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de Mariz E Miranda LS. The synergy between nucleotide biosynthesis inhibitors and antiviral nucleosides: New opportunities against viral infections? Arch Pharm (Weinheim) 2023; 356:e2200217. [PMID: 36122181 DOI: 10.1002/ardp.202200217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 01/04/2023]
Abstract
5'-Phosphorylated nucleoside derivatives are molecules that can be found in all living organisms and viruses. Over the last century, the development of structural analogs that could disrupt the transcription and translation of genetic information culminated in the development of clinically relevant anticancer and antiviral drugs. However, clinically effective broad-spectrum antiviral compounds or treatments are lacking. This viewpoint proposes that molecules that inhibit nucleotide biosynthesis may sensitize virus-infected cells toward direct-acting antiviral nucleosides. Such potentially synergistic combinations might allow the repurposing of drugs, leading to the development of new combination therapies.
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Affiliation(s)
- Leandro S de Mariz E Miranda
- Department of Organic Chemistry, Chemistry Institute, Biocatalysis and Organic Synthesis Group, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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2
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Zheng K, Wu SZ, Lv YW, Pang P, Deng L, Xu HC, Shi YC, Chen XY. Carvacrol inhibits the excessive immune response induced by influenza virus A via suppressing viral replication and TLR/RLR pattern recognition. JOURNAL OF ETHNOPHARMACOLOGY 2021; 268:113555. [PMID: 33152425 DOI: 10.1016/j.jep.2020.113555] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 05/24/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Carvacrol, a monoterpene phenol from Mosla chinensis Maxim, which is a commonly Chinese herbal medicine. The most important pharmacology of it is dispelling exogenous evils by increasing perspiration. And it is the gentleman medicine in the Chinese herbal compound prescription of Xin-Jia-Xiang-Ru-Yin, mainly for the treatment of summer colds with dampness including influenza virus A infection. AIM OF THE STUDY Our preliminary study verified that the Xin-Jia-Xiang-Ru-Yin could inhibit acute lung injury of mice with influenza virus A infection. And there have been some reports implicating the high antimicrobial activity of carvacrol for a wide range of product preservation, but little research including the effects of it on viral infection. The aim of this study was to reveal the antiviral effects of carvacrol, the main constituent in Mosla chinensis Maxim. MATERIALS AND METHODS Initially, C57BL/6 mice were grouped and intranasally administered FM1 virus to construct viral infection models. After treatment with ribavirin and carvacrol for 5 days, all mice were euthanized, and specimens were immediately obtained. Histology, flow cytometry and Meso Scale Discovery (MSD) analysis were used to analyze pathological changes in lung tissue, the expression levels of cytokines and the differentiation and proportion of CD4+ T cells subsets, while Western blot and qRT-PCR were used to detect the expression of related proteins and mRNA. RESULTS Carvacrol attenuated lung tissue damage, the proportions of Th1, Th2, Th17 and Treg in CD4+ T cells and the relative proportions of Th1/Th2 and Th17/Treg cells. Carvacrol inhibited the expression of inflammation-associated cytokines including IFN-γ, IL-2, IL-4, IL-5, IL-12 and TNF-ɑ, IL-1, IL-10, IL-6. Decreased levels of TLR7, MyD88, IRAK4, TRAK6, NF-κB, RIG-I, IPS-I and IRF mRNA in carvacrol-treated mice were observed comparing to the mice in VC group. Further, the total expression of RIG-I, MyD88 and NF-κB proteins had increased significantly in the VC group but reduced obviously in the group treated with ribavirin or carvacrol. CONCLUSIONS These results indicate that carvacrol is a potential alternative treatment for the excessive immune response induced by influenza virus A infection, the cold-fighting effect of Mosla chinensis Maxim may depend on the anti-virus of carvacrol.
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Affiliation(s)
- Ke Zheng
- College of Traditional Chinese Medicine, Jinan University, Guangzhou, China; The Hospital of the People's Liberation Army's 83rd Group, Xinxiang, China.
| | - Si-Zhi Wu
- College of Traditional Chinese Medicine, Jinan University, Guangzhou, China.
| | - Yi-Wen Lv
- College of Traditional Chinese Medicine, Jinan University, Guangzhou, China.
| | - Peng Pang
- College of Traditional Chinese Medicine, Jinan University, Guangzhou, China.
| | - Li Deng
- College of Traditional Chinese Medicine, Jinan University, Guangzhou, China.
| | - Hua-Chong Xu
- College of Traditional Chinese Medicine, Jinan University, Guangzhou, China.
| | - Yu-Cong Shi
- College of Traditional Chinese Medicine, Jinan University, Guangzhou, China.
| | - Xiao-Yin Chen
- College of Traditional Chinese Medicine, Jinan University, Guangzhou, China.
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Byléhn F, Menéndez CA, Perez-Lemus GR, Alvarado W, de Pablo JJ. Modeling the Binding Mechanism of Remdesivir, Favilavir, and Ribavirin to SARS-CoV-2 RNA-Dependent RNA Polymerase. ACS CENTRAL SCIENCE 2021; 7:164-174. [PMID: 33527086 PMCID: PMC7805600 DOI: 10.1021/acscentsci.0c01242] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Indexed: 05/05/2023]
Abstract
Recent efforts to repurpose drugs to combat COVID-19 have identified Remdesivir as a candidate. It acts on the RNA-dependent, RNA polymerase (RdRp) of the SARS-CoV-2 virus, a protein complex responsible for mediating replication of the virus's genome. However, its exact action mechanism, and that of other nucleotide analogue inhibitors, is not known. In this study, we examine at the molecular level the interaction of this drug and that of similar nucleotide analogue inhibitors, ribavirin and favilavir, by relying on atomistic molecular simulations and advanced sampling. By analyzing the binding free energies of these different drugs, it is found that all of them bind strongly at the active site. Surprisingly, however, ribavirin and favilavir do not bind the nucleotide on the complementary strand as effectively and seem to act by a different mechanism than remdesivir. Remdesivir exhibits similar binding interactions to the natural base adenine. Moreover, by analyzing remdesivir at downstream positions of the RNA, we also find that, consistent with a "delayed" termination mechanism, additional nucleotides can be incorporated after remdesivir is added, and its highly polar 1'-cyano group induces a set of conformational changes that can affect the normal RdRp complex function. By analyzing the fluctuations of residues that are altered by remdesivir binding, and comparing them to those induced by lethal point mutations, we find a possible secondary mechanism in which remdesivir destabilizes the protein complex and its interactions with the RNA strands.
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Affiliation(s)
- Fabian Byléhn
- Pritzker
School of Molecular Engineering, University
of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United
States
| | - Cintia A. Menéndez
- Pritzker
School of Molecular Engineering, University
of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United
States
| | - Gustavo R. Perez-Lemus
- Pritzker
School of Molecular Engineering, University
of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United
States
| | - Walter Alvarado
- Pritzker
School of Molecular Engineering, University
of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United
States
- Biophysical
Sciences, University of Chicago, 929 East 54th Street, Chicago, Illinois 60637, United States
| | - Juan J. de Pablo
- Pritzker
School of Molecular Engineering, University
of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United
States
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Mejer N, Galli A, Ramirez S, Fahnøe U, Benfield T, Bukh J. Ribavirin inhibition of cell-culture infectious hepatitis C genotype 1-3 viruses is strain-dependent. Virology 2019; 540:132-140. [PMID: 31778898 DOI: 10.1016/j.virol.2019.09.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 12/20/2022]
Abstract
Ribavirin remains relevant for successful treatment of chronic hepatitis C virus (HCV) infections in low-income settings, as well as for therapy of difficult-to-treat HCV patients. We studied the effect of ribavirin against cell-culture adapted HCV of genotypes 1, 2 and 3, representing ~80% of global infections. TNcc(1a) was the most sensitive to ribavirin, while J6/JFH1(2a) was the most resistant. EC50s ranged from 21 μM (95%CI: 20-22 μM) to 189 μM (95%CI: 173-207 μM). Substitutions at position 415 of NS5B resulted in little or no change to ribavirin sensitivity (0.7-0.9 fold) but conferred moderate drug resistance during extended treatment of genotype 1 (1.8-fold). NS5A and NS5B sequences could alter ribavirin sensitivity 2-4-fold, although their contribution was not simply additive. Finally, we detected limited accumulation of mutations associated with ribavirin treatment. Our findings show that the antiviral effect of ribavirin on HCV is strain-dependent and is influenced by the specific sequence of multiple HCV nonstructural proteins.
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Affiliation(s)
- Niels Mejer
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark
| | - Andrea Galli
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark
| | - Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark
| | - Thomas Benfield
- Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark.
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Kamiyama N, Soma R, Hidano S, Watanabe K, Umekita H, Fukuda C, Noguchi K, Gendo Y, Ozaki T, Sonoda A, Sachi N, Runtuwene LR, Miura Y, Matsubara E, Tajima S, Takasaki T, Eshita Y, Kobayashi T. Ribavirin inhibits Zika virus (ZIKV) replication in vitro and suppresses viremia in ZIKV-infected STAT1-deficient mice. Antiviral Res 2017; 146:1-11. [PMID: 28818572 PMCID: PMC7113888 DOI: 10.1016/j.antiviral.2017.08.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/27/2017] [Accepted: 08/13/2017] [Indexed: 02/08/2023]
Abstract
Zika fever, a mosquito-borne infectious disease caused by Zika virus (ZIKV), is an epidemic disease for which no effective therapy has been established. The recent outbreaks of ZIKV in Brazil and French Polynesia have been linked to a considerable increase in the incidence of fetal microcephaly and other diseases such as Guillain-Barre syndrome. Because there is currently no specific therapy or vaccine, the early exploitation of a method to prevent expansion of ZIKV is a high priority. To validate commonly used antiviral drugs, we evaluated the effect of ribavirin, a drug used to treat hepatitis C with interferon-β (IFN-β), on ZIKV replication. In mammalian cells, we observed an inhibitory effect of ribavirin on ZIKV replication and ZIKV-induced cell death without cytotoxic effect. Furthermore, we found that STAT1-deficient mice, which lack type I IFN signaling, were highly sensitive to ZIKV infection and exhibited lethal outcome. Ribavirin abrogated viremia in ZIKV-infected STAT-1-deficient mice. These data suggest that the inhibition of viral RNA-dependent RNA polymerases may be effective for treatment of ZIKV infection. Our data provide a new insight into the mechanisms for inhibition of ZIKV replication and prevention of Zika fever. Ribavirin inhibits ZIKV replication in mammalian cells. Ribavirin prevents ZIKV-induced apoptosis and cell death. Ribavirin administration abrogates viremia in ZIKV-infected STAT1-deficient mice. Leading to a prolonged survival.
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Affiliation(s)
- Naganori Kamiyama
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan.
| | - Ryusuke Soma
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Shinya Hidano
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Kei Watanabe
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Hiroshi Umekita
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Chiaki Fukuda
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Kaori Noguchi
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Yoshiko Gendo
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Takashi Ozaki
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Akira Sonoda
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Nozomi Sachi
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Lucky Ronald Runtuwene
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Yumako Miura
- Department of Neurology, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Etsuro Matsubara
- Department of Neurology, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Shigeru Tajima
- Department of Virology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Tomohiko Takasaki
- Department of Virology I, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Yuki Eshita
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Takashi Kobayashi
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan.
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7
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Fearns R, Plemper RK. Polymerases of paramyxoviruses and pneumoviruses. Virus Res 2017; 234:87-102. [PMID: 28104450 DOI: 10.1016/j.virusres.2017.01.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 11/13/2022]
Abstract
The paramyxo- and pneumoviruses are members of the order Mononegavirales, a group of viruses with non-segmented, negative strand RNA genomes. The polymerases of these viruses are multi-functional complexes, capable of transcribing subgenomic capped and polyadenylated mRNAs and replicating the genome. Although there is no native structure available for any complete paramyxo- or pneumovirus polymerase, functional and structural studies of a fragment of a pneumovirus polymerase protein and mutation analyses and resistance profiling of small-molecule inhibitors have generated a wealth of mechanistic information. This review integrates these data with the structure of a related polymerase, identifying similarities, differences, gaps in knowledge, and avenues for antiviral drug development.
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Affiliation(s)
- Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, United States.
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, United States
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8
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Ribavirin suppresses bacterial virulence by targeting LysR-type transcriptional regulators. Sci Rep 2016; 6:39454. [PMID: 27991578 PMCID: PMC5171790 DOI: 10.1038/srep39454] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 11/23/2016] [Indexed: 12/30/2022] Open
Abstract
Targeting bacterial virulence mechanisms without compromising bacterial growth is a promising strategy to prevent drug resistance. LysR-type transcriptional regulators (LTTRs) possess structural conservation across bacterial species and regulate virulence in numerous pathogens, making them attractive targets for antimicrobial agents. We targeted AphB, a Vibrio cholerae LTTR, which regulates the expression of genes encoding cholera toxin and toxin-co-regulated pilus for inhibitor designing. Since AphB ligand is unknown, we followed a molecular fragment-based approach for ligand designing using FDA-approved drugs and subsequent screen to identify molecules that exhibited high-affinity binding to AphB ligand-binding pocket. Among the identified compounds, ribavirin, an anti-viral drug, antagonized AphB functions. Ribavirin perturbed Vibrio cholerae pathogenesis in animal models. The inhibitory effects of the drug was limited to the bacteria expressing wild type AphB, but not its constitutively active mutant (AphBN100E), which represents the ligand-bound state, suggesting that ribavirin binds to the active site of AphB to exert its inhibitory role and there exists no AphB-independent mechanism of its action. Similarly, ribavirin suppressed the functions of Salmonella Typhi LTTR Hrg, indicating its broad spectrum efficacy. Moreover, ribavirin did not affect the bacterial viability in culture. This study cites an example of drug repurposing for anti-infective therapy.
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Tomei L, Altamura S, Paonessa G, De Francesco R, Migliaccio G. Review HCV Antiviral Resistance: The Impact of in vitro Studies on the Development of Antiviral Agents Targeting the Viral NS5B Polymerase. ACTA ACUST UNITED AC 2016; 16:225-45. [PMID: 16130521 DOI: 10.1177/095632020501600403] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The high prevalence of the disease caused by hepatitis C virus (HCV) and the limited efficacy of interferon-based therapies have stimulated the search for safer and more effective drugs. The development of inhibitors of the HCV NS5B RNA polymerase represents a promising strategy for identifying novel anti-HCV therapeutics. However, the high genetic diversity, mutation rate and turnover of HCV are expected to favour the emergence of drug resistance, limiting the clinical usefulness of polymerase inhibitors. Thus, the characterization of the drug-resistance profile of these antiviral agents is considered crucial for identifying the inhibitors with a higher probability of clinical success. In the absence of an efficient in vitro infection system, HCV sub-genomic replicons have been used to study viral resistance to both nucleoside and non-nucleoside NS5B inhibitors. While these studies suggest that drug-resistant viruses are likely to evolve in vivo, they provide a wealth of information that should help in the identification of inhibitors with improved and distinct resistance profiles that might be used for combination therapy.
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Affiliation(s)
- Licia Tomei
- Istituto di Ricerche di Biologia Molecolare P Angeletti, Pomezia-Roma, Italy
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de Ávila AI, Gallego I, Soria ME, Gregori J, Quer J, Esteban JI, Rice CM, Domingo E, Perales C. Lethal Mutagenesis of Hepatitis C Virus Induced by Favipiravir. PLoS One 2016; 11:e0164691. [PMID: 27755573 PMCID: PMC5068784 DOI: 10.1371/journal.pone.0164691] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/29/2016] [Indexed: 12/14/2022] Open
Abstract
Lethal mutagenesis is an antiviral approach that consists in extinguishing a virus by an excess of mutations acquired during replication in the presence of a mutagen. Here we show that favipiravir (T-705) is a potent mutagenic agent for hepatitis C virus (HCV) during its replication in human hepatoma cells. T-705 leads to an excess of G → A and C → U transitions in the mutant spectrum of preextinction HCV populations. Infectivity decreased significantly in the presence of concentrations of T-705 which are 2- to 8-fold lower than its cytotoxic concentration 50 (CC50). Passaging the virus five times in the presence of 400 μM T-705 resulted in virus extinction. Since T-705 has undergone advanced clinical trials for approval for human use, the results open a new approach based on lethal mutagenesis to treat hepatitis C virus infections. If proven effective for HCV in vivo, this new anti-HCV agent may be useful in patient groups that fail current therapeutic regimens.
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Affiliation(s)
- Ana I. de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain
| | - Isabel Gallego
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Maria Eugenia Soria
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d’Hebron Institut de Recerca-Hospital Universitari Vall d´Hebron, (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Josep Gregori
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d’Hebron Institut de Recerca-Hospital Universitari Vall d´Hebron, (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
- Roche Diagnostics, S.L., Sant Cugat del Vallés, Spain
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d’Hebron Institut de Recerca-Hospital Universitari Vall d´Hebron, (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
- Universitat Autónoma de Barcelona, Barcelona, Spain
| | - Juan Ignacio Esteban
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d’Hebron Institut de Recerca-Hospital Universitari Vall d´Hebron, (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
- Universitat Autónoma de Barcelona, Barcelona, Spain
| | - Charles M. Rice
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, United States of America
| | - Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Celia Perales
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d’Hebron Institut de Recerca-Hospital Universitari Vall d´Hebron, (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
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11
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Wang X, Pan C, Gong J, Liu X, Li H. Enhancing the Enrichment of Pharmacophore-Based Target Prediction for the Polypharmacological Profiles of Drugs. J Chem Inf Model 2016; 56:1175-83. [PMID: 27187084 DOI: 10.1021/acs.jcim.5b00690] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PharmMapper is a web server for drug target identification by reversed pharmacophore matching the query compound against an annotated pharmacophore model database, which provides a computational polypharmacology prediction approach for drug repurposing and side effect risk evaluation. But due to the inherent nondiscriminative feature of the simple fit scores used for prediction results ranking, the signal/noise ratio of the prediction results is high, posing a challenge for predictive reliability. In this paper, we improved the predictive accuracy of PharmMapper by generating a ligand-target pairwise fit score matrix from profiling all the annotated pharmacophore models against corresponding ligands in the original complex structures that were used to extract these pharmacophore models. The matrix reflects the noise baseline of fit score distribution of the background database, thus enabling estimation of the probability of finding a given target randomly with the calculated ligand-pharmacophore fit score. Two retrospective tests were performed which confirmed that the probability-based ranking score outperformed the simple fit score in terms of identification of both known drug targets and adverse drug reaction related off-targets.
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Affiliation(s)
- Xia Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, and ‡School of Information Science and Engineering, East China University of Science and Technology , Shanghai 200237, China
| | - Chenxu Pan
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, and ‡School of Information Science and Engineering, East China University of Science and Technology , Shanghai 200237, China
| | - Jiayu Gong
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, and ‡School of Information Science and Engineering, East China University of Science and Technology , Shanghai 200237, China
| | - Xiaofeng Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, and ‡School of Information Science and Engineering, East China University of Science and Technology , Shanghai 200237, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, and ‡School of Information Science and Engineering, East China University of Science and Technology , Shanghai 200237, China
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Cooper C, Naggie S, Saag M, Yang JC, Stamm LM, Dvory-Sobol H, Han L, Pang PS, McHutchison JG, Dieterich D, Sulkowski M. Successful Re-treatment of Hepatitis C Virus in Patients Coinfected With HIV Who Relapsed After 12 Weeks of Ledipasvir/Sofosbuvir. Clin Infect Dis 2016; 63:528-31. [PMID: 27225242 DOI: 10.1093/cid/ciw349] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 05/14/2016] [Indexed: 01/15/2023] Open
Abstract
UNLABELLED We assessed the efficacy and safety of ledipasvir/sofosbuvir plus ribavirin for 24 weeks in 9 human immunodeficiency virus/hepatitis C virus-coinfected patients who relapsed after receiving 12 weeks of treatment with ledipasvir/sofosbuvir. Eight of 9 (89%) achieved sustained virologic response 12 weeks after the end of treatment. One patient relapsed at posttreatment week 4. These results suggest an effective salvage therapy for patients for whom direct-acting antiviral treatment has failed. CLINICAL TRIALS REGISTRATION NCT02073656.
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Affiliation(s)
| | - Susanna Naggie
- Duke Clinical Research Institute and Duke University School of Medicine, Durham, North Carolina
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Trends in Antiviral Strategies. VIRUS AS POPULATIONS 2016. [PMCID: PMC7149557 DOI: 10.1016/b978-0-12-800837-9.00009-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Viral populations are true moving targets regarding the genomic sequences to be targeted in antiviral designs. Experts from different fields have expressed the need of new paradigms for antiviral interventions and viral disease control. This chapter reviews several strategies that aim at counteracting the adaptive capacity of viral quasispecies. The proposed designs are based on combinations of different antiviral drugs and immune modulators, or in the administration of virus-specific mutagenic agents, in an approach termed lethal mutagenesis of viruses. It consists of decreasing viral fitness by an excess of mutations that render viral proteins sub-optimal or non-functional. Viral extinction by lethal mutagenesis involves several sequential, overlapping steps that recapitulate the major concepts of intra-population interactions and genetic information stability discussed in preceding chapters. Despite the magnitude of the challenge, the chapter closes with some optimistic prospects for an effective control of viruses displaying error-prone replication, based on the combined targeting of replication fidelity and the induction of the innate immune response.
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Ribavirin Contributes to Hepatitis C Virus Suppression by Augmenting pDC Activation and Type 1 IFN Production. PLoS One 2015; 10:e0135232. [PMID: 26274905 PMCID: PMC4537094 DOI: 10.1371/journal.pone.0135232] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 07/20/2015] [Indexed: 01/14/2023] Open
Abstract
Ribavirin is used as a component of combination therapies for the treatment of chronic hepatitis C virus (HCV) infection together with pegylated interferon and/or direct-acting antiviral drugs. Its mechanism of action, however, is not clear. Direct antiviral activity and immunomodulatory functions have been implicated. Plasmacytoid dendritic cells (pDCs) are the principal source of type 1 interferon during viral infection. The interaction of pDCs with HCV-infected hepatocytes is the subject of intense recent investigation, but the effect of ribavirin on pDC activation has not been evaluated. In this study we showed that ribavirin augments toll-like receptors 7 and 9-mediated IFNα/β expression from pDCs and up-regulated numerous interferon-stimulated genes. Using the H77S.3 HCV infection and replication system, we showed that ribavirin enhanced the ability of activated pDCs to inhibit HCV replication, correlated with elevated induction of IFNα. Our findings provide novel evidence that ribavirin contributes to HCV inhibition by augmenting pDCs-derived type 1 IFN production.
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15
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Ribosomal protein S19-binding domain provides insights into hantavirus nucleocapsid protein-mediated translation initiation mechanism. Biochem J 2015; 464:109-21. [PMID: 25062117 DOI: 10.1042/bj20140449] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The hantaviral zoonotic diseases pose a significant threat to human health due to the lack of potential antiviral therapeutics or a vaccine against hantaviruses. N (Sin Nombre hantavirus nucleocapsid protein) augments mRNA translation. N binds to both the mRNA 5' cap and 40S ribosomal subunit via RPS19 (ribosomal protein S19). N with the assistance of the viral mRNA 5'-UTR preferentially favours the translation of a downstream ORF. We identified and characterized the RPS19-binding domain at the N-terminus of N. Its deletion did not influence the secondary structure, but affected the conformation of trimeric N molecules. The N variant lacking the RPS19-binding region was able to bind both the mRNA 5' cap and panhandle-like structure, formed by the termini of viral genomic RNA. In addition, the N variant formed stable trimers similar to wild-type N. Use of this variant in multiple experiments provided insights into the mechanism of ribosome loading during N-mediated translation strategy. The present study suggests that N molecules individually associated with the mRNA 5' cap and RPS19 of the 40S ribosomal subunit undergo N-N interaction to facilitate the engagement of N-associated ribosomes at the mRNA 5' cap. This has revealed new targets for therapeutic intervention of hantavirus infection.
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Ortega-Prieto AM, Sheldon J, Grande-Pérez A, Tejero H, Gregori J, Quer J, Esteban JI, Domingo E, Perales C. Extinction of hepatitis C virus by ribavirin in hepatoma cells involves lethal mutagenesis. PLoS One 2013; 8:e71039. [PMID: 23976977 PMCID: PMC3745404 DOI: 10.1371/journal.pone.0071039] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 06/26/2013] [Indexed: 12/14/2022] Open
Abstract
Lethal mutagenesis, or virus extinction produced by enhanced mutation rates, is under investigation as an antiviral strategy that aims at counteracting the adaptive capacity of viral quasispecies, and avoiding selection of antiviral-escape mutants. To explore lethal mutagenesis of hepatitis C virus (HCV), it is important to establish whether ribavirin, the purine nucleoside analogue used in anti-HCV therapy, acts as a mutagenic agent during virus replication in cell culture. Here we report the effect of ribavirin during serial passages of HCV in human hepatoma Huh-7.5 cells, regarding viral progeny production and complexity of mutant spectra. Ribavirin produced an increase of mutant spectrum complexity and of the transition types associated with ribavirin mutagenesis, resulting in HCV extinction. Ribavirin-mediated depletion of intracellular GTP was not the major contributory factor to mutagenesis since mycophenolic acid evoked a similar decrease in GTP without an increase in mutant spectrum complexity. The intracellular concentration of the other nucleoside-triphosphates was elevated as a result of ribavirin treatment. Mycophenolic acid extinguished HCV without an intervening mutagenic activity. Ribavirin-mediated, but not mycophenolic acid-mediated, extinction of HCV occurred via a decrease of specific infectivity, a feature typical of lethal mutagenesis. We discuss some possibilities to explain disparate results on ribavirin mutagenesis of HCV.
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Affiliation(s)
- Ana M Ortega-Prieto
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
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17
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Manvar D, Singh K, Pandey VN. Affinity labeling of hepatitis C virus replicase with a nucleotide analogue: identification of binding site. Biochemistry 2013; 52:432-44. [PMID: 23268692 DOI: 10.1021/bi301098g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We have used an ATP analogue 5'-[p-(fluorosulfonyl)benzoyl]adenosine (FSBA) to modify HCV replicase in order to identify the ATP binding site in the enzyme. FSBA inactivates HCV replicase activity in a concentration-dependent manner with a binding stoichiometry of 2 moles of FSBA per mole of enzyme. The enzyme activity is protected from FSBA in the presence of rNTP substrates or double-stranded RNA template primers that do not support ATP as the incoming nucleotide but not in the presence of polyrU.rA(26). HPLC analysis of tryptic peptides of FSBA-modified enzyme revealed the presence of two distinct peptides eluted at 23 and 36 min; these were absent in the control. Further we noted that both peptides were protected from FSBA modification in the presence of Mg·ATP. The LC/MS/MS analysis of the affinity-labeled tryptic peptides purified from HPLC, identified two major modification sites at positions 382 (Tyr), and 491 (Lys) and a minor site at position 38 (Tyr). To validate the functional significance of Tyr38, Tyr382, and Lys491 in catalysis, we individually substituted these residues by alanine and examined their ability to catalyze RdRp activity. We found that both Y382A and K491A mutants were significantly affected in their ability to catalyze RdRp activity while Y38A remained unaffected. We further observed that both Y382A and K491A mutants were not affected in their ability to bind template primer but were significantly affected in their ability to photo-cross-link ATP in the absence or presence of template primer.
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Affiliation(s)
- Dinesh Manvar
- Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, USA
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Inhibition of chikungunya virus replication by harringtonine, a novel antiviral that suppresses viral protein expression. Antimicrob Agents Chemother 2012; 57:155-67. [PMID: 23275491 DOI: 10.1128/aac.01467-12] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-transmitted virus that has reemerged as a significant public health threat in the last decade. Since the 2005-2006 chikungunya fever epidemic in the Indian Ocean island of La Réunion, millions of people in more than 40 countries have been infected. Despite this, there is currently no antiviral treatment for chikungunya infection. In this study, an immunofluorescence-based screening platform was developed to identify potential inhibitors of CHIKV infection. A primary screen was performed using a highly purified natural product compound library, and 44 compounds exhibiting ≥70% inhibition of CHIKV infection were identified as positive hits. Among these, four were selected for dose-dependent inhibition assays to confirm their anti-CHIKV activity. Harringtonine, a cephalotaxine alkaloid, displayed potent inhibition of CHIKV infection (50% effective concentration [EC(50)] = 0.24 μM) with minimal cytotoxicity and was selected for elucidation of its antiviral mechanism. Time-of-addition studies, cotreatment assays, and direct transfection of viral genomic RNA indicated that harringtonine inhibited an early stage of the CHIKV replication cycle which occurred after viral entry into cells. In addition, quantitative reverse transcription-PCR (qRT-PCR) and Western blot analyses indicated that harringtonine affects CHIKV RNA production as well as viral protein expression. Treatment of harringtonine against Sindbis virus, a related alphavirus, suggested that harringtonine could inhibit other alphaviruses. This study suggests for the first time that harringtonine exerts its antiviral effects by inhibiting CHIKV viral protein synthesis.
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Thomas E, Ghany MG, Liang TJ. The application and mechanism of action of ribavirin in therapy of hepatitis C. Antivir Chem Chemother 2012; 23:1-12. [PMID: 22592135 PMCID: PMC6271563 DOI: 10.3851/imp2125] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2012] [Indexed: 12/11/2022] Open
Abstract
Ribavirin has been used as an antiviral agent for several decades. Although it has activity against numerous viruses, its major use clinically has been in the treatment of respiratory syncytial virus in paediatric patients and chronic HCV infection in both children and adults. This review highlights the clinical application and mechanism of action of ribavirin and discusses the future role of ribavirin in treatment of HCV where there are intense research efforts to improve therapy.
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Affiliation(s)
- Emmanuel Thomas
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA.
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20
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Keppeke GD, Nunes E, Ferraz MLG, Silva EAB, Granato C, Chan EKL, Andrade LEC. Longitudinal study of a human drug-induced model of autoantibody to cytoplasmic rods/rings following HCV therapy with ribavirin and interferon-α. PLoS One 2012; 7:e45392. [PMID: 23028980 PMCID: PMC3454395 DOI: 10.1371/journal.pone.0045392] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 08/22/2012] [Indexed: 12/29/2022] Open
Abstract
Background A novel pattern in the indirect immunofluorescence antinuclear antibody assay on HEp-2 cells (IIF-HEp-2) characterized by cytoplasmic rods and rings (RR) was reported in HCV patients, but stringent disease specificity studies and longitudinal analysis are lacking. We investigated the clinical significance of anti-RR in an HCV cohort with up to a 12-month treatment follow up. Methodology/Results 597 patients (342 HCV, 55 HCV/HIV, 200 non-HCV) were screened and titered for anti-RR. Serial samples were available from 78 of 176 treated and 27 of 166 untreated patients. Anti-RR was detected in 14.1% of 342 HCV patients, 9.1% of 55 HCV/HIV, 3.4% of 29 Hepatitis B, and none of 171 non-HCV (p<0.0001; HCV versus non-HCV). Anti-RR was present in 38% of 108 patients receiving interferon-α/ribavirin, but none in 26 receiving either interferon-α or ribavirin, or 166 untreated patients (p<0.0001). Other IIF-HEp-2 patterns were more frequently associated with interferon-α treatment alone (52.2%) as compared to interferon-α/ribavirin (25%), ribavirin alone (33.3%), and no therapy (26.5%). Anti-RR frequency was not associated with sex, age, ethnicity, HCV genotype or viral load. Anti-RR occurred only after initiation of treatment, beginning as early as 1 month (6%), but by the sixth month >47% tested positive for anti-RR. The anti-RR titer generally increased with sustained treatment and remained high in 53% of patients. After treatment, anti-RR titer was negative in 41%. Non-responders to HCV therapy were 77% in anti-RR-positive versus 64% in anti-RR-negative patients. Response to treatment was not associated with anti-RR titer or the dynamics of anti-RR reactivity during and after treatment. Conclusions The exquisite association of anti-RR reactivity with combined interferon-α/ribavirin therapy in HCV patients represents a unique model for drug-induced autoantibody generation in humans as demonstrated by the fact that a significant fraction of patients who have anti-RR during therapy becomes anti-RR-negative after completion of therapy.
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Affiliation(s)
| | - Eunice Nunes
- Gastroenterology Division, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | | | - Celso Granato
- Infectious Diseases Division, Universidade Federal de São Paulo, São Paulo, Brazil
- Immunology Division, Fleury Medicine and Health Laboratories, São Paulo, Brazil
| | - Edward K. L. Chan
- Department of Oral Biology, University of Florida, Gainesville, Florida, United States of America
| | - Luís Eduardo C. Andrade
- Rheumatology Division, Universidade Federal de São Paulo, São Paulo, Brazil
- Immunology Division, Fleury Medicine and Health Laboratories, São Paulo, Brazil
- * E-mail:
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21
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Host-based ribavirin resistance influences hepatitis C virus replication and treatment response. J Virol 2011; 85:7273-83. [PMID: 21543469 DOI: 10.1128/jvi.00629-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Many individuals infected with hepatitis C virus (HCV) develop a chronic infection, and of those who are treated with pegylated interferon and ribavirin (RBV), many do not respond. While the nucleoside analog RBV improves treatment outcome, and will likely be an important component of therapy with next-generation viral inhibitors, RBV's mechanism is controversial. Most of RBV's proposed mechanisms require RBV import into cells. Therefore, we explored whether host-based RBV resistance develops through reduced cellular uptake, akin to chemotherapy resistance in some cancers. We examined the effect of host-based RBV resistance on HCV replication in cultured hepatoma Huh7.5 liver cells and whether RBV resistance develops in HCV patients. When Huh7.5 cells were exposed to RBV, resistance developed through reduced RBV uptake via the ENT1 nucleoside transporter and antiviral efficacy was reduced. The uptake defect in RBV-resistant cells was specific to RBV, since transport of another ENT1 substrate, cytidine, was unaffected. Importantly, RBV uptake significantly declined in HCV patient peripheral blood mononuclear cells (PBMCs) following 4 weeks of therapy. Furthermore, maintenance of RBV uptake correlated with rapid treatment response. Our results uncovered a novel form of antiviral drug resistance and suggest that host-based RBV resistance develops in HCV patients undergoing therapy and that maintenance of RBV uptake may contribute to rapid viral clearance.
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Li S, Kodama EN, Inoue Y, Tani H, Matsuura Y, Zhang J, Tanaka T, Hattori T. Procyanidin B1 purified from Cinnamomi cortex suppresses hepatitis C virus replication. Antivir Chem Chemother 2010; 20:239-48. [PMID: 20710064 DOI: 10.3851/imp1597] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND A combination of pegylated interferon and ribavirin is the current standard therapy for hepatitis C virus (HCV) infection, but this combination provides relatively low efficacy, especially in some patients with HCV genotype 1 infection; therefore, the development of novel therapeutic agents is required for further improvement in the treatment of chronic HCV infection. METHODS HCV pseudotype and subgenomic replicon assays were used in this study. The interaction of compounds with HCV receptors was examined using flow cytometry. Intracellular RNA levels were determined by semi-quantitative reverse transcriptase PCR. RESULTS Procyanidin B1 (PB1), a dimer of (-)-epicatechin and (+)-catechin, purified from Cinnamomi cortex, inhibits infection by vesicular stomatitis virus and HCV pseudotype virus in Huh-7 cells, with 50% effective concentrations of 29 and 15 microM, respectively. No inhibitory effects were observed in each component of PB1. We found that PB1 does not interfere with viral entry or receptor expression, but inhibits HCV RNA synthesis in a dose-dependent manner. CONCLUSIONS These results indicate that PB1 suppresses HCV RNA synthesis, possibly as a HCV RNA polymerase inhibitor. Our results might contribute towards the development of more effective inhibitors for HCV infection from natural plants.
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Affiliation(s)
- Shenwei Li
- Division of Emerging Infectious Diseases, Department of Internal Medicine, Tohoku University, Sendai, Japan
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Bollati M, Alvarez K, Assenberg R, Baronti C, Canard B, Cook S, Coutard B, Decroly E, de Lamballerie X, Gould EA, Grard G, Grimes JM, Hilgenfeld R, Jansson AM, Malet H, Mancini EJ, Mastrangelo E, Mattevi A, Milani M, Moureau G, Neyts J, Owens RJ, Ren J, Selisko B, Speroni S, Steuber H, Stuart DI, Unge T, Bolognesi M. Structure and functionality in flavivirus NS-proteins: perspectives for drug design. Antiviral Res 2010; 87:125-48. [PMID: 19945487 PMCID: PMC3918146 DOI: 10.1016/j.antiviral.2009.11.009] [Citation(s) in RCA: 241] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 09/08/2009] [Accepted: 11/21/2009] [Indexed: 12/28/2022]
Abstract
Flaviviridae are small enveloped viruses hosting a positive-sense single-stranded RNA genome. Besides yellow fever virus, a landmark case in the history of virology, members of the Flavivirus genus, such as West Nile virus and dengue virus, are increasingly gaining attention due to their re-emergence and incidence in different areas of the world. Additional environmental and demographic considerations suggest that novel or known flaviviruses will continue to emerge in the future. Nevertheless, up to few years ago flaviviruses were considered low interest candidates for drug design. At the start of the European Union VIZIER Project, in 2004, just two crystal structures of protein domains from the flaviviral replication machinery were known. Such pioneering studies, however, indicated the flaviviral replication complex as a promising target for the development of antiviral compounds. Here we review structural and functional aspects emerging from the characterization of two main components (NS3 and NS5 proteins) of the flavivirus replication complex. Most of the reviewed results were achieved within the European Union VIZIER Project, and cover topics that span from viral genomics to structural biology and inhibition mechanisms. The ultimate aim of the reported approaches is to shed light on the design and development of antiviral drug leads.
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Affiliation(s)
- Michela Bollati
- Department of Biomolecular Sciences and Biotechnology, University of Milano, Via Celoria 26, 20133 Milano, Italy
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Hang JQ, Yang Y, Harris SF, Leveque V, Whittington HJ, Rajyaguru S, Ao-Ieong G, McCown MF, Wong A, Giannetti AM, Le Pogam S, Talamás F, Cammack N, Nájera I, Klumpp K. Slow binding inhibition and mechanism of resistance of non-nucleoside polymerase inhibitors of hepatitis C virus. J Biol Chem 2009; 284:15517-29. [PMID: 19246450 PMCID: PMC2708848 DOI: 10.1074/jbc.m808889200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 01/20/2009] [Indexed: 01/03/2023] Open
Abstract
The binding affinity of four palm and thumb site representative non-nucleoside inhibitors (NNIs) of HCV polymerase NS5B to wild-type and resistant NS5B polymerase proteins was determined, and the influence of RNA binding on NNI binding affinity was investigated. NNIs with high binding affinity potently inhibited HCV RNA polymerase activity and replicon replication. Among the compounds tested, HCV-796 showed slow binding kinetics to NS5B. The binding affinity of HCV-796 to NS5B increased 27-fold over a 3-h incubation period with an equilibrium Kd of 71 +/- 2 nm. Slow binding kinetics of HCV-796 was driven by slow dissociation from NS5B with a k(off) of 4.9 +/- 0.5 x 10(-4) s(-1). NS5B bound a long, 378-nucleotide HCV RNA oligonucleotide with high affinity (Kd = 6.9 +/- 0.3 nm), whereas the binding affinity was significantly lower for a short, 21-nucleotide RNA (Kd = 155.1 +/- 16.2 nm). The formation of the NS5B-HCV RNA complex did not affect the slow binding kinetics profile and only slightly reduced NS5B binding affinity of HCV-796. The magnitude of reduction of NNI binding affinity for the NS5B proteins with various resistance mutations in the palm and thumb binding sites correlated well with resistance -fold shifts in NS5B polymerase activity and replicon assays. Co-crystal structures of NS5B-Con1 and NS5B-BK with HCV-796 revealed a deep hydrophobic binding pocket at the palm region of NS5B. HCV-796 interaction with the induced binding pocket on NS5B is consistent with slow binding kinetics and loss of binding affinity with mutations at amino acid position 316.
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Affiliation(s)
- Julie Qi Hang
- From Roche Palo Alto LLC, Palo Alto, California 94304
| | - Yanli Yang
- From Roche Palo Alto LLC, Palo Alto, California 94304
| | | | | | | | | | | | | | - April Wong
- From Roche Palo Alto LLC, Palo Alto, California 94304
| | | | | | | | - Nick Cammack
- From Roche Palo Alto LLC, Palo Alto, California 94304
| | - Isabel Nájera
- From Roche Palo Alto LLC, Palo Alto, California 94304
| | - Klaus Klumpp
- From Roche Palo Alto LLC, Palo Alto, California 94304
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Reduced ribavirin antiviral efficacy via nucleoside transporter-mediated drug resistance. J Virol 2009; 83:4538-47. [PMID: 19244331 DOI: 10.1128/jvi.02280-08] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Treatment for hepatitis C virus infection currently consists of pegylated interferon and ribavirin (RBV), a nucleoside analog. Although RBV clearly plays a role in aiding the treatment response, its antiviral mechanism is unclear. Regardless of the specific mechanism of RBV, we hypothesize that differences in levels of cellular uptake of RBV may affect antiviral efficacy and treatment success and that cells may become RBV resistant through reduced uptake. We monitored RBV uptake in various cell lines and determined the effect of uptake capacity on viral replication. RBV-resistant cells demonstrated reduced RBV uptake and increased growth of a model RNA virus, poliovirus, in the presence of RBV. Overexpression of equilibrative nucleoside transporter 1 (ENT1) or concentrative nucleoside transporter 3 (CNT3) increased RBV uptake in RBV-sensitive cell lines and restored the uptake defect in most RBV-resistant cell lines. However, CNT3 is not expressed in Huh-7 liver cells, and inhibition of concentrative transport did not affect RBV uptake. Blocking equilibrative transport using the inhibitor nitrobenzylmercaptopurine riboside recapitulated the RBV-resistant phenotype in RBV-sensitive cell lines, with a reduction in RBV uptake and increased poliovirus growth. Taken together, these results indicate that RBV uptake is restricted primarily to ENT1 in the cell lines examined. Interestingly, some RBV-resistant cell lines may compensate for reduced ENT1-mediated nucleoside uptake by increasing the activity of an alternative nucleoside transporter, ENT2. It is possible that RBV uptake affects the antiviral treatment response, either through natural differences in patients or through acquired resistance.
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Hofmann WP, Herrmann E, Sarrazin C, Zeuzem S. Ribavirin mode of action in chronic hepatitis C: from clinical use back to molecular mechanisms. Liver Int 2008; 28:1332-43. [PMID: 19055642 DOI: 10.1111/j.1478-3231.2008.01896.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ribavirin is an old broad-spectrum antiviral that is highly effective when used in combination with interferon-alpha and also as part of triple therapies containing new inhibitors of the hepatitis C virus (HCV) non-structural (NS)3/4 protease or HCV NS5B polymerase for the treatment of patients with chronic hepatitis C. However, the molecular mechanisms by which ribavirin enhances early and sustained virological response rates during interferon-based antiviral HCV therapy are still unknown. Several mechanisms including (i) immunomodulatory properties, (ii) inhibition of the inosine monophosphate dehydrogenase, (iii) direct inhibition of the HCV-encoded NS5B RNA polymerase, (iv) induction of lethal mutagenesis and (v) modulation of interferon-stimulated gene expression are currently proposed. Here, we discuss recent advances from in vitro data and their importance for the situation in patients with chronic hepatitis C. Furthermore, theoretical aspects from mathematical modelling of ribavirin action in chronic hepatitis C are reviewed.
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Affiliation(s)
- Wolf Peter Hofmann
- Department of Internal Medicine 1, Johann Wolfgang Goethe-University Hospital, Frankfurt, Germany
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Leyssen P, De Clercq E, Neyts J. Molecular strategies to inhibit the replication of RNA viruses. Antiviral Res 2008; 78:9-25. [PMID: 18313769 PMCID: PMC7114363 DOI: 10.1016/j.antiviral.2008.01.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 01/04/2008] [Accepted: 01/08/2008] [Indexed: 12/24/2022]
Abstract
There are virtually no antiviral drugs available for the treatment of infections with RNA viruses. This is particularly worrisome since most of the highly pathogenic and emerging viruses are, and will likely continue to be, RNA viruses. These viruses can cause acute, severe illness, including severe respiratory disease, hemorrhagic fever and encephalitis, with a high case fatality rate. It is important to have potent and safe drugs at hand that can be used for the treatment or prophylaxis of such infections. Drugs approved for the treatment of RNA virus infections (other than HIV) are the influenza M2 channel inhibitors, amantadine and rimantadine; the influenza neuraminidase inhibitors, oseltamivir and zanamivir, and ribavirin for the treatment of infections with respiratory syncytial virus and hepatitis C virus. The molecular mechanism(s) by which ribavirin inhibits viral replication, such as depletion of intracellular GTP pools and induction of error catastrophe, may not readily allow the design of analogues that are more potent/selective than the parent drug. Highly pathogenic RNA viruses belong to a variety of virus families, each having a particular replication strategy, thus offering a wealth of potential targets to selectively inhibit viral replication. We here provide a non-exhaustive review of potential experimental strategies, using small molecules, to inhibit the replication of several RNA viruses. Other approaches, such as the use of interferon or other host-response modifiers, immune serum or neutralizing antibodies, are not addressed in this review.
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Affiliation(s)
| | | | - Johan Neyts
- Rega Institute for Medical Research, Catholic University Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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Picard-Jean F, Bougie I, Bisaillon M. Characterization of the DNA- and dNTP-binding activities of the human cytomegalovirus DNA polymerase catalytic subunit UL54. Biochem J 2007; 407:331-41. [PMID: 17672827 PMCID: PMC2275067 DOI: 10.1042/bj20070853] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The catalytic subunit of the human cytomegalovirus DNA polymerase is critical for the replication of the virus. In the present study, we report the expression and purification of a recombinant catalytic subunit of the human cytomegalovirus DNA polymerase expressed in bacteria which retains polymerase activity. As a first step towards elucidating the nature of the interaction between the enzyme, DNA and dNTPs, we have utilized endogenous tryptophan fluorescence to evaluate the binding of ligands to the enzyme. Using this technique, we demonstrate that the minimal DNA-binding site of the enzyme is 6 nt. We also report the first detailed study of the binding kinetics and thermodynamic parameters involved in the interaction between the enzyme, DNA and dNTPs. Our thermodynamic analyses indicate that the initial formation of the enzyme-DNA binary complex is driven by a favourable entropy change, but is also clearly associated with an unfavourable enthalpic contribution. In contrast, the interaction of dNTPs to the binary complex was shown to depend on a completely different mode of binding that is dominated by a favourable enthalpy change and associated with an unfavourable entropy change. In order to provide additional insights into the structural modifications that occur during catalysis, we correlated the effect of DNA and dNTP binding on protein structure using CD. Our results indicate that the enzyme undergoes a first conformational change upon the formation of the protein-DNA binary complex, which is followed by a second structural modification upon dNTP binding. The present study provides a better understanding of the molecular basis of DNA and dNTP recognition by the catalytic subunit of the human cytomegalovirus DNA polymerase.
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Affiliation(s)
- Frédéric Picard-Jean
- Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4
| | - Isabelle Bougie
- Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4
| | - Martin Bisaillon
- Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4
- To whom correspondence should be addressed (email )
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Wohnsland A, Hofmann WP, Sarrazin C. Viral determinants of resistance to treatment in patients with hepatitis C. Clin Microbiol Rev 2007; 20:23-38. [PMID: 17223621 PMCID: PMC1797633 DOI: 10.1128/cmr.00010-06] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chronic hepatitis C virus (HCV) infection affects more than 170 million persons worldwide and is responsible for the development of liver cirrhosis in many cases. Standard treatment with pegylated alpha interferon (IFN-alpha) in combination with the nucleoside analogue ribavirin leads to a sustained virologic response in approximately half of the patients. IFN-alpha is classified as an indirect treatment, as it interacts with the host's immune response. The mechanism of action of ribavirin is still unknown. The benefit of triple therapy by adding other antiviral agents, e.g., amantadine, is controversial. Currently, new direct antiviral drugs (HCV protease/polymerase inhibitors) are being evaluated in phase 1/phase 2 trials. Phenotypic resistance to antiviral therapy has been attributed to amino acid variations within distinct regions of the HCV polyprotein. While sensitivity to IFN-alpha-based antiviral therapy in vivo is clearly correlated with the number of mutations within the HCV NS5A protein, the underlying functional mechanisms for this association are unknown. In turn, in vitro, several mechanisms to circumvent the host immune defense or to block treatment-induced antiviral activities have been described for different HCV proteins. By the introduction of direct antiviral drugs, hepatitis C therapy now is entering a new era in which the development of resistance may become the most important parameter for treatment success or failure.
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Affiliation(s)
- Anette Wohnsland
- Department of Internal Medicine II, Saarland University Hospital, Kirrbergerstrasse, 66421 Homburg/Saar, Germany
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Sallie R. Replicative homeostasis III: implications for antiviral therapy and mechanisms of response and non-response. Virol J 2007; 4:29. [PMID: 17355620 PMCID: PMC1847443 DOI: 10.1186/1743-422x-4-29] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Accepted: 03/13/2007] [Indexed: 12/27/2022] Open
Abstract
While improved drug regimens have greatly enhanced outcomes for patients with chronic viral infection, antiviral therapy is still not ideal due to drug toxicities, treatment costs, primary drug failure and emergent resistance. New antiviral agents, alternative treatment strategies and a better understanding of viral pathobiology, host responses and drug action are desperately needed. Interferon (IFN) and ribavirin, are effective drugs used to treat hepatitis C (HCV), but the mechanism(s) of their action are uncertain. Error catastrophe (EC), or precipitous loss of replicative fitness caused by genomic mutation, is postulated to mediate ribavirin action, but is a deeply flawed hypothesis lacking empirical confirmation. Paradoxically ribavirin, a proven RNA mutagen, has no impact on HCV viraemia long term, suggesting real viruses, replicating in-vitro, as opposed to mathematical models, replicating in-silico, are likely to resist EC by highly selective replication of fit (~consensus sequence) genomes mediated, in part, by replicative homeostasis (RH), an epicyclic mechanism that dynamically links RNApol fidelity and processivity and other viral protein functions. Replicative homeostasis provides a rational explanation for the various responses seen during treatment of HCV, including genotype-specific and viral load-dependent differential response rates, as well as otherwise unexplained phenomena like the transient inhibition and rebound of HCV viraemia seen during ribavirin monotherapy. Replicative homeostasis also suggests a primarily non-immunological mechanism that mediates increased immune responsiveness during treatment with ribavirin (and other nucleos(t)ide analogues), explicating the enhanced second-phase clearance of HCV ribavirin promotes and, thus, the apparent immunomodulatory action of ribavirin. More importantly, RH suggests specific new antiviral therapeutic strategies.
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Abstract
Thirty years after its synthesis, the mechanism of action of ribavirin is still not completely understood. Although much is known about the metabolism and biochemical effects of ribavirin in human cells, there is still much to be learned about the precise mechanism of action of ribavirin with the various viruses. New information about its ability to induce mutations in viral genomes has led to new questions about its mechanism of action. There is considerable evidence that indicates that ribavirin triphosphate (RTP) can interact with the various viral RNA polymerases, and it seems likely that this interaction is important to the mechanism of action of ribavirin. It seems likely that ribavirin will not have one universal mechanism of action, but will inhibit different viruses in different ways. In some cases, inhibition of IMP dehydrogenase may be sufficient for antiviral activity. Whereas, in other cases, inhibition of viral RNA polymerases by RTP may be more important. It is also likely that RTP will interact with the different viral RNA polymerases in different ways leading to different mechanisms of actions. More comprehensive studies are needed that address all aspects of ribavirin metabolism and biochemical actions to gain a thorough understanding of the activity of this agent. Finally, the differences in the metabolism and biochemical actions of ribavirin, selenazofurin, and tiazofurin indicate that small structural changes can have profound effects on biological activity. This observation is well known by investigators familiar with nucleoside analogs, but indicate that one should not assume that agents of similar structure have identical activities.
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Affiliation(s)
- William B Parker
- Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205, USA.
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Mir MA, Panganiban AT. The hantavirus nucleocapsid protein recognizes specific features of the viral RNA panhandle and is altered in conformation upon RNA binding. J Virol 2005; 79:1824-35. [PMID: 15650206 PMCID: PMC544099 DOI: 10.1128/jvi.79.3.1824-1835.2005] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Hantaviruses are tripartite negative-sense RNA viruses and members of the Bunyaviridae family. The nucleocapsid (N) protein is the principal structural component of the viral capsid. N forms a stable trimer that specifically recognizes the panhandle structure formed by the viral RNA termini. We used trimeric glutathione S-transferase (GST)-N protein and small RNA panhandles to examine the requirements for specific recognition by Sin Nombre hantavirus N. Trimeric GST-N recognizes the panhandles of the three viral RNAs (S, M, and L) with high affinity, whereas the corresponding plus-strand panhandles of the complementary RNA are recognized with lower affinity. Based on analysis of nucleotide substitutions that alter either the higher-order structure of the panhandle or the primary sequence of the panhandle, both secondary structure and primary sequence are necessary for stable interaction with N. A panhandle 23 nucleotides long is necessary and sufficient for high-affinity binding by N, and stoichiometry calculations indicate that a single N trimer interacts with a single panhandle. Surprisingly, displacement of the panhandle structure away from the terminus does not eliminate recognition by N. The binding of N to the panhandle is an entropy-driven process resulting in initial stable N-RNA interaction followed by a conformational change in N. Taken together, these data provide insight into the molecular events that take place during interaction of N with the panhandle and suggest that specific high-affinity interaction between an RNA binding domain of trimeric N and the panhandle is required for encapsidation of the three viral RNAs.
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Affiliation(s)
- M A Mir
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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Ng KKS, Pendás-Franco N, Rojo J, Boga JA, Machín A, Alonso JMM, Parra F. Crystal structure of norwalk virus polymerase reveals the carboxyl terminus in the active site cleft. J Biol Chem 2004; 279:16638-45. [PMID: 14764591 DOI: 10.1074/jbc.m400584200] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Norwalk virus is a major cause of acute gastroenteritis for which effective treatments are sorely lacking. To provide a basis for the rational design of novel antiviral agents, the main replication enzyme in Norwalk virus, the virally encoded RNA-dependent RNA polymerase (RdRP), has been expressed in an enzymatically active form, and its structure has been crystallographically determined both in the presence and absence of divalent metal cations. Although the overall fold of the enzyme is similar to that seen previously in the RdRP from rabbit hemorrhagic disease virus, the carboxyl terminus, surprisingly, is located in the active site cleft in five independent copies of the protein in three distinct crystal forms. The location of this carboxyl-terminal segment appears to interfere with the binding of double-stranded RNA in the active site cleft and may play a role in the initiation of RNA synthesis or mediate interactions with accessory replication proteins.
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Affiliation(s)
- Kenneth K-S Ng
- Division of Biochemistry, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
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