151
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Ma Z, Zhang W, Wang L, Zhu M, Wang H, Feng WH, Ng TB. A novel compound from the mushroom Cryptoporus volvatus inhibits porcine reproductive and respiratory syndrome virus (PRRSV) in vitro. PLoS One 2013; 8:e79333. [PMID: 24260198 PMCID: PMC3832501 DOI: 10.1371/journal.pone.0079333] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 09/29/2013] [Indexed: 11/20/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS), caused by PRRS virus (PRRSV), is a serious contagious disease in the swine industry. At present, there are no effective control strategies against PRRSV. Thus, there is an urgent need for new treatment regimens that have efficacious antiviral activity to compensate for vaccines. The anti-infective effect of Cryptoporus volvatus has previously been demonstrated in Tradational Chinese Medicine. In this report, we expected to identify a new anti-PRRSV agent in the aqueous extract of C. volvatus, by employing a combination of modern chromatographic purification techniques and indirect immunofluorescence assay (IFA). Our results showed that C. volvatus extracts from every separation step differed in their inhibitory potency on PRRSV. One anti-PRRSV component designated as CM-H-L-5 was isolated from water-soluble fraction of C. volvatus. The inhibition induced by CM-H-L-5 occurred in a dose-dependent manner. CM-H-L-5 appeared to be a low-molecular-weight polyol fragment with amide groups and carboxylic acid groups. Collectively, our findings imply that CM-H-L-5 from the aqueous extract of C. volvatus has the potential to be used for anti-PRRSV therapy.
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Affiliation(s)
- Zengqiang Ma
- State Key Laboratory for Agrobiotechnology and Department of Microbiology, China Agricultural University, Beijing, China
| | - Weiwei Zhang
- State Key Laboratory for Agrobiotechnology and Department of Microbiology, China Agricultural University, Beijing, China
| | - Li Wang
- State Key Laboratory for Agrobiotechnology and Department of Microbiology, China Agricultural University, Beijing, China
| | - Mengjuan Zhu
- State Key Laboratory for Agrobiotechnology and Department of Microbiology, China Agricultural University, Beijing, China
| | - Hexiang Wang
- State Key Laboratory for Agrobiotechnology and Department of Microbiology, China Agricultural University, Beijing, China
- * E-mail: (HW); (WF); (TN)
| | - Wen-hai Feng
- State Key Laboratory for Agrobiotechnology and Department of Microbiology, China Agricultural University, Beijing, China
- * E-mail: (HW); (WF); (TN)
| | - Tzi Bun Ng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
- * E-mail: (HW); (WF); (TN)
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152
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Wasik S, Jackowiak P, Figlerowicz M, Blazewicz J. Multi-agent model of hepatitis C virus infection. Artif Intell Med 2013; 60:123-31. [PMID: 24309221 DOI: 10.1016/j.artmed.2013.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 10/23/2013] [Accepted: 11/01/2013] [Indexed: 01/04/2023]
Abstract
OBJECTIVES The objective of this study is to design a method for modeling hepatitis C virus (HCV) infection using multi-agent simulation and to verify it in practice. METHODS AND MATERIALS In this paper, first, the modeling of HCV infection using a multi-agent system is compared with the most commonly used model type, which is based on differential equations. Then, the implementation and results of the model using a multi-agent simulation is presented. To find the values of the parameters used in the model, a method using inverted simulation flow and genetic algorithm is proposed. All of the data regarding HCV infection are taken from the paper describing the model based on the differential equation to which the proposed method is compared. RESULTS Important advantages of the proposed method are noted and demonstrated: these include flexibility, clarity, re-usability and the possibility to model more complex dependencies. Then, the simulation framework that uses the proposed approach is successfully implemented in C++ and is verified by comparing it to the approach based on differential equations. The verification proves that an objective function that performs the best is the function that minimizes the maximal differences in the data. Finally, an analysis of one of the already known models is performed, and it is proved that it incorrectly models a decay in the hepatocytes number by 40%. CONCLUSIONS The proposed method has many advantages in comparison to the currently used model types and can be used successfully for analyzing HCV infection. With almost no modifications, it can also be used for other types of viral infections.
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Affiliation(s)
- Szymon Wasik
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jacek Blazewicz
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland
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153
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Ciotti M, D'Agostini C, Marrone A. Advances in the Diagnosis and Monitoring of Hepatitis C Virus Infection. Gastroenterology Res 2013; 6:161-170. [PMID: 27785248 PMCID: PMC5051090 DOI: 10.4021/gr576e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/03/2013] [Indexed: 12/18/2022] Open
Abstract
Hepatitis C virus (HCV) infection represents a major health problem worldwide. Approximately 350,000 people die every year from hepatitis C related diseases. Antiviral therapy is given to prevent such complications. Advances in serological and molecular assays greatly improved the diagnosis of hepatitis C virus infection and the management of chronically infected patients. Sensitive real-time PCR methods are currently used to monitor the response to antiviral therapy, to guide treatment decisions, and to assess the sustained virological response 24 weeks after the end of therapy. HCV genotyping is part of the pretreatment evaluation. Determination of HCV genotype is important both for tailoring antiviral treatment and for determining treatment duration. It predicts also response to therapy. With the recent introduction of the serine protease inhibitors telaprevir and boceprevir, approved for the treatment of genotype 1 chronic hepatitis C in combination with INF-a and ribavirin, subtyping has become clinically relevant. Indeed, subtypes 1a and 1b may respond differently to current telaprevir-based or boceprevir-based triple therapy. This review summarizes the most recent advances in the diagnosis and monitoring of HCV chronic infection.
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Affiliation(s)
- Marco Ciotti
- Laboratory of Molecular Virology, Polyclinic Tor Vergata Foundation, Viale Oxford 81-00133, Rome, Italy
| | - Cartesio D'Agostini
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy; Laboratory of Clinical Microbiology and Virology, Polyclinic "Tor Vergata" Foundation, Viale Oxford 81, 00133, Rome, Italy
| | - Aldo Marrone
- Internal Medicine and Hepatology, School of Medicine of Naples, Second University of Naples, Via Pansini 5, Edificio 10, 80131, Napoli, Italy
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154
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Hazuda DJ, Burroughs M, Howe AYM, Wahl J, Venkatraman S. Development of boceprevir: a first-in-class direct antiviral treatment for chronic hepatitis C infection. Ann N Y Acad Sci 2013; 1291:69-76. [PMID: 23859802 DOI: 10.1111/nyas.12218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The identification of hepatitis C virus (HCV) as the causative agent of non-A and non-B hepatitis, over 20 years ago, fueled an intensive effort to develop direct-acting antivirals targeting the viral polymerase and protease, two key proteins critical for HCV replication. However, it took more than two decades for these efforts to be realized with boceprevir, one of the two HCV protease inhibitors approved for treatment of HCV infection in 2011. The development of boceprevir is a major advancement in the ability to treat HCV infection and a significant step toward the long-term goal of eradicating chronic HCV infection. Both as a first-in-class agent and an entirely new modality for treating HCV infection, many challenges were encountered during the discovery and development of this compound. The lessons learned in overcoming these obstacles offer insights and pave the way for the newly emerging field of HCV antiviral therapeutics. This paper will describe the discovery and development of a first-in-class direct antiviral treatment for chronic hepatitis C infection, boceprevir, marketed around the world as Victrelis™.
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Affiliation(s)
- Daria J Hazuda
- Merck Research Laboratories, West Point, Pennsylvania 19486, USA.
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155
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In vitro phenotypic characterization of hepatitis C virus NS3 protease variants observed in clinical studies of telaprevir. Antimicrob Agents Chemother 2013; 57:6236-45. [PMID: 24100495 DOI: 10.1128/aac.01578-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Telaprevir is a linear, peptidomimetic small molecule that inhibits hepatitis C virus (HCV) replication by specifically inhibiting the NS3·4A protease. In phase 3 clinical studies, telaprevir in combination with peginterferon and ribavirin (PR) significantly improved sustained virologic response (SVR) rates in genotype 1 chronic HCV-infected patients compared with PR alone. In patients who do not achieve SVR after treatment with telaprevir-based regimens, variants with mutations in the NS3·4A protease region have been observed. Such variants can contribute to drug resistance and limit the efficacy of treatment. To gain a better understanding of the viral resistance profile, we conducted phenotypic characterization of the variants using HCV replicons carrying site-directed mutations. The most frequently observed (significantly enriched) telaprevir-resistant variants, V36A/M, T54A/S, R155K/T, and A156S, conferred lower-level resistance (3- to 25-fold), whereas A156T and V36M+R155K conferred higher-level resistance (>25-fold) to telaprevir. Rarely observed (not significantly enriched) variants included V36I/L and I132V, which did not confer resistance to telaprevir; V36C/G, R155G/I/M/S, V36A+T54A, V36L+R155K, T54S+R155K, and R155T+D168N, which conferred lower-level resistance to telaprevir; and A156F/N/V, V36A+R155K/T, V36M+R155T, V36A/M+A156T, T54A+A156S, T54S+A156S/T, and V36M+T54S+R155K, which conferred higher-level resistance to telaprevir. All telaprevir-resistant variants remained fully sensitive to alpha interferon, ribavirin, and HCV NS5B nucleoside and nonnucleoside polymerase inhibitors. In general, the replication capacity of telaprevir-resistant variants was lower than that of the wild-type replicon.
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156
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Resistance to HCV nucleoside analogue inhibitors of hepatitis C virus RNA-dependent RNA polymerase. Curr Opin Virol 2013; 3:508-13. [DOI: 10.1016/j.coviro.2013.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 08/12/2013] [Accepted: 08/20/2013] [Indexed: 11/20/2022]
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157
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Capobianchi MR, Giombini E, Rozera G. Next-generation sequencing technology in clinical virology. Clin Microbiol Infect 2013; 19:15-22. [PMID: 23279287 DOI: 10.1111/1469-0691.12056] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/17/2012] [Accepted: 09/22/2012] [Indexed: 12/18/2022]
Abstract
Recent advances in nucleic acid sequencing technologies, referred to as 'next-generation' sequencing (NGS), have produced a true revolution and opened new perspectives for research and diagnostic applications, owing to the high speed and throughput of data generation. So far, NGS has been applied to metagenomics-based strategies for the discovery of novel viruses and the characterization of viral communities. Additional applications include whole viral genome sequencing, detection of viral genome variability, and the study of viral dynamics. These applications are particularly suitable for viruses such as human immunodeficiency virus, hepatitis B virus, and hepatitis C virus, whose error-prone replication machinery, combined with the high replication rate, results, in each infected individual, in the formation of many genetically related viral variants referred to as quasi-species. The viral quasi-species, in turn, represents the substrate for the selective pressure exerted by the immune system or by antiviral drugs. With traditional approaches, it is difficult to detect and quantify minority genomes present in viral quasi-species that, in fact, may have biological and clinical relevance. NGS provides, for each patient, a dataset of clonal sequences that is some order of magnitude higher than those obtained with conventional approaches. Hence, NGS is an extremely powerful tool with which to investigate previously inaccessible aspects of viral dynamics, such as the contribution of different viral reservoirs to replicating virus in the course of the natural history of the infection, co-receptor usage in minority viral populations harboured by different cell lineages, the dynamics of development of drug resistance, and the re-emergence of hidden genomes after treatment interruptions. The diagnostic application of NGS is just around the corner.
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Affiliation(s)
- M R Capobianchi
- National Institute for Infectious Diseases 'L. Spallanzani', Rome, Italy.
| | - E Giombini
- National Institute for Infectious Diseases 'L. Spallanzani', Rome, Italy
| | - G Rozera
- National Institute for Infectious Diseases 'L. Spallanzani', Rome, Italy
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158
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Binder M, Sulaimanov N, Clausznitzer D, Schulze M, Hüber CM, Lenz SM, Schlöder JP, Trippler M, Bartenschlager R, Lohmann V, Kaderali L. Replication vesicles are load- and choke-points in the hepatitis C virus lifecycle. PLoS Pathog 2013; 9:e1003561. [PMID: 23990783 PMCID: PMC3749965 DOI: 10.1371/journal.ppat.1003561] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 07/02/2013] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) infection develops into chronicity in 80% of all patients, characterized by persistent low-level replication. To understand how the virus establishes its tightly controlled intracellular RNA replication cycle, we developed the first detailed mathematical model of the initial dynamic phase of the intracellular HCV RNA replication. We therefore quantitatively measured viral RNA and protein translation upon synchronous delivery of viral genomes to host cells, and thoroughly validated the model using additional, independent experiments. Model analysis was used to predict the efficacy of different classes of inhibitors and identified sensitive substeps of replication that could be targeted by current and future therapeutics. A protective replication compartment proved to be essential for sustained RNA replication, balancing translation versus replication and thus effectively limiting RNA amplification. The model predicts that host factors involved in the formation of this compartment determine cellular permissiveness to HCV replication. In gene expression profiling, we identified several key processes potentially determining cellular HCV replication efficiency. Hepatitis C is a severe disease and a prime cause for liver transplantation. Up to 3% of the world's population are chronically infected with its causative agent, the Hepatitis C virus (HCV). This capacity to establish long (decades) lasting persistent infection sets HCV apart from other plus-strand RNA viruses typically causing acute, self-limiting infections. A prerequisite for its capacity to persist is HCV's complex and tightly regulated intracellular replication strategy. In this study, we therefore wanted to develop a comprehensive understanding of the molecular processes governing HCV RNA replication in order to pinpoint the most vulnerable substeps in the viral life cycle. For that purpose, we used a combination of biological experiments and mathematical modeling. Using the model to study HCV's replication strategy, we recognized diverse but crucial roles for the membraneous replication compartment of HCV in regulating RNA amplification. We further predict the existence of an essential limiting host factor (or function) required for establishing active RNA replication and thereby determining cellular permissiveness for HCV. Our model also proved valuable to understand and predict the effects of pharmacological inhibitors of HCV and might be a solid basis for the development of similar models for other plus-strand RNA viruses.
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Affiliation(s)
- Marco Binder
- Heidelberg University, Medical Faculty, Department of Infectious Diseases, Molecular Virology, Heidelberg, Germany
| | - Nurgazy Sulaimanov
- Technische Universität Dresden, Institute for Medical Informatics and Biometry, Dresden, Germany
- Heidelberg University, ViroQuant Research Group Modeling, BioQuant BQ26, Heidelberg, Germany
| | - Diana Clausznitzer
- Technische Universität Dresden, Institute for Medical Informatics and Biometry, Dresden, Germany
| | - Manuel Schulze
- Technische Universität Dresden, Institute for Medical Informatics and Biometry, Dresden, Germany
| | - Christian M. Hüber
- Heidelberg University, Medical Faculty, Department of Infectious Diseases, Molecular Virology, Heidelberg, Germany
| | - Simon M. Lenz
- Heidelberg University, Interdisciplinary Center for Scientific Computing (IWR), Simulation and Optimization Group, Heidelberg, Germany
| | - Johannes P. Schlöder
- Heidelberg University, Interdisciplinary Center for Scientific Computing (IWR), Simulation and Optimization Group, Heidelberg, Germany
| | - Martin Trippler
- University Hospital of Essen, Department of Gastroenterology and Hepatology, Essen, Germany
| | - Ralf Bartenschlager
- Heidelberg University, Medical Faculty, Department of Infectious Diseases, Molecular Virology, Heidelberg, Germany
| | - Volker Lohmann
- Heidelberg University, Medical Faculty, Department of Infectious Diseases, Molecular Virology, Heidelberg, Germany
| | - Lars Kaderali
- Technische Universität Dresden, Institute for Medical Informatics and Biometry, Dresden, Germany
- Heidelberg University, ViroQuant Research Group Modeling, BioQuant BQ26, Heidelberg, Germany
- * E-mail:
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159
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Bartolini B, Giombini E, Zaccaro P, Selleri M, Rozera G, Abbate I, Comandini UV, Ippolito G, Solmone M, Capobianchi MR. Extent of HCV NS3 protease variability and resistance-associated mutations assessed by next generation sequencing in HCV monoinfected and HIV/HCV coinfected patients. Virus Res 2013; 177:205-8. [PMID: 23954579 DOI: 10.1016/j.virusres.2013.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 02/07/2023]
Abstract
HCV quasispecies variability represents the background for the selection of mutations and for the development of drug resistance. Natural aminoacid changes in NS3, associated with reduced protease inhibitor susceptibility, have been observed in treatment-naïve patients. Massively parallel sequencing has been used to analyze NS3 quasispecies in patients infected with HCV genotype 1, naive to anti-HCV treatment, with/without HIV-coinfection, to establish the genetic heterogeneity and the presence of amino acid substitutions at positions responsible for drug resistance. Genomes carrying substitutions represented either predominant or minority components of viral quasispecies, and were observed in 85.7% of patients. Multiple substitutions, frequently associated on the same haplotype, were observed in 46.4% of patients. High resistance combinations were not detected, neither on the same genome, nor in the whole quasispecies. Heterogeneity of HCV NS3 was lower in HIV-coinfected as compared to HCV-monoinfected patients, but factors underlying this difference remain to be established. Although the relevance of naturally occurring mutations with respect of resistance development and probability of success of direct acting antivirals is questioned, UDPS may be beneficial to help understanding viral dynamics, providing high resolution view of viral diversity.
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Affiliation(s)
- Barbara Bartolini
- "L. Spallanzani" National Institute for Infectious Diseases, Via Portuense 292, 00149 Rome, Italy
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160
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Deep sequencing analysis of HCV NS3 resistance-associated variants and mutation linkage in liver transplant recipients. PLoS One 2013; 8:e69698. [PMID: 23922778 PMCID: PMC3726766 DOI: 10.1371/journal.pone.0069698] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 06/11/2013] [Indexed: 12/22/2022] Open
Abstract
Viral variants with decreased susceptibility to HCV protease inhibitors (PIs) occur naturally and preexist at low levels within HCV populations. In patients failing PI monotherapy, single and double mutants conferring intermediate to high-level resistance to PIs have been selected in vivo. The abundance, temporal dynamics and linkage of naturally occurring resistance-associated variants (RAVs), however, have not been characterized in detail. Here, using high-density pyrosequencing, we analyzed HCV NS3 gene segments from 20 subjects with chronic HCV infection, including 12 subjects before and after liver transplantation. Bioinformatics analysis revealed that Q80 substitution was a dominant variant in 40% of the subjects, whereas other RAVs circulate at low levels within quasispecies populations. Low frequency mutation linkage was detectable by Illumina paired-end sequencing in as low as 0.5% of the mock populations constructed from in vitro RNA transcripts but were uncommon in vivo. We show that naturally occurring RAVs are common and can persist long term following liver transplant at low levels not readily detectable by conventional sequencing. Our results indicate that mutation linkage at low levels could be identified using the Illumina paired-end approach. The methods described here should facilitate the analysis of low frequency HCV drug resistance, mutation linkage and evolution, which may inform future therapeutic strategies in patients undergoing direct acting antiviral therapies.
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161
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Rapid virological response tailors the duration of treatment in hepatitis C virus genotype 3 patients treated with pegylated interferon alfa-2a and ribavirin in Pakistan. Int J Infect Dis 2013; 17:e1017-21. [PMID: 23896656 DOI: 10.1016/j.ijid.2013.05.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 05/09/2013] [Accepted: 05/22/2013] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Rapid virological response (RVR) is now thought to be the strongest predictor of sustained virological response (SVR) in hepatitis C virus (HCV) patients undergoing antiviral therapy. It can be used as a guide to individualize treatment duration. The aim of this study was to assess the role of RVR in tailoring the duration of treatment. METHODS Patients with HCV genotype 3 infections were enrolled and treated with pegylated interferon alfa-2a (PEG IFN alfa-2a) 180 μg/week and ribavirin. HCV RNA was analyzed at weeks 4, 12, 16, and 24. Treatment duration was individualized on the basis of RVR. Patients who achieved RVR and who were aged ≤ 40 years with a body mass index (BMI) ≤ 27 kg/m(2) received 16 weeks of treatment (group A). Patients who achieved RVR and were aged >40 years with a BMI >27 kg/m(2), aged >40 years with a BMI ≤ 27 kg/m(2), and aged ≤ 40 years with a BMI >27 kg/m(2) received 24 weeks of treatment (group B). Patients who did not achieve RVR but who achieved an early virological response (EVR; HCV PCR-negative or ≥ 2 log drop in HCV RNA at week 12) were treated with 24 weeks of therapy (group C). RESULTS SVR was observed in 86% in group A, 82.2% in group B, and 46.8% in group C. A difference was observed in SVR for patients with and without RVR and receiving the standard duration of treatment (82.2% vs. 46.8%, p<0 .001). The results show that the rate of SVR is not inferior in those with RVR treated with 16 weeks of therapy compared to 24 weeks (86% vs. 82.2%, p=0.004). CONCLUSIONS RVR is useful to individualize the duration of treatment and to predict the treatment outcome. A short treatment of 16 weeks is as effective as 24 weeks in HCV genotype 3 patients who achieve RVR, who have a low BMI, and are younger in age.
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162
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Ali A, Aydin C, Gildemeister R, Romano KP, Cao H, Özen A, Soumana D, Newton A, Petropoulos CJ, Huang W, Schiffer CA. Evaluating the role of macrocycles in the susceptibility of hepatitis C virus NS3/4A protease inhibitors to drug resistance. ACS Chem Biol 2013; 8:1469-78. [PMID: 23594083 DOI: 10.1021/cb400100g] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The hepatitis C virus (HCV) infects an estimated 150 million people worldwide and is the major cause of viral hepatitis, cirrhosis, and liver cancer. The available antiviral therapies, which include PEGylated interferon, ribavirin, and one of the HCV NS3/4A protease inhibitors telaprevir or boceprevir, are ineffective for some patients and cause severe side effects. More potent NS3/4A protease inhibitors are in clinical development, but the long-term effectiveness of these drugs is challenged by the development of drug resistance. Here, we investigated the role of macrocycles in the susceptibility of NS3/4A protease inhibitors to drug resistance in asunaprevir, danoprevir, vaniprevir, and MK-5172, with similar core structures but varied P2 moieties and macrocyclizations. Linear and macrocyclic analogues of these drugs were designed, synthesized, and tested against wild-type and drug-resistant variants R155K, V36M/R155K, A156T, and D168A in enzymatic and antiviral assays. Macrocyclic inhibitors were generally more potent, but the location of the macrocycle was critical for retaining activity against drug-resistant variants: the P1-P3 macrocyclic inhibitors were less susceptible to drug resistance than the linear and P2-P4 macrocyclic analogues. In addition, the heterocyclic moiety at P2 largely determined the inhibitor resistance profile, susceptibility to drug resistance, and the extent of modulation by the helicase domain. Our findings suggest that to design robust inhibitors that retain potency to drug-resistant NS3/4A protease variants, inhibitors should combine P1-P3 macrocycles with flexible P2 moieties that optimally contact with the invariable catalytic triad of this enzyme.
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Affiliation(s)
- Akbar Ali
- Department of Biochemistry and
Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Cihan Aydin
- Department of Biochemistry and
Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Reinhold Gildemeister
- Department of Biochemistry and
Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | | | - Hong Cao
- Department of Biochemistry and
Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Ayşegül Özen
- Department of Biochemistry and
Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Djade Soumana
- Department of Biochemistry and
Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Alicia Newton
- Monogram Biosciences, South San Francisco, California 94080, United States
| | | | - Wei Huang
- Monogram Biosciences, South San Francisco, California 94080, United States
| | - Celia A. Schiffer
- Department of Biochemistry and
Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
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163
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Analysis of boceprevir resistance associated amino acid variants (RAVs) in two phase 3 boceprevir clinical studies. Virology 2013; 444:329-36. [PMID: 23876458 DOI: 10.1016/j.virol.2013.06.029] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/10/2013] [Accepted: 06/25/2013] [Indexed: 12/23/2022]
Abstract
BACKGROUND We investigated the frequency of RAVs among patients failing to achieve SVR in two clinical trials. We also investigated the impact of interferon responsiveness on RAVs and specific baseline RAVs relationship with boceprevir treatment failure. METHODS Data are from 1020 patients enrolled into either SPRINT-2 or RESPOND-2; patients received a 4-week PR lead-in prior to receiving boceprevir or placebo. RAVs were analyzed via population-based sequence analysis of the NS3 protease gene (success rate of >90% at a virus level of ≥ 10,000IU/mL) RESULTS: The high SVR rate in patients who received boceprevir resulted in a low rate of RAVs; 7% was detected at baseline in all patients, which rose to 15% after treatment. However, RAVs were detected in 53% of patients that failed to achieve SVR, which declined to 22.8% 6-14 months following cessation of boceprevir therapy. Baseline RAVs alone were not predictive of virologic outcome; poor interferon responsiveness was highly predictive of non-SVR. RAVs were more frequently detected in poor interferon responders. CONCLUSIONS We detected no association between the presence of baseline amino acid variants at boceprevir resistance-associated loci and outcome in the context of good IFN response.
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164
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Guedj J, Dahari H, Uprichard SL, Perelson AS. The hepatitis C virus NS5A inhibitor daclatasvir has a dual mode of action and leads to a new virus half-life estimate. Expert Rev Gastroenterol Hepatol 2013; 7:397-9. [PMID: 23899277 PMCID: PMC4067513 DOI: 10.1586/17474124.2013.811050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jeremie Guedj
- University Paris Diderot, Sorbonne Paris Cité, 75018 Paris, France,INSERM, UMR 738, 75018 Paris, France
| | - Harel Dahari
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545,Department of Medicine, Loyola University Chicago, Maywood, IL 60153
| | | | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545,Corresponding author: Alan S. Perelson, , Phone: 505-667-6829, MS-K710, Los Alamos National Laboratory, NM 87545 USA
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Belema M, Meanwell NA, Bender JA, Lopez OD, Hewawasam P, Langley DR. Discovery and Clinical Validation of HCV Inhibitors Targeting the NS5A Protein. SUCCESSFUL STRATEGIES FOR THE DISCOVERY OF ANTIVIRAL DRUGS 2013. [DOI: 10.1039/9781849737814-00003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
HCV non‐structural protein 5A (NS5A) is a multifunctional protein that plays a diverse set of roles in the replication cycle of the virus. Although a significant level of effort has been invested over the past decade at characterizing this protein, our understanding and appreciation of its full structure and function remain far from complete. Despite these drawbacks, however, great strides have been made towards discovering potent HCV NS5A inhibitors that have exhibited promising efficacy in early clinical trials, and these inhibitors have the potential to become an integral component of effective combination therapies that are expected to emerge in the near future. Highlights of the biochemical characterization of the HCV NS5A protein, aspects of the seminal drug discovery effort that culminated in the identification of daclatasvir with which clinical proof‐of‐concept was obtained for NS5A as a target and the follow‐up efforts that identified additional inhibitors, along with findings from mode‐of‐action studies, are discussed.
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Affiliation(s)
| | | | | | | | | | - David R. Langley
- Department of Computer‐Assisted Drug Design Bristol‐Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492 USA
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166
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Rong L, Perelson AS. Mathematical analysis of multiscale models for hepatitis C virus dynamics under therapy with direct-acting antiviral agents. Math Biosci 2013; 245:22-30. [PMID: 23684949 DOI: 10.1016/j.mbs.2013.04.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 04/25/2013] [Accepted: 04/26/2013] [Indexed: 12/12/2022]
Abstract
Chronic hepatitis C virus (HCV) infection remains a world-wide public health problem. Therapy with interferon and ribavirin leads to viral elimination in less than 50% of treated patients. New treatment options aiming at a higher cure rate are focused on direct-acting antiviral agents (DAAs), which directly interfere with different steps in the HCV life cycle. In this paper, we describe and analyze a recently developed multiscale model that predicts HCV dynamics under therapy with DAAs. The model includes both intracellular viral RNA replication and extracellular viral infection. We calculate the steady states of the model and perform a detailed stability analysis. With certain assumptions we obtain analytical approximations of the viral load decline after treatment initiation. One approximation agrees well with the prediction of the model, and can conveniently be used to fit patient data and estimate parameter values. We also discuss other possible ways to incorporate intracellular viral dynamics into the multiscale model.
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Affiliation(s)
- Libin Rong
- Department of Mathematics and Statistics, Oakland University, Rochester, MI 48309, United States
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167
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Laouénan C, Guedj J, Mentré F. Clinical trial simulation to evaluate power to compare the antiviral effectiveness of two hepatitis C protease inhibitors using nonlinear mixed effect models: a viral kinetic approach. BMC Med Res Methodol 2013; 13:60. [PMID: 23617810 PMCID: PMC3651343 DOI: 10.1186/1471-2288-13-60] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 04/12/2013] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Models of hepatitis C virus (HCV) kinetics are increasingly used to estimate and to compare in vivo drug's antiviral effectiveness of new potent anti-HCV agents. Viral kinetic parameters can be estimated using non-linear mixed effect models (NLMEM). Here we aimed to evaluate the performance of this approach to precisely estimate the parameters and to evaluate the type I errors and the power of the Wald test to compare the antiviral effectiveness between two treatment groups when data are sparse and/or a large proportion of viral load (VL) are below the limit of detection (BLD). METHODS We performed a clinical trial simulation assuming two treatment groups with different levels of antiviral effectiveness. We evaluated the precision and the accuracy of parameter estimates obtained on 500 replication of this trial using the stochastic approximation expectation-approximation algorithm which appropriately handles BLD data. Next we evaluated the type I error and the power of the Wald test to assess a difference of antiviral effectiveness between the two groups. Standard error of the parameters and Wald test property were evaluated according to the number of patients, the number of samples per patient and the expected difference in antiviral effectiveness. RESULTS NLMEM provided precise and accurate estimates for both the fixed effects and the inter-individual variance parameters even with sparse data and large proportion of BLD data. However Wald test with small number of patients and lack of information due to BLD resulted in an inflation of the type I error as compared to the results obtained when no limit of detection of VL was considered. The corrected power of the test was very high and largely outperformed what can be obtained with empirical comparison of the mean VL decline using Wilcoxon test. CONCLUSION This simulation study shows the benefit of viral kinetic models analyzed with NLMEM over empirical approaches used in most clinical studies. When designing a viral kinetic study, our results indicate that the enrollment of a large number of patients is to be preferred to small population sample with frequent assessments of VL.
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Affiliation(s)
- Cédric Laouénan
- INSERM, UMR 738, Université Paris Diderot, Sorbonne Paris Cité, Paris F-75018, France.
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168
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Abstract
The addition of hepatitis C virus NS3 protease inhibitors to interferon-based regimens has dramatically improved response rates. Despite these improvements treatment is now more complex, associated with increased side effects, and has the potential to select resistant variants in those who are not cured. This article discusses the virologic underpinnings for the development of hepatitis C virus-resistant variants (with a focus on telaprevir and boceprevir) and their impact on therapeutic success. Interim guidance on the use of resistance testing and management is provided based on the limited data. Finally, resistance considerations for other classes of inhibitors and the rapidly approaching interferon-free therapeutics regimens are offered.
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Affiliation(s)
- David L Wyles
- Division of Infectious Diseases, University of California, San Diego, 9500 Gilman Drive, MC 0711, La Jolla, CA 92093, USA.
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169
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Abstract
Recent advances in understanding of the molecular characteristics of the hepatitis C virus have led to the development of novel antiviral therapeutics. Direct-acting antivirals are designed to inhibit viral targets, whereas host-targeted antivirals block host factors that are used by the virus for its own life cycle. The rapid development of agents in multiple classes has led to the promise of shorter therapy duration, an improved side effect profile, and eventually interferon-sparing regimens. This article reviews novel hepatitis C virus therapeutics in development, including mechanism of action, efficacy, and adverse effects.
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Affiliation(s)
- Jennifer Y Chen
- GI Unit, Massachusetts General Hospital, GRJ724, 55 Fruit Street, Boston, MA 02114, USA
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170
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Miller JF, Chong PY, Shotwell JB, Catalano JG, Tai VWF, Fang J, Banka AL, Roberts CD, Youngman M, Zhang H, Xiong Z, Mathis A, Pouliot JJ, Hamatake RK, Price DJ, Seal JW, Stroup LL, Creech KL, Carballo LH, Todd D, Spaltenstein A, Furst S, Hong Z, Peat AJ. Hepatitis C Replication Inhibitors That Target the Viral NS4B Protein. J Med Chem 2013; 57:2107-20. [DOI: 10.1021/jm400125h] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- John F. Miller
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Pek Y. Chong
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - J. Brad Shotwell
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - John G. Catalano
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Vincent W.-F. Tai
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Jing Fang
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Anna L. Banka
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Christopher D. Roberts
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Michael Youngman
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Huichang Zhang
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Zhiping Xiong
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Amanda Mathis
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Jeffery J. Pouliot
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Robert K. Hamatake
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Daniel J. Price
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - John W. Seal
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Lisa L. Stroup
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Katrina L. Creech
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Luz H. Carballo
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Dan Todd
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Andrew Spaltenstein
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Sylvia Furst
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Zhi Hong
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
| | - Andrew J. Peat
- GlaxoSmithKline Research and Development, 5 Moore Drive, Research Triangle Park,
North Carolina 27709, United States
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171
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Sullivan JC, De Meyer S, Bartels DJ, Dierynck I, Zhang EZ, Spanks J, Tigges AM, Ghys A, Dorrian J, Adda N, Martin EC, Beumont M, Jacobson IM, Sherman KE, Zeuzem S, Picchio G, Kieffer TL. Evolution of treatment-emergent resistant variants in telaprevir phase 3 clinical trials. Clin Infect Dis 2013; 57:221-9. [PMID: 23575197 DOI: 10.1093/cid/cit226] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Telaprevir (TVR), a hepatitis C virus (HCV) NS3/4A protease inhibitor, has been approved to treat genotype 1 HCV. To understand the clinical impact of TVR-resistant variants, we analyzed samples from patients in phase 3 clinical trials to determine the frequency and retention of TVR-resistant variants in patients who did not achieve sustained virologic response (SVR). METHODS A total of 1797 patients were treated with TVR. Resistant variants (V36A/G/I/L/M, T54A/S, I132V [subtype 1a only], R155G/K/T/M, A156F/N/S/T/V, and D168N) were identified after treatment failure and at visits thereafter, by direct (population) sequencing of the NS3/4A region. Kaplan-Meier analysis was used to determine median time to loss of these variants. RESULTS Resistant variants were observed in 77% (299/388) of patients who did not achieve SVR. Resistance occurred more commonly in subtype 1a (86%; 232/269) than subtype 1b infections (56%; 67/119). After treatment failure, 355 patients had at least 1 follow-up visit (median follow-up period: 9.6 months). Of patients with resistance at time of failure and at least 1 follow-up visit, 60% (153/254) lost resistance. Kaplan-Meier analysis, including all patients with any sequence data after treatment failure, indicated that median time to wild type was 10.6 months (95% confidence interval [CI], 9.47-12.20) in subtype 1a and 0.9 months (95% CI, 0.00-2.07) in subtype 1b infections. CONCLUSIONS After failure to achieve SVR with TVR-based treatment, resistant variants are observed in most patients. However, presumably due to the lower fitness of those variants, they tend to be replaced with wild-type virus over time.
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172
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Wyles DL. Antiviral resistance and the future landscape of hepatitis C virus infection therapy. J Infect Dis 2013; 207 Suppl 1:S33-9. [PMID: 23390303 DOI: 10.1093/infdis/jis761] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The addition of hepatitis C virus (HCV) protease inhibitors (PIs) to interferon and ribavirin therapy has significantly improved the efficacy of treatment for HCV infection. However, for patients who do not respond to therapy, the selection of HCV variants with resistance to PIs is likely. Resistant variants, such as R155K and A156T/V, result in extensive cross-resistance to other HCV PIs. Despite the rapid and frequent appearance of PI-resistant HCV variants, the long-term clinical implications are unknown. In particular, progress in the development of other HCV antivirals, such as NS5A inhibitors, next-generation NS3 protease inhibitors, and NS5B nucleoside and nonnucleoside inhibitors, has provided a broad selection of potent antivirals such that interferon-free therapy is a reality. Promising results from early stages of interferon-free trials will be reviewed.
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Affiliation(s)
- David L Wyles
- Division of Infectious Diseases, University of California-San Diego, La Jolla, CA, USA.
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173
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Watkins WJ, Desai MC. HCV versus HIV drug discovery: Déjà vu all over again? Bioorg Med Chem Lett 2013; 23:2281-7. [DOI: 10.1016/j.bmcl.2013.02.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 02/13/2013] [Accepted: 02/16/2013] [Indexed: 12/23/2022]
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174
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Dahari H, Cotler SJ, Layden TJ, Perelson AS. Understanding triphasic HCV decline during treatment in the era of IL28B polymorphisms and direct acting antiviral agents via mathematical modeling. J Hepatol 2013; 58:840-2. [PMID: 23246507 PMCID: PMC3667977 DOI: 10.1016/j.jhep.2012.08.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 07/10/2012] [Accepted: 08/28/2012] [Indexed: 01/19/2023]
Affiliation(s)
- Harel Dahari
- Department of Medicine, University of Illinois at Chicago, IL 60612 USA
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Scott J. Cotler
- Department of Medicine, University of Illinois at Chicago, IL 60612 USA
| | - Thomas J. Layden
- Department of Medicine, University of Illinois at Chicago, IL 60612 USA
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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175
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Rong L, Guedj J, Dahari H, Coffield DJ, Levi M, Smith P, Perelson AS. Analysis of hepatitis C virus decline during treatment with the protease inhibitor danoprevir using a multiscale model. PLoS Comput Biol 2013; 9:e1002959. [PMID: 23516348 PMCID: PMC3597560 DOI: 10.1371/journal.pcbi.1002959] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 01/16/2013] [Indexed: 01/05/2023] Open
Abstract
The current paradigm for studying hepatitis C virus (HCV) dynamics in patients utilizes a standard viral dynamic model that keeps track of uninfected (target) cells, infected cells, and virus. The model does not account for the dynamics of intracellular viral replication, which is the major target of direct-acting antiviral agents (DAAs). Here we describe and study a recently developed multiscale age-structured model that explicitly considers the potential effects of DAAs on intracellular viral RNA production, degradation, and secretion as virus into the circulation. We show that when therapy significantly blocks both intracellular viral RNA production and virus secretion, the serum viral load decline has three phases, with slopes reflecting the rate of serum viral clearance, the rate of loss of intracellular viral RNA, and the rate of loss of intracellular replication templates and infected cells, respectively. We also derive analytical approximations of the multiscale model and use one of them to analyze data from patients treated for 14 days with the HCV protease inhibitor danoprevir. Analysis suggests that danoprevir significantly blocks intracellular viral production (with mean effectiveness 99.2%), enhances intracellular viral RNA degradation about 5-fold, and moderately inhibits viral secretion (with mean effectiveness 56%). The multiscale model can be used to study viral dynamics in patients treated with other DAAs and explore their mechanisms of action in treatment of hepatitis C. Chronic infection with hepatitis C virus (HCV) remains an important health-care problem worldwide despite significant progress in the development of HCV therapy since the discovery of the virus in 1989. Current treatment options are focused on direct-acting antiviral agents (DAAs) that target specific steps of the HCV life cycle. Danoprevir, one of the DAAs that inhibit the HCV NS3-4A protease, has induced substantial viral load reductions in patients receiving therapy. We study the viral decline during therapy using a multiscale age-structured model that accounts for the dynamics of intracellular viral replication, and which includes the major steps in the HCV life cycle that are targeted by DAAs. We examine the biological parameters contributing to different phases of the viral decline after treatment initiation. We also explore the mechanisms of action of danoprevir and estimate its treatment effectiveness. The multiscale model provides a theoretical framework for studying virus dynamics in hepatitis C patients treated with other DAAs currently in clinical development, and may help one to optimally combine drugs with complementary modes of action to maximize the HCV cure rate.
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Affiliation(s)
- Libin Rong
- Department of Mathematics and Statistics and Center for Biomedical Research, Oakland University, Rochester, Michigan, United States of America
| | - Jeremie Guedj
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- University Paris Diderot, Sorbonne Paris Cite, 75018 Paris, France
- INSERM, UMR 738, 75018 Paris, France
| | - Harel Dahari
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Medicine, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Daniel J. Coffield
- University of Michigan-Flint, Mathematics Department, Flint, Michigan, United States of America
| | - Micha Levi
- Clinical Pharmacology, Pharma Research and Early Development, Roche, Nutley, New Jersey, United States of America
| | - Patrick Smith
- Clinical Pharmacology, Pharma Research and Early Development, Roche, Nutley, New Jersey, United States of America
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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176
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Tillmann HL. Hepatitis C infection and presence of advanced fibrosis: wait or treat? Why wait? There is no time to lose, is there? J Hepatol 2013; 58:412-4. [PMID: 23247067 DOI: 10.1016/j.jhep.2012.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 12/04/2012] [Indexed: 12/04/2022]
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177
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Waheed Y, Bhatti A, Ashraf M. RNA dependent RNA polymerase of HCV: a potential target for the development of antiviral drugs. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2013; 14:247-57. [PMID: 23291407 DOI: 10.1016/j.meegid.2012.12.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 11/07/2012] [Accepted: 12/11/2012] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) is a major cause of hepatocellular carcinoma, cirrhosis and end stage liver disease. More than 200million people are living with HCV worldwide with high morbidity and mortality. There is no vaccine available for this virus; the approved treatment option for the majority of HCV genotypes is the combination of pegylated (Peg) interferon and ribavirin. The therapy has a different response rate on different HCV genotypes and has a number of side effects. Recently, as well as Peg interferon and ribavirin, two protease inhibitors have been introduced to treat patients with HCV genotype 1 infection. The protease inhibitors have rapid onset of resistance and are not approved for use for infections with other HCV genotypes. The HCV NS5B gene encodes RNA dependent RNA polymerase (RdRp), which is the key player in viral replication and is a promising target for the development of antiviral drugs. HCV NS5B has been studied in various biochemical assays, cell based assays and animal model systems. So far, a number of nucleoside and non-nucleoside inhibitors have been screened for effects on viral replication. This review presents a deep insight into the structure and function of HCV polymerase and the effect of various nucleoside and non-nucleoside inhibitors on viral replication.
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Affiliation(s)
- Yasir Waheed
- Atta ur Rahman School of Applied Biosciences, National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan.
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178
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Salvatierra K, Fareleski S, Forcada A, López-Labrador FX. Hepatitis C virus resistance to new specifically-targeted antiviral therapy: A public health perspective. World J Virol 2013; 2:6-15. [PMID: 24175225 PMCID: PMC3785043 DOI: 10.5501/wjv.v2.i1.6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Revised: 12/30/2012] [Accepted: 01/17/2013] [Indexed: 02/05/2023] Open
Abstract
Until very recently, treatment for chronic hepatitis C virus (HCV) infection has been based on the combination of two non-viral specific drugs: pegylated interferon-α and ribavirin, which is effective in, overall, about 40%-50% of cases. To improve the response to treatment, novel drugs have been designed to specifically block viral proteins. Multiple compounds are under development, and the approval for clinical use of the first of such direct-acting antivirals in 2011 (Telaprevir and Boceprevir), represents a milestone in HCV treatment. HCV therapeutics is entering a new expanding era, and a highly-effective cure is envisioned for the first time since the discovery of the virus in 1989. However, any antiviral treatment may be limited by the capacity of the virus to overcome the selective pressure of new drugs, generating antiviral resistance. Here, we try to provide a basic overview of new treatments, HCV resistance to new antivirals and some considerations derived from a Public Health perspective, using HCV resistance to protease and polymerase inhibitors as examples.
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Affiliation(s)
- Karina Salvatierra
- Karina Salvatierra, Sabrina Fareleski, F Xavier López-Labrador, Joint Unit in Genomics and Health, Centre for Public Health Research, Public Health Department, Generalitat Valenciana/Institut Cavanilles, University of Valencia, 46020 Valencia, Spain
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179
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Cruz-Rivera M, Carpio-Pedroza JC, Escobar-Gutiérrez A, Lozano D, Vergara-Castaneda A, Rivera-Osorio P, Martinez-Guarneros A, Chacon CAV, Fonseca-Coronado S, Vaughan G. Rapid hepatitis C virus divergence among chronically infected individuals. J Clin Microbiol 2013; 51:629-32. [PMID: 23224093 PMCID: PMC3553878 DOI: 10.1128/jcm.03042-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 11/26/2012] [Indexed: 12/17/2022] Open
Abstract
Here, we analyze the viral divergence among hepatitis C virus (HCV) chronic cases infected with genotype 1. The intrahost viral evolution was assessed by deep sequencing using the 454 Genome Sequencer platform. The results showed a rapid nucleotide sequence divergence. This notorious short-term viral evolution is of the utmost importance for the study of HCV transmission, because direct links between related samples were virtually lost. Thus, rapid divergence of HCV significantly affects genetic relatedness studies and outbreak investigations.
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Affiliation(s)
- Mayra Cruz-Rivera
- Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | - Daniela Lozano
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | | | | | | | - Salvador Fonseca-Coronado
- Laboratorio de Inmunobiología de Enfermedades Infecciosas, Unidad de Investigación Multidisciplinaria, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, Mexico
| | - Gilberto Vaughan
- Instituto de Diagnóstico y Referencia Epidemiológicos, Mexico City, Mexico
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180
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Abstract
Mathematical modeling of hepatitis C viral kinetics has been an important tool in understanding hepatitis C virus (HCV) infection dynamics and in estimating crucial in vivo parameters characterizing the effectiveness of HCV therapy. Because of the introduction of direct-acting antiviral agents, there is a need to extend previous models so as to understand, characterize, and compare various new HCV treatment regimens. Here we review recent modeling efforts in this direction.
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Affiliation(s)
- Anushree Chatterjee
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87545, USA,Center for Nonlinear Studies, Los Alamos National Laboratory, NM 87545, USA
| | - Patrick F. Smith
- Clinical Pharmacology, Pharma Research and Early Development, Roche, Nutley, NJ, USA
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87545, USA,Corresponding author.
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181
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Martel-Laferrière V, Dieterich DT. Update on combinations of DAAs with and without pegylated-interferon and ribavirin: triple and quadruple therapy more than doubles SVR. Clin Liver Dis 2013. [PMID: 23177285 DOI: 10.1016/j.cld.2012.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Monotherapy is an ineffective way to treat hepatitis C and it leads to rapid development of resistance. An increasing number of drugs are currently being developed for the treatment of hepatitis C. This allows combination strategies that can overcome the development of resistance and improve sustained virologic response rates. This article focuses on the 2 main strategies in development: quadruple combination therapies, including pegylated-interferon and triple/quadruple pegylated-interferon free combination therapies. If the first combinations are leading to extremely high sustained virologic responses, the second ones offer hope that the era of pegylated-interferon will end soon.
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Affiliation(s)
- Valérie Martel-Laferrière
- Division of Liver Diseases, Department of Medicine, Mount Sinai School of Medicine, New York, NY 10029, USA.
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182
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Yang X, Marcucci K, Anguela X, Couto LB. Preclinical evaluation of an anti-HCV miRNA cluster for treatment of HCV infection. Mol Ther 2013; 21:588-601. [PMID: 23295950 DOI: 10.1038/mt.2012.247] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We developed a strategy to treat hepatitis C virus (HCV) infection by replacing five endogenous microRNA (miRNA) sequences of a natural miRNA cluster (miR-17-92) with sequences that are complementary to the HCV genome. This miRNA cluster (HCV-miR-Cluster 5) is delivered to cells using adeno-associated virus (AAV) vectors and the miRNAs are expressed in the liver, the site of HCV replication and assembly. AAV-HCV-miR-Cluster 5 inhibited bona fide HCV replication in vitro by up to 95% within 2 days, and the spread of HCV to uninfected cells was prevented by continuous expression of the anti-HCV miRNAs. Furthermore, the number of cells harboring HCV RNA replicons decreased dramatically by sustained expression of the anti-HCV miRNAs, suggesting that the vector is capable of curing cells of HCV. Delivery of AAV-HCV-miR-Cluster 5 to mice resulted in efficient transfer of the miRNA gene cluster and expression of all five miRNAs in liver tissue, at levels up to 1,300 copies/cell. These levels achieved up to 98% gene silencing of cognate HCV sequences, and no liver toxicity was observed, supporting the safety of this approach. Therefore, AAV-HCV-miR-Cluster 5 represents a different paradigm for the treatment of HCV infection.
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Affiliation(s)
- Xiao Yang
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
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183
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Stedman CAM. Current prospects for interferon-free treatment of hepatitis C in 2012. J Gastroenterol Hepatol 2013; 28:38-45. [PMID: 23137126 DOI: 10.1111/jgh.12028] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/06/2012] [Indexed: 12/21/2022]
Abstract
Present interferon-based therapy for chronic hepatitis C is limited by both efficacy and tolerability. Telaprevir and boceprevir are the first two direct-acting antiviral drugs (DAAs) that inhibit hepatitis C virus replication to be licensed for use in conjunction with pegylated interferon and ribavirin. Numerous other DAAs are in clinical development, and phases 2 and 3 trials are evaluating interferon-free combination DAA therapy. Interferon-free sustained virologic responses have now been achieved with combinations of asunaprevir and daclatasvir; sofosbuvir and ribavirin; sofosbuvir and daclatasvir; faldaprevir and BI207127; ABT-450, ritonovir and ABT-333; ABT-450, ritonovir and ABT-072; miracitabine, danoprevir and ritonavir; and alisporivir and ribavirin. Some drugs are genotype-specific in their activity, whereas others are pan-genotypic, and differential responses for the genotype 1 subtypes 1a and 1b have emerged with many DAA combinations. Viral breakthrough and resistance are important considerations for future trial design. The prospect of interferon-free combination DAA therapy for hepatitis C virus is now finally becoming a reality.
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184
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Treatment of Hepatitis C in Patients Infected with Human Immunodeficiency Virus in the Direct-Acting Antiviral Era. Infect Dis Clin North Am 2012; 26:931-48. [DOI: 10.1016/j.idc.2012.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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185
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Alexander HK, Bonhoeffer S. Pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics. Epidemics 2012; 4:187-202. [DOI: 10.1016/j.epidem.2012.10.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 10/15/2012] [Accepted: 10/16/2012] [Indexed: 11/30/2022] Open
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186
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Li X, Liu Y, Zhang YK, Plattner JJ, Baker SJ, Bu W, Liu L, Zhou Y, Ding CZ, Zhang S, Kazmierski WM, Hamatake R, Duan M, Wright LL, Smith GK, Jarvest RL, Ji JJ, Cooper JP, Tallant MD, Crosby RM, Creech K, Wang A. Synthesis and antiviral activity of novel HCV NS3 protease inhibitors with P4 capping groups. Bioorg Med Chem Lett 2012; 22:7351-6. [DOI: 10.1016/j.bmcl.2012.10.075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/08/2012] [Accepted: 10/15/2012] [Indexed: 12/29/2022]
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187
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Jackman JA, Cho NJ. Model membrane platforms for biomedicine: case study on antiviral drug development. Biointerphases 2012; 7:18. [PMID: 22589061 PMCID: PMC7099340 DOI: 10.1007/s13758-011-0018-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 12/29/2011] [Indexed: 01/28/2023] Open
Abstract
As one of the most important interfaces in cellular systems, biological membranes have essential functions in many activities such as cellular protection and signaling. Beyond their direct functions, they also serve as scaffolds to support the association of proteins involved in structural support, adhesion, and transport. Unfortunately, biological processes sometimes malfunction and require therapeutic intervention. For those processes which occur within or upon membranes, it is oftentimes difficult to study the mechanism in a biologically relevant, membranous environment. Therefore, the identification of direct therapeutic targets is challenging. In order to overcome this barrier, engineering strategies offer a new approach to interrogate biological activities at membrane interfaces by analyzing them through the principles of the interfacial sciences. Since membranes are complex biological interfaces, the development of simplified model systems which mimic important properties of membranes can enable fundamental characterization of interaction parameters for such processes. We have selected the hepatitis C virus (HCV) as a model viral pathogen to demonstrate how model membrane platforms can aid antiviral drug discovery and development. Responsible for generating the genomic diversity that makes treating HCV infection so difficult, viral replication represents an ideal step in the virus life cycle for therapeutic intervention. To target HCV genome replication, the interaction of viral proteins with model membrane platforms has served as a useful strategy for target identification and characterization. In this review article, we demonstrate how engineering approaches have led to the discovery of a new functional activity encoded within the HCV nonstructural 5A protein. Specifically, its N-terminal amphipathic, α-helix (AH) can rupture lipid vesicles in a size-dependent manner. While this activity has a number of exciting biotechnology and biomedical applications, arguably the most promising one is in antiviral medicine. Based on the similarities between lipid vesicles and the lipid envelopes of virus particles, experimental findings from model membrane platforms led to the prediction that a range of medically important viruses might be susceptible to rupturing treatment with synthetic AH peptide. This hypothesis was tested and validated by molecular virology studies. Broad-spectrum antiviral activity of the AH peptide has been identified against HCV, HIV, herpes simplex virus, and dengue virus, and many more deadly pathogens. As a result, the AH peptide is the first in class of broad-spectrum, lipid envelope-rupturing antiviral agents, and has entered the drug pipeline. In summary, engineering strategies break down complex biological systems into simplified biomimetic models that recapitulate the most important parameters. This approach is particularly advantageous for membrane-associated biological processes because model membrane platforms provide more direct characterization of target interactions than is possible with other methods. Consequently, model membrane platforms hold great promise for solving important biomedical problems and speeding up the translation of biological knowledge into clinical applications.
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Affiliation(s)
- Joshua A. Jackman
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798 Singapore
- Centre for Biomimetic Sensor Science, Nanyang Technological University, 50 Nanyang Drive, Singapore, 637553 Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798 Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
- Centre for Biomimetic Sensor Science, Nanyang Technological University, 50 Nanyang Drive, Singapore, 637553 Singapore
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, 269 Campus Drive, Stanford, CA 94305 USA
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188
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Hepatitis C virus variants with decreased sensitivity to direct-acting antivirals (DAAs) were rarely observed in DAA-naive patients prior to treatment. J Virol 2012; 87:1544-53. [PMID: 23152524 DOI: 10.1128/jvi.02294-12] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The prevalence of naturally occurring hepatitis C virus (HCV) variants that are less sensitive to direct-acting antiviral (DAA) inhibitors has not been fully characterized. We used population sequence analysis to assess the frequency of such variants in plasma samples from 3,447 DAA-naive patients with genotype 1 HCV. In general, HCV variants with lower-level resistance (3- to 25-fold increased 50% inhibitor concentration [IC(50)]) to telaprevir were observed as the dominant species in 0 to 3% of patients, depending on the specific variant, whereas higher-level resistant variants (>25-fold-increased IC(50)) were not observed. Specific variants resistant to NS5A inhibitors were predominant in up to 6% of patients. Most variants resistant to nucleo(s/t)ide active-site NS5B polymerase inhibitors were not observed, whereas variants resistant to non-nucleoside allosteric inhibitors were observed in up to 18% of patients. The presence of DAA-resistant variants in NS5A, NS5B, or NS3 (including telaprevir-resistant variants), in baseline samples of treatment-naive patients receiving a telaprevir-based regimen in phase 3 studies did not affect the sustained viral response (SVR). Treatment-naive patients with viral populations containing the telaprevir-resistant variants NS3 V36M, T54S, or R155K at baseline achieved a 74% SVR rate, whereas patients with no resistant variants detected prior to treatment achieved a 76% SVR rate. The effect of specific resistant variant frequency on response to various DAA treatments in different patient populations, including interferon nonresponders, should be further studied.
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Abstract
Two selective inhibitors of the hepatitis C virus (HCV) protease nearly double the cure rates for this infection when combined with peginterferon alfa and ribavirin. These drugs, boceprevir and telaprevir, received regulatory approval in 2011 and are the first direct-acting antiviral agents (DAAs) that selectively target HCV. During 2012, at least 30 additional DAAs were in various stages of clinical development. HCV protease inhibitors, polymerase inhibitors, and NS5A inhibitors (among others) can achieve high cure rates when combined with peginterferon alfa and ribavirin and demonstrate promise when used in combination with one another. Current research is attempting to improve the pharmacokinetics and tolerability of these agents, define the best regimens, and determine treatment strategies that produce the best outcomes. Several DAAs will reach the market simultaneously, and resources will be needed to guide the use of these drugs. We review the clinical pharmacology, trial results, and remaining challenges of DAAs for the treatment of HCV.
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Affiliation(s)
- Jennifer J. Kiser
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, Colorado 80045;
| | - Charles Flexner
- Division of Clinical Pharmacology, Johns Hopkins University, Baltimore, Maryland 21287;
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190
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D’Ambrosio R, Aghemo A, Colombo M. Treatment of experienced and naïve patients with hepatitis C: focus on telaprevir. Biologics 2012; 6:363-70. [PMID: 23118525 PMCID: PMC3484502 DOI: 10.2147/btt.s20673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Telaprevir (TVR) is an orally available protease inhibitor of the hepatitis C virus that in association with pegylated interferon and ribavirin (PR) was shown to improve the rates of sustained virological response and potentially reduce treatment duration in adult patients with chronic hepatitis C genotype. Despite its robust activity in both treatment-naïve and experienced patients, the addition of TVR to PR is counterbalanced by increased costs and adverse events; moreover, there are still areas of uncertainty that regard treatment of patients with advanced liver disease, the role of patient stratification by genetic predictors, and the use/need for a lead-in phase with PR. Since TVR regimens have been associated with the risk of viral mutants that may cause treatment failure and jeopardize future therapeutic strategies with direct-acting antiviral agents, early stopping rules have been designed to protect patients with a poor virological response to TVR regimens against such a risk.
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Affiliation(s)
- Roberta D’Ambrosio
- Centro A.M. e A. Migliavacca, First Division of Gastroenterology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Alessio Aghemo
- Centro A.M. e A. Migliavacca, First Division of Gastroenterology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Massimo Colombo
- Centro A.M. e A. Migliavacca, First Division of Gastroenterology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
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191
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Hepatitis C virus: a critical appraisal of new approaches to therapy. HEPATITIS RESEARCH AND TREATMENT 2012; 2012:138302. [PMID: 23094146 PMCID: PMC3472509 DOI: 10.1155/2012/138302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 07/16/2012] [Indexed: 01/22/2023]
Abstract
The HCV council 2011 convened 11 leading clinicians and researchers in hepatitis C virus from academic medical centers in the United States to provide a forum for the practical and comprehensive evaluation of current data regarding best practices for integrating new direct-acting antiviral agents into existing treatment paradigms. The council investigated 10 clinical practice statements related to HCV treatment that reflect key topical areas. Faculty members reviewed and discussed the data related to each statement, and voted on the nature of the evidence and their level of support for each statement. In this new era of DAAs, a comprehensive and critical analysis of the literature is needed to equip clinicians with the knowledge necessary to design, monitor, and modify treatment regimens in order to optimize patient outcomes.
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192
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Chatterjee A, Guedj J, Perelson AS. Mathematical modelling of HCV infection: what can it teach us in the era of direct-acting antiviral agents? Antivir Ther 2012. [PMID: 23186606 DOI: 10.3851/imp2428] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
HCV infection is a major cause of chronic liver disease and affects nearly 170 million people worldwide. Whereas the previous standard of care with pegylated interferon and ribavirin had a modest effectiveness, the recent approval of two highly potent protease inhibitors and the ongoing development of dozens of direct-acting antiviral agents (DAAs) constitute a major milestone for HCV therapy. Mathematical modelling of viral kinetics under treatment has played an instrumental role in improving our understanding of virus pathogenesis and in guiding drug development. Here, we review the current state of HCV kinetic modelling, and challenges to the standard biphasic viral decline model that arise when fitting viral kinetic models to data obtained with DAAs.
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Affiliation(s)
- Anushree Chatterjee
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
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193
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Götte M. The distinct contributions of fitness and genetic barrier to the development of antiviral drug resistance. Curr Opin Virol 2012; 2:644-50. [DOI: 10.1016/j.coviro.2012.08.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 08/15/2012] [Indexed: 01/14/2023]
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194
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Welsch C, Zeuzem S. Clinical relevance of HCV antiviral drug resistance. Curr Opin Virol 2012; 2:651-5. [DOI: 10.1016/j.coviro.2012.08.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 08/24/2012] [Accepted: 08/24/2012] [Indexed: 11/25/2022]
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195
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Ribeiro RM, Li H, Wang S, Stoddard MB, Learn GH, Korber BT, Bhattacharya T, Guedj J, Parrish EH, Hahn BH, Shaw GM, Perelson AS. Quantifying the diversification of hepatitis C virus (HCV) during primary infection: estimates of the in vivo mutation rate. PLoS Pathog 2012; 8:e1002881. [PMID: 22927817 PMCID: PMC3426522 DOI: 10.1371/journal.ppat.1002881] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 07/12/2012] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) is present in the host with multiple variants generated by its error prone RNA-dependent RNA polymerase. Little is known about the initial viral diversification and the viral life cycle processes that influence diversity. We studied the diversification of HCV during acute infection in 17 plasma donors, with frequent sampling early in infection. To analyze these data, we developed a new stochastic model of the HCV life cycle. We found that the accumulation of mutations is surprisingly slow: at 30 days, the viral population on average is still 46% identical to its transmitted viral genome. Fitting the model to the sequence data, we estimate the median in vivo viral mutation rate is 2.5×10−5 mutations per nucleotide per genome replication (range 1.6–6.2×10−5), about 5-fold lower than previous estimates. To confirm these results we analyzed the frequency of stop codons (N = 10) among all possible non-sense mutation targets (M = 898,335), and found a mutation rate of 2.8–3.2×10−5, consistent with the estimate from the dynamical model. The slow accumulation of mutations is consistent with slow turnover of infected cells and replication complexes within infected cells. This slow turnover is also inferred from the viral load kinetics. Our estimated mutation rate, which is similar to that of other RNA viruses (e.g., HIV and influenza), is also compatible with the accumulation of substitutions seen in HCV at the population level. Our model identifies the relevant processes (long-lived cells and slow turnover of replication complexes) and parameters involved in determining the rate of HCV diversification. Hepatitis C virus (HCV) is a RNA virus that infects over 170 million people across the world. It leads to a chronic infection in the majority of people who are infected (>70%). Most people only discover that they are infected long after initial infection. Thus, it is difficult to study the very early events in infection. Here we study 17 individuals during the earliest possible stages of infection, from before the virus is detectable in the plasma to around 35 days post-infection. We focus on understanding the viral kinetics and the diversification of HCV during this acute phase of infection. During chronic infection HCV is present in the host as a swarm of multiple variants generated by its error prone copying. We studied the early diversification of HCV during acute infection using a new mathematical model of HCV replication. We found that after a phase of fast increase in viral load, accompanied by viral diversification, there is a stabilization of viral load and diversity levels. Using our model, we were able to estimate for the first time the HCV mutation rate during acute infection. We estimated the median in vivo viral mutation rate is 2.5×10−5 mutations per nucleotide per genome replication (range 1.6–6.2×10−5), about 5-fold lower than previous estimates. We also used a different approach, based on results of classical genetics, to calculate HCV's mutation rate and obtained consistent results (2.8–3.2×10−5).
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Affiliation(s)
- Ruy M. Ribeiro
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shuyi Wang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mark B. Stoddard
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gerald H. Learn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Bette T. Korber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tanmoy Bhattacharya
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jeremie Guedj
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Erica H. Parrish
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Beatrice H. Hahn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George M. Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alan S. Perelson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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196
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Characterization of hepatitis C virus (HCV) quasispecies dynamics upon short-term dual therapy with the HCV NS5B nucleoside polymerase inhibitor mericitabine and the NS3/4 protease inhibitor danoprevir. Antimicrob Agents Chemother 2012; 56:5494-502. [PMID: 22869576 DOI: 10.1128/aac.01035-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In the INFORM-1 study, 73 patients with chronic hepatitis C virus infection received mericitabine plus danoprevir for up to 13 days. Seventy-two patients experienced a continuous decline in HCV RNA levels during treatment, and of these patients, 14 had viral loads that remained >1,000 IU/ml by day 13 and 1 met the definition for viral breakthrough. In-depth NS5B and NS3/4A population and clonal sequencing studies and mericitabine and danoprevir drug susceptibility testing were performed to assess the variability and quasispecies dynamics before and upon monotherapy or dual therapy. Sequence analysis of the viral quasispecies indicated that the mericitabine resistance mutation S282T was not present at baseline, nor was it selected (even at a low level) during treatment. Protease inhibitor resistance mutations, either as predominant or as minority species, were detected in 18 patients at baseline. No enrichment of minority protease inhibitor-resistant variants present at baseline was observed during treatment; viral population samples were fully susceptible to mericitabine and/or danoprevir, despite the presence within their quasispecies of minority variants confirmed to have reduced susceptibility to danoprevir or other protease inhibitors. It was also observed that certain NS3 amino acid substitutions affected protease inhibitor drug susceptibility in a compound-specific manner and varied with the genetic context. In summary, the slower kinetics of viral load decline observed in some patients was not due to the selection of danoprevir or mericitabine resistance during treatment. Over 2 weeks' therapy, mericitabine suppressed the selection of danoprevir resistance, results that could differ upon longer treatment periods.
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197
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No influence of antiretroviral therapy on the mutation rate of the HCV NS5B polymerase in HIV/HCV-coinfected patients. Antiviral Res 2012; 95:67-71. [DOI: 10.1016/j.antiviral.2012.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 05/26/2012] [Accepted: 05/30/2012] [Indexed: 01/11/2023]
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198
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Abstract
The recent development of small molecule compounds that directly inhibit the viral life cycle represents a major milestone for the treatment of chronic hepatitis C virus (HCV) infection. These new drugs that are collectively termed direct-acting antivirals (DAA) include a range of inhibitors of the non-structural (NS) 3/4A protease, NS5B polymerase and NS5A protein. Two NS3/4A protease inhibitors (boceprevir and telaprevir) in combination with pegylated interferon and ribavirin have now been approved for the treatment of chronic HCV genotype 1 infection and cure rates could be increased by 20-30%. However, the majority of DAAs is still in early clinical development. The rapid replication rate of HCV, along with the error-prone polymerase activity leads to a high genetic diversity among HCV virions that includes mutants with reduced susceptibility to DAA-therapy. These resistance-associated variants often occur at very low frequencies. However, during DAA-based treatment, rapid selection of resistance mutations may occur, eventually leading to viral break-through. A number of variants with different levels of resistance have been described in vitro and in vivo for virtually all DAAs. We review the parameters that determine DAA resistance as well as the clinical implications of resistance testing. In addition, the most recent literature and conference data on resistance profiles of DAAs in clinical development and future strategies to avoid the emergence of viral resistance are also discussed.
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Affiliation(s)
- Johannes Vermehren
- Medizinische Klinik 1, Klinikum der J. W. Goethe-Universität, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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199
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Romano KP, Ali A, Aydin C, Soumana D, Özen A, Deveau LM, Silver C, Cao H, Newton A, Petropoulos CJ, Huang W, Schiffer CA. The molecular basis of drug resistance against hepatitis C virus NS3/4A protease inhibitors. PLoS Pathog 2012; 8:e1002832. [PMID: 22910833 PMCID: PMC3406087 DOI: 10.1371/journal.ppat.1002832] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 06/13/2012] [Indexed: 01/16/2023] Open
Abstract
Hepatitis C virus (HCV) infects over 170 million people worldwide and is the leading cause of chronic liver diseases, including cirrhosis, liver failure, and liver cancer. Available antiviral therapies cause severe side effects and are effective only for a subset of patients, though treatment outcomes have recently been improved by the combination therapy now including boceprevir and telaprevir, which inhibit the viral NS3/4A protease. Despite extensive efforts to develop more potent next-generation protease inhibitors, however, the long-term efficacy of this drug class is challenged by the rapid emergence of resistance. Single-site mutations at protease residues R155, A156 and D168 confer resistance to nearly all inhibitors in clinical development. Thus, developing the next-generation of drugs that retain activity against a broader spectrum of resistant viral variants requires a comprehensive understanding of the molecular basis of drug resistance. In this study, 16 high-resolution crystal structures of four representative protease inhibitors – telaprevir, danoprevir, vaniprevir and MK-5172 – in complex with the wild-type protease and three major drug-resistant variants R155K, A156T and D168A, reveal unique molecular underpinnings of resistance to each drug. The drugs exhibit differential susceptibilities to these protease variants in both enzymatic and antiviral assays. Telaprevir, danoprevir and vaniprevir interact directly with sites that confer resistance upon mutation, while MK-5172 interacts in a unique conformation with the catalytic triad. This novel mode of MK-5172 binding explains its retained potency against two multi-drug-resistant variants, R155K and D168A. These findings define the molecular basis of HCV N3/4A protease inhibitor resistance and provide potential strategies for designing robust therapies against this rapidly evolving virus. Hepatitis C virus (HCV) infects over 170 million people worldwide and is the leading cause of chronic liver diseases, including cirrhosis, liver failure, and liver cancer. New classes of directly-acting antiviral agents that target various HCV enzymes are being developed. Two such drugs that target the essential HCV NS3/4A protease are approved by the FDA and several others are at various stages of clinical development. These drugs, when used in combination with pegylated interferon and ribavirin, significantly improve treatment outcomes. However HCV evolves very quickly and drug resistance develops against directly-acting antiviral agents. Thus, despite the therapeutic success of NS3/4A protease inhibitors, their long-term effectiveness is challenged by drug resistance. Our study explains in atomic detail how and why drug resistance occurs for four chemically representative protease inhibitors –telaprevir, danoprevir, vaniprevir and MK-5172. Potentially with this knowledge, new drugs could be developed that are less susceptible to drug resistance. More generally, understanding the underlying mechanisms by which drug resistance occurs can be incorporated in drug development to many quickly evolving diseases.
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Affiliation(s)
- Keith P. Romano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Cihan Aydin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Djade Soumana
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Ayşegül Özen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Laura M. Deveau
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Casey Silver
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Hong Cao
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Alicia Newton
- Monogram Biosciences, San Francisco, California, United States of America
| | | | - Wei Huang
- Monogram Biosciences, San Francisco, California, United States of America
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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Hepatitis C variability, patterns of resistance, and impact on therapy. Adv Virol 2012; 2012:267483. [PMID: 22851970 PMCID: PMC3407602 DOI: 10.1155/2012/267483] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 05/10/2012] [Indexed: 12/17/2022] Open
Abstract
Hepatitis C (HCV), a leading cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma, is the most common indication for liver transplantation in the United States. Although annual incidence of infection has declined since the 1980s, aging of the currently infected population is expected to result in an increase in HCV burden. HCV is prone to develop resistance to antiviral drugs, and despite considerable efforts to understand the virus for effective treatments, our knowledge remains incomplete. This paper reviews HCV resistance mechanisms, the traditional treatment with and the new standard of care for hepatitis C treatment. Although these new treatments remain PEG-IFN-α- and ribavirin-based, they add one of the newly FDA approved direct antiviral agents, telaprevir or boceprevir. This new “triple therapy” has resulted in greater viral cure rates, although treatment failure remains a possibility. The future may belong to nucleoside/nucleotide analogues, non-nucleoside RNA-dependent RNA polymerase inhibitors, or cyclophilin inhibitors, and the treatment of HCV may ultimately parallel that of HIV. However, research should focus not only on effective treatments, but also on the development of a HCV vaccine, as this may prove to be the most cost-effective method of eradicating this disease.
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