy for HCV infection has limited efficacy, particularly against genotype 1 virus, and is hampered by a range of adverse effects. Therefore, there is a clear unmet medical need for efficacious and safe direct antiviral drugs for use in combination with current treatments to increase cure rates and shorten treatment times. The broad genotypic coverage achievable with nucleosides or nucleotides and the high genetic barrier to resistance of these compounds observed in vitro and in vivo suggest that this class of inhibitors could be a valuable component of future therapeutic regimens. Here, we report the in vitro inhibitory activity and mode of action of 2'-deoxy-2'-spirocyclopropylcytidine (TMC647078), a novel and potent nucleoside inhibitor of the HCV NS5B RNA-dependent RNA polymerase that causes chain termination of the nascent HCV RNA chain. In vitro combination studies with a protease inhibitor resulted in additive efficacy in the suppression of HCV RNA replication, highlighting the potential for the combination of these two classes in the treatment of chronic HCV infection. No cytotoxic effects were observed in various cell lines. Biochemical studies indicated that TMC647078 is phosphorylated mainly by deoxycytidine kinase (dCK) without inhibiting the phosphorylation of the natural substrate, and high levels of triphosphate were observed in Huh7 cells and in primary hepatocytes in vitro. TMC647078 is a potent novel nucleoside inhibitor of HCV replication with a promising in vitro virology and biology profile.
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18
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Selection of clinically relevant protease inhibitor-resistant viruses using the genotype 2a hepatitis C virus infection system. Antimicrob Agents Chemother 2011; 55:2197-205. [PMID: 21357305 DOI: 10.1128/aac.01382-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Treatment of patients infected with hepatitis C virus (HCV) with direct acting antivirals can lead to the emergence of drug-resistant variants that may pose a long-term threat to viral eradication. HCV replicons have been used to select resistance mutations; however, genotype 2a JFH-1-based viruses provide the opportunity to perform resistance selection in a bona fide infection system. In this study, we used a tissue culture-adapted J6/JFH-1 virus to select resistance to the NS3 protease inhibitors BILN-2061 and VX-950. Lunet-CD81 cells were infected with J6/JFH-1 virus and maintained in the presence of inhibitors until high-titer viral supernatant was produced. Viral supernatants were passaged over naive cells at escalating drug concentrations, and the resulting viruses were then characterized. Three NS3 resistance mutations were identified in BILN-2061-resistant viruses: A156G, D168A, and D168V. Interestingly, D168A, D168V, and A156T/V, but not A156G, were selected in parallel using a genotype 2a replicon. For VX-950, the T54A and A156S NS3 resistance mutations were identified in the virus selections, whereas only A156T/V emerged in genotype 2a replicon selections. Of note, VX-950 resistance mutations selected using the 2a virus (T54A and A156S) were also observed during VX-950 clinical studies in genotype 2 patients. We also performed viral fitness evaluations and determined that the mutations selected in the viral system did not confer marked reductions in virus production kinetics or peak titers. Overall, the HCV infection system is an efficient tool for drug resistance selections and has advantages for the rapid identification and characterization of clinically relevant resistance mutations.
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19
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Yan R, Zhao Z, He Y, Wu L, Cai D, Hong W, Wu Y, Cao Z, Zheng C, Li W. A new natural α-helical peptide from the venom of the scorpion Heterometrus petersii kills HCV. Peptides 2011; 32:11-9. [PMID: 20950663 DOI: 10.1016/j.peptides.2010.10.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/06/2010] [Accepted: 10/06/2010] [Indexed: 11/29/2022]
Abstract
Hepatitis C virus (HCV) is a major cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma. There is no vaccine available for HCV, and almost half of patients cannot be cured using standard combination therapy. Thus, new anti-HCV strategies and drugs are urgently needed. Here, the gene encoding a new α-helical peptide, Hp1090, was screened from the venomous gland cDNA library of the scorpion Heterometrus petersii. Structural analysis showed that Hp1090 is an amphipathic α-helical peptide. In vitro HCV RNA inhibitory assays indicated that Hp1090 peptide inhibited HCV infection with an IC(50) of 7.62 μg/ml (5.0 μM), whereas Hp1035 peptide, showing high homology to Hp1090, exhibited no anti-HCV activity. Hp1090 acted as a viricide against HCV particles in vitro and prevented the initiation of HCV infection. Furthermore, this peptide interacted with HCV particles directly and rapidly permeabilized phospholipid membranes. Collectively, it seems that Hp1090 is virocidal for HCV in vitro, directly interacting with the viral membrane and decreasing the virus infectivity. These results suggest that Hp1090 could be considered an anti-HCV lead compound with virocidal mechanism that offers a potential therapeutic approach to HCV infection. Our work opens a new avenue for antiviral drug discovery in natural scorpion venom.
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Affiliation(s)
- Ran Yan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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20
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Zhu T, Fawzi MB, Flint M, Kong F, Szeliga J, Tsao R, Howe AY, Pan W. Design and synthesis of HCV agents with sequential triple inhibitory potentials. Bioorg Med Chem Lett 2010; 20:5212-6. [DOI: 10.1016/j.bmcl.2010.06.156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 06/30/2010] [Indexed: 12/26/2022]
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21
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Tracking the evolution of multiple in vitro hepatitis C virus replicon variants under protease inhibitor selection pressure by 454 deep sequencing. J Virol 2010; 84:11124-33. [PMID: 20739521 DOI: 10.1128/jvi.01217-10] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Resistance to hepatitis C virus (HCV) inhibitors targeting viral enzymes has been observed in in vitro replicon studies and during clinical trials. The factors determining the emergence of resistance and the changes in the viral quasispecies population under selective pressure are not fully understood. To assess the dynamics of variants emerging in vitro under various selective pressures with TMC380765, a potent macrocyclic HCV NS3/4A protease inhibitor, HCV genotype 1b replicon-containing cells were cultured in the presence of a low, high, or stepwise-increasing TMC380765 concentration(s). HCV replicon RNA from representative samples thus obtained was analyzed using (i) population, (ii) clonal, and (iii) 454 deep sequencing technologies. Depending on the concentration of TMC380765, distinct mutational patterns emerged. In particular, culturing with low concentrations resulted in the selection of low-level resistance mutations (F43S and A156G), whereas high concentrations resulted in the selection of high-level resistance mutations (A156V, D168V, and D168A). Clonal and 454 deep sequencing analysis of the replicon RNA allowed the identification of low-frequency preexisting mutations possibly contributing to the mutational pattern that emerged. Stepwise-increasing TMC380765 concentrations resulted in the emergence and disappearance of multiple replicon variants in response to the changing selection pressure. Moreover, two different codons for the wild-type amino acids were observed at certain NS3 positions within one population of replicons, which may contribute to the emerging mutational patterns. Deep sequencing technologies enabled the study of minority variants present in the HCV quasispecies population present at baseline and during antiviral drug pressure, giving new insights into the dynamics of resistance acquisition by HCV.
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22
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Viral response to specifically targeted antiviral therapy for hepatitis C and the implications for treatment success. CANADIAN JOURNAL OF GASTROENTEROLOGY = JOURNAL CANADIEN DE GASTROENTEROLOGIE 2010; 24:385-90. [PMID: 20559582 DOI: 10.1155/2010/125435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Currently, hepatitis C virus (HCV) antiviral therapy is characterized by long duration, a multitude of side effects, difficult administration and suboptimal success; clearly, alternatives are needed. Collectively, specifically targeted antiviral therapy for HCV (STAT-C) molecules achieve rapid viral suppression and very high rapid virological response rates, and improve sustained virological response rates. The attrition rate of agents within this class has been high due to various toxicities. Regardless, several STAT-C molecules are poised to become the standard of care for HCV treatment in the foreseeable future. Optimism must be tempered with concerns related to the rapid development of drug resistance with resulting HCV rebound. Strategies including induction dosing with interferon and ribavirin, use of combination high-potency STAT-C molecules and an intensive emphasis on adherence to HCV antiviral therapy will be critical to the success of this promising advance in HCV therapy.
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23
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Raney KD, Sharma SD, Moustafa IM, Cameron CE. Hepatitis C virus non-structural protein 3 (HCV NS3): a multifunctional antiviral target. J Biol Chem 2010; 285:22725-31. [PMID: 20457607 PMCID: PMC2906261 DOI: 10.1074/jbc.r110.125294] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hepatitis C virus non-structural protein 3 contains a serine protease and an RNA helicase. Protease cleaves the genome-encoded polyprotein and inactivates cellular proteins required for innate immunity. Protease has emerged as an important target for the development of antiviral therapeutics, but drug resistance has turned out to be an obstacle in the clinic. Helicase is required for both genome replication and virus assembly. Mechanistic and structural studies of helicase have hurled this enzyme into a prominent position in the field of helicase enzymology. Nevertheless, studies of helicase as an antiviral target remain in their infancy.
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Affiliation(s)
- Kevin D. Raney
- From the
Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and
| | - Suresh D. Sharma
- the
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Ibrahim M. Moustafa
- the
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Craig E. Cameron
- the
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
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Cummings MD, Lindberg J, Lin TI, de Kock H, Lenz O, Lilja E, Felländer S, Baraznenok V, Nyström S, Nilsson M, Vrang L, Edlund M, Rosenquist A, Samuelsson B, Raboisson P, Simmen K. Induced-fit binding of the macrocyclic noncovalent inhibitor TMC435 to its HCV NS3/NS4A protease target. Angew Chem Int Ed Engl 2010; 49:1652-5. [PMID: 20166108 DOI: 10.1002/anie.200906696] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Salloum S, Kluge SF, Kim AY, Roggendorf M, Timm J. The resistance mutation R155K in the NS3/4A protease of hepatitis C virus also leads the virus to escape from HLA-A*68-restricted CD8 T cells. Antiviral Res 2010; 87:272-5. [PMID: 20488208 DOI: 10.1016/j.antiviral.2010.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 05/06/2010] [Accepted: 05/12/2010] [Indexed: 12/31/2022]
Abstract
The NS3/4A serine protease of the hepatitis C virus (HCV) is one of the most attractive targets for specific antiviral agents. However, mutations conferring resistance may decrease the efficacy of these drugs. Although the level of resistance associated with specific mutations differs between different compounds, substitutions R155K and A156T reduce susceptibility to all protease inhibitors published so far. Interestingly, variants harboring the resistant mutation R155K were also detected as the predominant quasispecies in some treatment-naïve patients. Of note, key positions for resistance overlap with the HLA-A*68-restricted epitope HAVGIFRAAV(1175-1184). The aim of our study was to analyze the impact of protease inhibitor resistance mutations on the replication level and the antiviral CD8 T cell response against this HCV epitope. Our findings suggest that the R155K variant is associated with a relatively high replication level and with a substantial loss of cross-recognition by specific CD8 T cells targeting the epitope HAVGIFRAAV(1175-1184), providing a possible explanation for its existence in the absence of drug selection pressure.
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Affiliation(s)
- Shadi Salloum
- Institute for Virology, University of Duisburg-Essen, Virchowstrasse 179, 45147 Essen, Germany
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26
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Andrew Knight D, Hickey TE, Bongard JE, Thach DC, Yngard R, Chang EL. Differential effects of Co(III), Ni(II), and Ru(III) amine complexes on Sindbis virus. J Inorg Biochem 2010; 104:592-8. [DOI: 10.1016/j.jinorgbio.2010.01.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 01/27/2010] [Accepted: 01/28/2010] [Indexed: 11/16/2022]
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27
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In vitro resistance profile of the hepatitis C virus NS3/4A protease inhibitor TMC435. Antimicrob Agents Chemother 2010; 54:1878-87. [PMID: 20176898 DOI: 10.1128/aac.01452-09] [Citation(s) in RCA: 198] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
TMC435 is a small-molecule inhibitor of the NS3/4A serine protease of hepatitis C virus (HCV) currently in phase 2 development. The in vitro resistance profile of TMC435 was characterized by selection experiments with HCV genotype 1 replicon cells and the genotype 2a JFH-1 system. In 80% (86/109) of the sequences from genotype 1 replicon cells analyzed, a mutation at NS3 residue D168 was observed, with changes to V or A being the most frequent. Mutations at NS3 positions 43, 80, 155, and 156, alone or in combination, were also identified. A transient replicon assay confirmed the relevance of these positions for TMC435 inhibitory activity. The change in the 50% effective concentrations (EC(50)s) observed for replicons with mutations at position 168 ranged from <10-fold for those with the D168G or D168N mutation to approximately 2,000-fold for those with the D168V or D168I mutation, compared to the EC(50) for the wild type. Of the positions identified, mutations at residue Q80 had the least impact on the activity of TMC435 (<10-fold change in EC(50)s), while greater effects were observed for some replicons with mutations at positions 43, 155, and 156. TMC435 remained active against replicons with the specific mutations observed after in vitro or in vivo exposure to telaprevir or boceprevir, including most replicons with changes at positions 36, 54, and 170 (<3-fold change in EC(50)s). Replicons carrying mutations affecting the activity of TMC435 remained fully susceptible to alpha interferon and NS5A and NS5B inhibitors. Finally, combinations of TMC435 with alpha interferon and NS5B polymerase inhibitors prevented the formation of drug-resistant replicon colonies.
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Cummings M, Lindberg J, Lin TI, de Kock H, Lenz O, Lilja E, Felländer S, Baraznenok V, Nyström S, Nilsson M, Vrang L, Edlund M, Rosenquist Å, Samuelsson B, Raboisson P, Simmen K. Induced-Fit Binding of the Macrocyclic Noncovalent Inhibitor TMC435 to its HCV NS3/NS4A Protease Target. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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29
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Abstract
Hepatitis C virus (HCV) causes significant morbidity and mortality worldwide with nearly 3% of the world population infected by this virus. Fortunately, this virus does not establish latency, and hence it may be possible to eradicate it. HCV is strongly associated with liver cirrhosis and hepatocellular carcinoma and is currently treated with pegylated interferon-alpha (peg-IFN-alpha) and ribavirin. Unfortunately, these limited treatment options often produce significant side effects, and currently, complete eradication of virus with combined drug modalities has not yet been achieved for the majority of chronically HCV-infected individuals. Restricted treatment options, lack of a universal cure for HCV and the link between chronic infection, liver cirrhosis and hepatocellular carcinoma necessitate design of novel drugs and treatment options. Understanding the relationship between the immune response, viral clearance and inhibition of viral replication with pharmacology-based design can ultimately allow for complete eradication of HCV. This review focuses upon significant novel preclinical and clinical specifically targeted antiviral therapy (STAT-C) drugs under development, highlights their mechanism of action, and discusses their impact on systemic viral loads and permanent clearance of infection.
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Affiliation(s)
- R F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Veterans Affairs Medical Center/Emory University School of Medicine, Atlanta, GA, USA.
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30
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Beaulieu PL. Recent advances in the development of NS5B polymerase inhibitors for the treatment of hepatitis C virus infection. Expert Opin Ther Pat 2009; 19:145-64. [PMID: 19441916 DOI: 10.1517/13543770802672598] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND 170 to 200 million people worldwide are believed to suffer from chronic hepatitis C virus (HCV) infection, a blood-born disease that targets the liver and progresses to organ cirrhosis and primary cancer in a significant proportion of patients. The currently available treatment has limited efficacy and suffers from restricting side effects. HCV infection is the principal cause of liver transplant in industrialized nations and between 8000 and 10,000 deaths result annually from the disease in the United States alone. Virus-specific, more efficacious, and better-tolerated anti-HCV therapies are thus required to address the unmet medical need. OBJECTIVE To review progress achieved since 2005 in the development of HCV NS5B polymerase inhibitors as potential therapy for the treatment of HCV infection with a primary focus on available patent and medical literature. RESULTS/CONCLUSION Several classes of small-molecule inhibitors of HCV NS5B have progressed into clinical development and demonstrated efficacy in reducing viral load in infected patients. The results so far provide an encouraging foundation for the development of novel, more tolerable therapies and addressing emergence of resistance through combination of antiviral agents with complementary mechanisms of action.
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WEISS JJ, BRÄU N, STIVALA A, SWAN T, FISHBEIN D. Review article: adherence to medication for chronic hepatitis C - building on the model of human immunodeficiency virus antiretroviral adherence research. Aliment Pharmacol Ther 2009; 30:14-27. [PMID: 19416131 PMCID: PMC3102513 DOI: 10.1111/j.1365-2036.2009.04004.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Treatment of hepatitis C virus (HCV) infection with pegylated interferon/ribavirin achieves sustained virological response in up to 56% of HCV mono-infected patients and 40% of HCV/human immunodeficiency virus (HIV)-co-infected patients. The relationship of patient adherence to outcome warrants study. AIM To review comprehensively research on patient-missed doses to HCV treatment and discuss applicable research from adherence to HIV antiretroviral therapy. METHODS Publications were identified by PubMed searches using the keywords: adherence, compliance, hepatitis C virus, interferon and ribavirin. RESULTS The term 'non-adherence' differs in how it is used in the HCV from the HIV literature. In HCV, 'non-adherence' refers primarily to dose reductions by the clinician and early treatment discontinuation. In contrast, in HIV, 'non-adherence' refers primarily to patient-missed doses. Few data have been published on the rates of missed dose adherence to pegylated interferon/ribavirin and its relationship to virological response. CONCLUSIONS As HCV treatment becomes more complex with new classes of agents, adherence will be increasingly important to treatment success as resistance mutations may develop with suboptimal dosing of HCV enzyme inhibitors. HIV adherence research can be applied to that on HCV to establish accurate methods to assess adherence, investigate determinants of non-adherence and develop strategies to optimize adherence.
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Affiliation(s)
- J. J. WEISS
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
| | - N. BRÄU
- Department of Medicine, Mount Sinai School of Medicine, New York, NY, USA
,Veterans Affairs Medical Center, Infectious Disease Section, Bronx, NY, USA
| | - A. STIVALA
- Department of Medicine, Mount Sinai School of Medicine, New York, NY, USA
| | - T. SWAN
- Treatment Action Group, New York, NY, USA
| | - D. FISHBEIN
- Department of Medicine, Mount Sinai School of Medicine, New York, NY, USA
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32
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Abstract
Hepatitis C virus (HCV) has a high propensity to establish chronic infection with end-stage liver disease. The high turnover of virus particles and high transcription error rates due to lack of proof-reading function of the viral polymerase imply that HCV exists as quasispecies, thus enabling the virus to evade the host immune response. Clearance of the virus is characterized by a multispecific, vigorous and persistent T-cell response, whereas T-cell responses are weak, narrow and transient in patients who develop chronic infection. At present, standard treatment is a combination of pegylated interferon-alpha and ribavirin, with a sustained viral response rate of 40-80%, depending on genotype. The mechanisms for the observed synergistic effects of the two drugs are still not known in detail, but in addition to direct antiviral mechanisms, the immunomodulatory effects of both drugs seem to be important, with a shift from Th2- to Th1-cytokine profiles in successfully treated patients. This article describes virus-host relations in the natural course of HCV infection and during treatment.
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Affiliation(s)
- Helge Myrmel
- Department of Microbiology and Immunology, Haukeland University Hospital, Bergen, Norway.
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33
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Novel imino sugar derivatives demonstrate potent antiviral activity against flaviviruses. Antimicrob Agents Chemother 2009; 53:1501-8. [PMID: 19223639 DOI: 10.1128/aac.01457-08] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Imino sugars, such as N-butyl-deoxynojirimycin and N-nonyl-deoxynojirimycin (NNDNJ), are glucose analogues that selectively inhibit cellular alpha-glucosidase I and II in the endoplasmic reticulum and exhibit antiviral activities against many types of enveloped viruses. Although these molecules have broad-spectrum antiviral activity, their development has been limited by a lack of efficacy and/or selectivity. We have previously reported that a DNJ derivative with a hydroxylated cyclohexyl side chain, called OSL-95II, has an antiviral efficacy similar to that of NNDNJ but significantly less toxicity. Building upon this observation, a family of imino sugar derivatives containing an oxygenated side chain and terminally restricted ring structures were synthesized and shown to have low cytotoxicity and superior antiviral activity against members of the Flaviviridae family, including bovine viral diarrhea virus, dengue virus (DENV), and West Nile virus. Of particular interest is that several of these novel imino sugar derivatives, such as PBDNJ0801, PBDNJ0803, and PBDNJ0804, potently inhibit DENV infection in vitro, with 90% effective concentration values at submicromolar concentrations and selectivity indices greater than 800. Therefore, these compounds represent the best in their class and may offer realistic candidates for the development of antiviral therapeutics against human DENV infections.
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34
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Soriano V, Peters MG, Zeuzem S. New therapies for hepatitis C virus infection. Clin Infect Dis 2009; 48:313-20. [PMID: 19123867 DOI: 10.1086/595848] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Chronic hepatitis C virus (HCV) infection remains a global health threat with approximately 175 million carriers worldwide. Currently, treatment consists of pegylated interferon alpha plus ribavirin for 12-72 weeks, depending on HCV genotype, baseline viral load, and initial virological response to therapy. Serious adverse effects and limited sustained virological responses with this therapy warrant the need for novel HCV therapies. Specifically targeted antiviral therapies designed to inhibit the HCV serine protease and the RNA-dependent RNA polymerase have recently entered clinical development. Herein, the main characteristics of these new antiviral agents and the most important challenges arising with their use--namely, toxicities and rapid selection of resistance--are discussed.
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Affiliation(s)
- Vincent Soriano
- Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain.
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35
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Meanwell NA, Kadow JF, Scola PM. Chapter 20 Progress towards the Discovery and Development of Specifically Targeted Inhibitors of Hepatitis C Virus. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2009. [DOI: 10.1016/s0065-7743(09)04420-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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36
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Kim AY, Timm J. Resistance mechanisms in HCV: from evolution to intervention. Expert Rev Anti Infect Ther 2008; 6:463-78. [PMID: 18662114 DOI: 10.1586/14787210.6.4.463] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Recent advances in our understanding of the HCV life cycle and the functions of virally encoded proteins enabled the development of specifically targeted antiviral therapies for HCV, which directly inhibit HCV replication. Early clinical trials show great efficacy; however, from the first trials it became evident that, similar to HIV and HBV, selection of resistant variants will be problematic. Error-prone replication of HCV, resulting in a complex quasispecies population within each infected individual, enables rapid adaptation to changing environments. In this review, the evolutionary mechanisms involved in the selection process resulting in drug resistance are discussed. We give an overview of the resistance profiles to recently developed HCV protease and polymerase inhibitors and discuss potential implications for future treatment developments.
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Affiliation(s)
- Arthur Y Kim
- Partners AIDS Research Center, Massachusetts General Hospital/Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA.
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37
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Combinations of cyclophilin inhibitor NIM811 with hepatitis C Virus NS3-4A Protease or NS5B polymerase inhibitors enhance antiviral activity and suppress the emergence of resistance. Antimicrob Agents Chemother 2008; 52:3267-75. [PMID: 18591281 DOI: 10.1128/aac.00498-08] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Chronic hepatitis C virus (HCV) infection remains a major global health burden while current interferon-based therapy is suboptimal. Efforts to develop more effective antiviral agents mainly focus on two viral targets: NS3-4A protease and NS5B polymerase. However, resistant mutants against these viral specific inhibitors emerge quickly both in vitro and in patients, particularly in the case of monotherapy. An alternative and complementary strategy is to target host factors such as cyclophilins that are also essential for viral replication. Future HCV therapies will most likely be combinations of multiple drugs of different mechanisms to maximize antiviral activity and to suppress the emergence of resistance. Here, the effects of combining a host cyclophilin inhibitor NIM811 with other viral specific inhibitors were investigated in vitro using HCV replicon. All of the combinations led to more pronounced antiviral effects than any single agent, with no significant increase of cytotoxicity. Moreover, the combination of NIM811 with a nucleoside (NM107) or a non-nucleoside (thiophene-2-carboxylic acid) polymerase inhibitor was synergistic, while the combination with a protease inhibitor (BILN2061) was additive. Resistant clones were selected in vitro with these inhibitors. Interestingly, it was much more difficult to develop resistance against NIM811 than viral specific inhibitors. No cross-resistance was observed among these inhibitors. Most notably, NIM811 was highly effective in blocking the emergence of resistance when used in combination with viral protease or polymerase inhibitors. Taken together, these results illustrate the significant advantages of combining inhibitors targeting both viral and host factors as key components of future HCV therapies.
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38
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Mascolini M, Richman D, Larder B, Mellors J, Boucher CAB. Clinical Implications of Resistance to Antiretrovirals: New Resistance Technologies and Interpretations. Antivir Ther 2008. [DOI: 10.1177/135965350801300211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Understanding resistance to antiretroviral therapy plays an ever more crucial role in managing HIV infection as new agents – including several in new antiretroviral classes – promise better control of multidrug-resistant virus in the developed world. Yet these new drugs have different, and often complex, resistance profiles. At the same time, resistance has assumed a key role in developing countries as access to additional antiretrovirals expands in the face of first-line regimen failures. Every year the International HIV Drug Resistance Workshop gathers leading investigators and resistance-savvy clinicians to share unpublished, peer-reviewed research on the mechanisms, pathogenesis, epidemiology, and clinical implications of resistance to licensed and experimental antivirals. The 2007 workshop, held on 12–16 June, proved particularly notable for its exploration of resistance to two new antiretroviral classes, integrase inhibitors and CCR5 antagonists, as well as to agents that control hepatitis C virus (HCV) infection. This report summarizes most oral presentations from the workshop and many posters.
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Affiliation(s)
| | - Douglas Richman
- VA San Diego Healthcare System and University of California, San Diego, USA
| | | | | | - Charles AB Boucher
- Erasmus Medical Center Rotterdam and University Hospital Utrecht, the Netherlands
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