1
|
Giannakopoulou E, Akrani I, Mpekoulis G, Frakolaki E, Dimitriou M, Myrianthopoulos V, Vassilaki N, Zoidis G. Novel Pyrazino[1,2- a]indole-1,3(2 H,4 H)-dione Derivatives Targeting the Replication of Flaviviridae Viruses: Structural and Mechanistic Insights. Viruses 2024; 16:1238. [PMID: 39205212 PMCID: PMC11360281 DOI: 10.3390/v16081238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/27/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024] Open
Abstract
Infections with Flaviviridae viruses, such as hepatitis C (HCV), dengue (DENV), and yellow fever (YFV) viruses, are major public health problems worldwide. In the case of HCV, treatment is associated with drug resistance and high costs, while there is no clinically approved therapy for DENV and YFV. Consequently, there is still a need for new chemotherapies with alternative modes of action. We have previously identified novel 2-hydroxypyrazino[1,2-a]indole-1,3(2H,4H)-diones as metal-chelating inhibitors targeting HCV RNA replication. Here, by utilizing a structure-based approach, we rationally designed a second series of compounds by introducing various substituents at the indole core structure and at the imidic nitrogen, to improve specificity against the RNA-dependent RNA polymerase (RdRp). The resulting derivatives were evaluated for their potency against HCV genotype 1b, DENV2, and YFV-17D using stable replicon cell lines. The most favorable substitution was nitro at position 6 of the indole ring (compound 36), conferring EC50 1.6 μM against HCV 1b and 2.57 μΜ against HCV 1a, with a high selectivity index. Compound 52, carrying the acetohydroxamic acid functionality (-CH2CONHOH) on the imidic nitrogen, and compound 78, the methyl-substituted molecule at the position 4 indolediketopiperazine counterpart, were the most effective against DENV and YFV, respectively. Interestingly, compound 36 had a high genetic barrier to resistance and only one resistance mutation was detected, T181I in NS5B, suggesting that the compound target HCV RdRp is in accordance with our predicted model.
Collapse
Affiliation(s)
- Erofili Giannakopoulou
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece; (E.G.); (I.A.); (V.M.)
| | - Ifigeneia Akrani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece; (E.G.); (I.A.); (V.M.)
| | - George Mpekoulis
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, GR-11521 Athens, Greece; (G.M.); (M.D.)
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, GR-11521 Athens, Greece; (G.M.); (M.D.)
| | - Marios Dimitriou
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, GR-11521 Athens, Greece; (G.M.); (M.D.)
| | - Vassilios Myrianthopoulos
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece; (E.G.); (I.A.); (V.M.)
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, GR-11521 Athens, Greece; (G.M.); (M.D.)
| | - Grigoris Zoidis
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece; (E.G.); (I.A.); (V.M.)
| |
Collapse
|
2
|
Zahedipour F, Zahedipour F, Zamani P, Jaafari MR, Sahebkar A. Harnessing CRISPR technology for viral therapeutics and vaccines: from preclinical studies to clinical applications. Virus Res 2024; 341:199314. [PMID: 38211734 PMCID: PMC10825633 DOI: 10.1016/j.virusres.2024.199314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
The CRISPR/Cas system, identified as a type of bacterial adaptive immune system, have attracted significant attention due to its remarkable ability to precisely detect and eliminate foreign genetic material and nucleic acids. Expanding upon these inherent capabilities, recent investigations have unveiled the potential of reprogrammed CRISPR/Cas 9, 12, and 13 systems for treating viral infections associated with human diseases, specifically targeting DNA and RNA viruses, respectively. Of particular interest is the RNA virus responsible for the recent global outbreak of coronavirus disease 2019 (COVID-19), which presents a substantial public health risk, coupled with limited efficacy of current prophylactic and therapeutic techniques. In this regard, the utilization of CRISPR/Cas technology offers a promising gene editing approach to overcome the limitations of conventional methods in managing viral infections. This comprehensive review provides an overview of the latest CRISPR/Cas-based therapeutic and vaccine strategies employed to combat human viral infections. Additionally, we discuss significant challenges and offer insights into the future prospects of this cutting-edge gene editing technology.
Collapse
Affiliation(s)
- Farzaneh Zahedipour
- Microbiology Department, Medical Sciences Branch, Islamic Azad University (IAU), Tehran, Iran
| | - Fatemeh Zahedipour
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parvin Zamani
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahmoud Reza Jaafari
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
3
|
Liu C, Guo M, Han L, Lu J, Xiang X, Xie Q, Nouhin J, Duong V, Tong Y, Zhong J. Construction and characterization of a new hepatitis C virus genotype 6a subgenomic replicon that is prone to render the sofosbuvir resistance. J Med Virol 2023; 95:e29103. [PMID: 37721366 DOI: 10.1002/jmv.29103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/19/2023]
Abstract
Hepatitis C virus (HCV) infection remains a challenge to human public health despite the development of highly effective direct-acting antivirals (DAAs). Sofosbuvir (SOF), a key component in most DAA-based anti-HCV cocktail regimens, is a potent viral RNA polymerase (NS5B) inhibitor with a high barrier to drug resistance. The serine-to-threonine mutation at NS5B 282 (S282T) confers the SOF resistance, but severely impairs viral replication in most HCV genotypes (GTs) and cannot be stably maintained after the termination of the SOF-based therapies. In this study, we first developed a new HCV GT-6a subgenomic replicon PR58D6. Next, we selected SOF-resistant PR58D6 variants by culturing the replicon cells in the presence of SOF. Interestingly, unlike many other HCV replicons which require additional mutations to compensate for the S282T-inducing fitness loss, S282T alone in PR58D6 is genetically stable and confers the SOF resistance without significantly impairing viral replication. Furthermore, we showed that amino acid residue at NS5B 74 (R74) and 556 (D556) which are conserved in GT 6a HCV contribute to efficient replication of PR58D6 containing S282T. Finally, we showed that the G556D mutation in NS5B could rescue the replication deficiency of the S282T in JFH1, a GT-2a replicon. In conclusion, we showed that a novel GT-6a HCV replicon may easily render SOF resistance, which may call for attention to potential drug resistance during DAA therapies of HCV GT-6a patients.
Collapse
Affiliation(s)
- Chaolun Liu
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Mingzhe Guo
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Lin Han
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Lu
- Department of Infectious Disease, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaogang Xiang
- Department of Infectious Disease, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qing Xie
- Department of Infectious Disease, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Janin Nouhin
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
- Sequencing Platform, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
- Sequencing Platform, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
| | - Yimin Tong
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jin Zhong
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
4
|
Kumar S, Verma R, Saha S, Agrahari AK, Shukla S, Singh ON, Berry U, Anurag, Maiti TK, Asthana S, Ranjith-Kumar CT, Surjit M. RNA-Protein Interactome at the Hepatitis E Virus Internal Ribosome Entry Site. Microbiol Spectr 2023; 11:e0282722. [PMID: 37382527 PMCID: PMC10434006 DOI: 10.1128/spectrum.02827-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/11/2023] [Indexed: 06/30/2023] Open
Abstract
Multiple processes exist in a cell to ensure continuous production of essential proteins either through cap-dependent or cap-independent translation processes. Viruses depend on the host translation machinery for viral protein synthesis. Therefore, viruses have evolved clever strategies to use the host translation machinery. Earlier studies have shown that genotype 1 hepatitis E virus (g1-HEV) uses both cap-dependent and cap-independent translation machineries for its translation and proliferation. Cap-independent translation in g1-HEV is driven by an 87-nucleotide-long RNA element that acts as a noncanonical, internal ribosome entry site-like (IRESl) element. Here, we have identified the RNA-protein interactome of the HEV IRESl element and characterized the functional significance of some of its components. Our study identifies the association of HEV IRESl with several host ribosomal proteins, demonstrates indispensable roles of ribosomal protein RPL5 and DHX9 (RNA helicase A) in mediating HEV IRESl activity, and establishes the latter as a bona fide internal translation initiation site. IMPORTANCE Protein synthesis is a fundamental process for survival and proliferation of all living organisms. The majority of cellular proteins are produced through cap-dependent translation. Cells also use a variety of cap-independent translation processes to synthesize essential proteins during stress. Viruses depend on the host cell translation machinery to synthesize their own proteins. Hepatitis E virus (HEV) is a major cause of hepatitis worldwide and has a capped positive-strand RNA genome. Viral nonstructural and structural proteins are synthesized through a cap-dependent translation process. An earlier study from our laboratory reported the presence of a fourth open reading frame (ORF) in genotype 1 HEV, which produces the ORF4 protein using a cap-independent internal ribosome entry site-like (IRESl) element. In the current study, we identified the host proteins that associate with the HEV-IRESl RNA and generated the RNA-protein interactome. Through a variety of experimental approaches, our data prove that HEV-IRESl is a bona fide internal translation initiation site.
Collapse
Affiliation(s)
- Shiv Kumar
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Rohit Verma
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Sandhini Saha
- Laboratory of Functional Proteomics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Ashish Kumar Agrahari
- Noncommunicable Disease Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Shivangi Shukla
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Oinam Ningthemmani Singh
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Umang Berry
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Anurag
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Tushar Kanti Maiti
- Laboratory of Functional Proteomics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Shailendra Asthana
- Noncommunicable Disease Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - C. T. Ranjith-Kumar
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Milan Surjit
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| |
Collapse
|
5
|
Sherwood AV, Rivera-Rangel LR, Ryberg LA, Larsen HS, Anker KM, Costa R, Vågbø CB, Jakljevič E, Pham LV, Fernandez-Antunez C, Indrisiunaite G, Podolska-Charlery A, Grothen JER, Langvad NW, Fossat N, Offersgaard A, Al-Chaer A, Nielsen L, Kuśnierczyk A, Sølund C, Weis N, Gottwein JM, Holmbeck K, Bottaro S, Ramirez S, Bukh J, Scheel TKH, Vinther J. Hepatitis C virus RNA is 5'-capped with flavin adenine dinucleotide. Nature 2023:10.1038/s41586-023-06301-3. [PMID: 37407817 DOI: 10.1038/s41586-023-06301-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/08/2023] [Indexed: 07/07/2023]
Abstract
RNA viruses have evolved elaborate strategies to protect their genomes, including 5' capping. However, until now no RNA 5' cap has been identified for hepatitis C virus1,2 (HCV), which causes chronic infection, liver cirrhosis and cancer3. Here we demonstrate that the cellular metabolite flavin adenine dinucleotide (FAD) is used as a non-canonical initiating nucleotide by the viral RNA-dependent RNA polymerase, resulting in a 5'-FAD cap on the HCV RNA. The HCV FAD-capping frequency is around 75%, which is the highest observed for any RNA metabolite cap across all kingdoms of life4-8. FAD capping is conserved among HCV isolates for the replication-intermediate negative strand and partially for the positive strand. It is also observed in vivo on HCV RNA isolated from patient samples and from the liver and serum of a human liver chimeric mouse model. Furthermore, we show that 5'-FAD capping protects RNA from RIG-I mediated innate immune recognition but does not stabilize the HCV RNA. These results establish capping with cellular metabolites as a novel viral RNA-capping strategy, which could be used by other viruses and affect anti-viral treatment outcomes and persistence of infection.
Collapse
Affiliation(s)
- Anna V Sherwood
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Lizandro R Rivera-Rangel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Line A Ryberg
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Helena S Larsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Klara M Anker
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Rui Costa
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Cathrine B Vågbø
- Proteomics and Modomics Experimental Core (PROMEC), Norwegian University of Science and Technology and the Central Norway Regional Health Authority, Trondheim, Norway
| | - Eva Jakljevič
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Long V Pham
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Gabriele Indrisiunaite
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Agnieszka Podolska-Charlery
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Julius E R Grothen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Nicklas W Langvad
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Nicolas Fossat
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Anna Offersgaard
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Amal Al-Chaer
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Louise Nielsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Anna Kuśnierczyk
- Proteomics and Modomics Experimental Core (PROMEC), Norwegian University of Science and Technology and the Central Norway Regional Health Authority, Trondheim, Norway
| | - Christina Sølund
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen N, Denmark
| | - Nina Weis
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen N, Denmark
| | - Judith M Gottwein
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Kenn Holmbeck
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Sandro Bottaro
- Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark.
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark.
| | - Troels K H Scheel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark.
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark.
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
| | - Jeppe Vinther
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
| |
Collapse
|
6
|
Nasr T, Aboshanab AM, Mpekoulis G, Drakopoulos A, Vassilaki N, Zoidis G, Abouzid KAM, Zaghary W. Novel 6-Aminoquinazolinone Derivatives as Potential Cross GT1-4 HCV NS5B Inhibitors. Viruses 2022; 14:v14122767. [PMID: 36560772 PMCID: PMC9782603 DOI: 10.3390/v14122767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
Chronic hepatitis C virus (HCV) infections are a worldwide medical problem responsible for diverse types of liver diseases. The NS5B polymerase enzyme has become a very interesting target for the development of anti-HCV drugs owing to its fundamental role in viral replication. Here we report the synthesis of a novel series of 1-substituted phenyl-4(1H)-quinazolinone and 2-methyl-1-substituted phenyl-4(1H)-quinazolinone derivatives and evaluate their activity against HCV in HCV subgenomic replicon assays. The biological data revealed that compound 11a showed the highest activity against HCV GT1b at a micromolar concentration (EC50 = 0.984 µM) followed by compound 11b (EC50 = 1.38 µM). Both compounds 11a and 11b had high selectivity indices (SI = CC50/EC50), 160.71 and 71.75, respectively, which make them very interesting candidates for further development of more potent and selective anti-HCV agents.
Collapse
Affiliation(s)
- Tamer Nasr
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Ain-Helwan, Cairo 11795, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, MTI University, Cairo 12055, Egypt
- Correspondence: (T.N.); (G.Z.)
| | - Ahmed M. Aboshanab
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Ain-Helwan, Cairo 11795, Egypt
| | - George Mpekoulis
- Molecular Virology Laboratory, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Antonios Drakopoulos
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Grigoris Zoidis
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
- Correspondence: (T.N.); (G.Z.)
| | - Khaled A. M. Abouzid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo 11566, Egypt
| | - Wafaa Zaghary
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Ain-Helwan, Cairo 11795, Egypt
| |
Collapse
|
7
|
Hamdy J, Emadeldin N, Hamed MM, Frakolaki E, Katsamakas S, Vassilaki N, Zoidis G, Hirsch AKH, Abdel-Halim M, Abadi AH. Design and Synthesis of Novel Bis-Imidazolyl Phenyl Butadiyne Derivatives as HCV NS5A Inhibitors. Pharmaceuticals (Basel) 2022; 15:632. [PMID: 35631457 PMCID: PMC9146377 DOI: 10.3390/ph15050632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/08/2022] [Accepted: 05/12/2022] [Indexed: 11/17/2022] Open
Abstract
In today’s global plan to completely eradicate hepatitis C virus (HCV), the essential list of medications used for HCV treatment are direct-acting antivirals (DAAs), as interferon-sparing regimens have become the standard-of-care (SOC) treatment. HCV nonstructural protein 5A (NS5A) inhibitors are a very common component of these regimens. Food and Drug Administration (FDA)-approved NS5A inhibitors, although very potent, do not have the same potency against all eight genotypes of HCV. Therefore, this study aims to synthesize NS5A inhibitor analogues with high potency pan-genotypic activity and high metabolic stability. Starting from an NS5A inhibitor scaffold previously identified by our research group, we made several modifications. Two series of compounds were created to test the effect of changing the length and spatial conformation (para-para vs. meta-meta-positioned bis-imidazole-proline-carbamate), replacing amide groups in the linker with imidazole groups, as well as different end-cap compositions and sizes. The frontrunner inhibits genotype 1b (Con1) replicon, with an EC50 value in the picomolar range, and showed high genotypic coverage with nanomolar range EC50 values against four more genotypes. This together with its high metabolic stability (t½ > 120 min) makes it a potential preclinical candidate.
Collapse
Affiliation(s)
- Jehad Hamdy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (J.H.); (N.E.)
| | - Nouran Emadeldin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (J.H.); (N.E.)
| | - Mostafa M. Hamed
- Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)—Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; (M.M.H.); (A.K.H.H.)
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Department of Microbiology, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521 Athens, Greece; (E.F.); (N.V.)
| | - Sotirios Katsamakas
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece;
| | - Niki Vassilaki
- Molecular Virology Laboratory, Department of Microbiology, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521 Athens, Greece; (E.F.); (N.V.)
| | - Grigoris Zoidis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece;
| | - Anna K. H. Hirsch
- Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)—Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; (M.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (J.H.); (N.E.)
| | - Ashraf H. Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (J.H.); (N.E.)
| |
Collapse
|
8
|
Pham LV, Pedersen MS, Fahnøe U, Fernandez-Antunez C, Humes D, Schønning K, Ramirez S, Bukh J. HCV genome-wide analysis for development of efficient culture systems and unravelling of antiviral resistance in genotype 4. Gut 2022; 71:627-642. [PMID: 33833066 PMCID: PMC8862099 DOI: 10.1136/gutjnl-2020-323585] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/17/2021] [Accepted: 02/03/2021] [Indexed: 01/14/2023]
Abstract
OBJECTIVE HCV-genotype 4 infections are a major cause of liver diseases in the Middle East/Africa with certain subtypes associated with increased risk of direct-acting antiviral (DAA) treatment failures. We aimed at developing infectious genotype 4 cell culture systems to understand the evolutionary genetic landscapes of antiviral resistance, which can help preserve the future efficacy of DAA-based therapy. DESIGN HCV recombinants were tested in liver-derived cells. Long-term coculture with DAAs served to induce antiviral-resistance phenotypes. Next-generation sequencing (NGS) of the entire HCV-coding sequence identified mutation networks. Resistance-associated substitutions (RAS) were studied using reverse-genetics. RESULT The in-vivo infectious ED43(4a) clone was adapted in Huh7.5 cells, using substitutions identified in ED43(Core-NS5A)/JFH1-chimeric viruses combined with selected NS5B-changes. NGS, and linkage analysis, permitted identification of multiple genetic branches emerging during culture adaptation, one of which had 31 substitutions leading to robust replication/propagation. Treatment of culture-adapted ED43 with nine clinically relevant protease-DAA, NS5A-DAA and NS5B-DAA led to complex dynamics of drug-target-specific RAS with coselection of genome-wide substitutions. Approved DAA combinations were efficient against the original virus, but not against variants with RAS in corresponding drug targets. However, retreatment with glecaprevir/pibrentasvir remained efficient against NS5A inhibitor and sofosbuvir resistant variants. Recombinants with specific RAS at NS3-156, NS5A-28, 30, 31 and 93 and NS5B-282 were viable, but NS3-A156M and NS5A-L30Δ (deletion) led to attenuated phenotypes. CONCLUSION Rapidly emerging complex evolutionary landscapes of mutations define the persistence of HCV-RASs conferring resistance levels leading to treatment failure in genotype 4. The high barrier to resistance of glecaprevir/pibrentasvir could prevent persistence and propagation of antiviral resistance.
Collapse
Affiliation(s)
- Long V. Pham
- 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
| | - Martin Schou Pedersen
- 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 Clinical Microbiology, 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
| | - Carlota Fernandez-Antunez
- 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
| | - Daryl Humes
- 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
| | - Kristian Schønning
- Department of Clinical Microbiology, Hvidovre Hospital, Hvidovre, Denmark,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 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
| | - 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
| |
Collapse
|
9
|
Abdallah M, Hamed MM, Frakolaki E, Katsamakas S, Vassilaki N, Bartenschlager R, Zoidis G, Hirsch AKH, Abdel-Halim M, Abadi AH. Redesigning of the cap conformation and symmetry of the diphenylethyne core to yield highly potent pan-genotypic NS5A inhibitors with high potency and high resistance barrier. Eur J Med Chem 2021; 229:114034. [PMID: 34959173 DOI: 10.1016/j.ejmech.2021.114034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 11/15/2022]
Abstract
Herein, we report the discovery of several NS5A inhibitors with potency against HCV genotype 1b in the picomolar range. Compounds (15, 33) were of extremely high potency against HCV genotype 1b (EC50 ≈ 1 pM), improved activity against genotype 3a (GT 3a) and good metabolic stability. We studied the impact of changing the cap conformation relative to the diphenylethyne core and/or compound symmetry on both potency and metabolic stability. The analogs obtained exhibited improved potency against HCV genotypes 1a, 1b, 3a and 4a compared to the clinically approved candidate daclatasvir with EC50 values in the low picomolar range and SI50s > 7 orders of magnitude. Compound 15, a symmetrically m-, m'-substituted diphenyl ethyne analog, was 150-fold more potent than daclatasvir against GT 3a, while compound 33, an asymmetrically m-, p-substituted diphenyl ethyne analog, was 35-fold more potent than daclatasvir against GT 3a. In addition, compound 15 exhibited a higher resistance barrier than daclatasvir against genotype 1b.
Collapse
Affiliation(s)
- Mennatallah Abdallah
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt
| | - Mostafa M Hamed
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus E8.1, 66123, Saarbrücken, Germany
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521, Athens, Greece
| | - Sotirios Katsamakas
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771, Athens, Greece
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521, Athens, Greece
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, Germany
| | - Grigoris Zoidis
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771, Athens, Greece.
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus E8.1, 66123, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, Saarbrücken, 66123, Germany
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt.
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt.
| |
Collapse
|
10
|
BAWONO RHEZAGANDI, ABE TAKAYUKI, SHIBATA YASUAKI, MATSUI CHIEKO, DENG LIN, SHOJI IKUO. NS5A-ISGylation via Lysine 26 Has a Critical Role for Efficient Propagation of Hepatitis C Virus Genotype 2a. THE KOBE JOURNAL OF MEDICAL SCIENCES 2021; 67:E38-E47. [PMID: 34795154 PMCID: PMC8622218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
We previously reported that hepatitis C virus (HCV) NS5A (1b, Con1) protein accepts covalent ISG15 conjugation at specific lysine (Lys) residues (K44, K68, K166, K215 and K308), exhibiting proviral effects on HCV RNA replication. Here we investigated a role of NS5A-ISGylation via Lys residues in HCV propagation using HCV infectious clone. The alignment of amino acid sequences revealed that 5 Lys residues (K20, K26, K44, K139, and K166) of the 13 Lys residues within NS5A (genotype 2a, JFH1 strain) were conserved compared to those of HCV (genotype 1b, Con1 strain). The cell-based ISGylation assay revealed that the K26 residue in the amphipathic helix (AH) domain and the K139 residue in domain I of NS5A (2a, JFH1) had the potential to accept ISGylation. Use of the HCV replicon carrying luciferase gene revealed that the K26 residue but not K139 residue of NS5A (2a, JFH1) was important for HCV RNA replication. Furthermore, cell culture HCV revealed that the mutation with the K26 residue in combination with K139 or K166 on NS5A (2a, JFH1) resulted in complete abolishment of viral propagation, suggesting that the K26 residue collaborates with either the K139 residue or K166 residue for efficient HCV propagation. Taken together, these results suggest that HCV NS5A protein has the potential to accept ISGylation via specific Lys residues, involving efficient viral propagation in a genotype-specific manner.
Collapse
Affiliation(s)
| | | | | | | | | | - IKUO SHOJI
- Corresponding author: Phone: +81-78-382-5500, Fax: +81-78-382-5519, E-mail:
| |
Collapse
|
11
|
Nageswara Rao D, Zephyr J, Henes M, Chan ET, Matthew AN, Hedger AK, Conway HL, Saeed M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A. Discovery of Quinoxaline-Based P1-P3 Macrocyclic NS3/4A Protease Inhibitors with Potent Activity against Drug-Resistant Hepatitis C Virus Variants. J Med Chem 2021; 64:11972-11989. [PMID: 34405680 PMCID: PMC9228641 DOI: 10.1021/acs.jmedchem.1c00554] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The three pan-genotypic HCV NS3/4A protease inhibitors (PIs) currently in clinical use-grazoprevir, glecaprevir, and voxilaprevir-are quinoxaline-based P2-P4 macrocycles and thus exhibit similar resistance profiles. Using our quinoxaline-based P1-P3 macrocyclic lead compounds as an alternative chemical scaffold, we explored structure-activity relationships (SARs) at the P2 and P4 positions to develop pan-genotypic PIs that avoid drug resistance. A structure-guided strategy was used to design and synthesize two series of compounds with different P2 quinoxalines in combination with diverse P4 groups of varying sizes and shapes, with and without fluorine substitutions. Our SAR data and cocrystal structures revealed the interplay between the P2 and P4 groups, which influenced inhibitor binding and the overall resistance profile. Optimizing inhibitor interactions in the S4 pocket led to PIs with excellent antiviral activity against clinically relevant PI-resistant HCV variants and genotype 3, providing potential pan-genotypic inhibitors with improved resistance profiles.
Collapse
Affiliation(s)
- Desaboini Nageswara Rao
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Jacqueto Zephyr
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Elise T Chan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Ashley N Matthew
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Adam K Hedger
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Hasahn L Conway
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts 02118, United States
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts 02118, United States
| | - Alicia Newton
- Monogram Biosciences, South San Francisco, California 94080, United States
| | | | - Wei Huang
- Monogram Biosciences, South San Francisco, California 94080, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| |
Collapse
|
12
|
Leumi S, El Kassas M, Zhong J. Hepatitis C virus genotype 4: A poorly characterized endemic genotype. J Med Virol 2021; 93:6079-6088. [PMID: 34185316 DOI: 10.1002/jmv.27165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/26/2021] [Indexed: 12/16/2022]
Abstract
Globally, 13% of all hepatitis C virus (HCV) infections are caused by genotype 4 (GT4), which consists of 17 subtypes with various levels of susceptibility to anti-HCV therapy. This genotype is endemic in the Middle East and Africa and has considerably spread to Europe lately. The molecular features of HCV-GT4 infection, as well as its appropriate therapeutics, are poorly characterized as it has not been the subject of widespread basic research. As such, in this review, we aim to gather the current state of knowledge of this genotype with a particular emphasis on its heterogeneity, sequence signatures, resistance-associated substitutions, and available in vivo and in vitro models used for its study. We urge developing more cell-culture models based on different GT4 subtypes to better understand the virology and therapeutic response of this particular genotype. This review may raise more awareness about this genotype and trigger more basic research work to develop its research tools. This will be critical to design better therapeutics and help to provide adequate guidelines for physicians working with HCV-GT4 patients.
Collapse
Affiliation(s)
- Steve Leumi
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mohamed El Kassas
- Department of Endemic Medicine, Faculty of Medicine, Helwan University, Cairo, Egypt
| | - Jin Zhong
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
13
|
Mousa MHA, Ahmed NS, Schwedtmann K, Frakolaki E, Vassilaki N, Zoidis G, Weigand JJ, Abadi AH. Design and Synthesis of Novel Symmetric Fluorene-2,7-Diamine Derivatives as Potent Hepatitis C Virus Inhibitors. Pharmaceuticals (Basel) 2021; 14:ph14040292. [PMID: 33806139 PMCID: PMC8064491 DOI: 10.3390/ph14040292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatitis C virus (HCV) is an international challenge. Since the discovery of NS5A direct-acting antivirals, researchers turned their attention to pursue novel NS5A inhibitors with optimized design and structure. Herein we explore highly potent hepatitis C virus (HCV) NS5A inhibitors; the novel analogs share a common symmetrical prolinamide 2,7-diaminofluorene scaffold. Modification of the 2,7-diaminofluorene backbone included the use of (S)-prolinamide or its isostere (S,R)-piperidine-3-caboxamide, both bearing different amino acid residues with terminal carbamate groups. Compound 26 exhibited potent inhibitory activity against HCV genotype (GT) 1b (effective concentration (EC50) = 36 pM and a selectivity index of >2.78 × 106). Compound 26 showed high selectivity on GT 1b versus GT 4a. Interestingly, it showed a significant antiviral effect against GT 3a (EC50 = 1.2 nM). The structure-activity relationship (SAR) analysis revealed that picomolar inhibitory activity was attained with the use of S-prolinamide capped with R- isoleucine or R-phenylglycine residues bearing a terminal alkyl carbamate group.
Collapse
Affiliation(s)
- Mai H. A. Mousa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
| | - Nermin S. Ahmed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
- Correspondence: (N.S.A.); (A.H.A.); Tel.: +202-27590700 (ext. 3429) (N.S.A.); +202-27590700 (ext. 3400) (A.H.A.); Fax: +202-27581041 (N.S.A. & A.H.A.)
| | - Kai Schwedtmann
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany; (K.S.); (J.J.W.)
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, 11521 Athens, Greece; (E.F.); (N.V.)
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, 11521 Athens, Greece; (E.F.); (N.V.)
| | - Grigoris Zoidis
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece;
| | - Jan J. Weigand
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany; (K.S.); (J.J.W.)
| | - Ashraf H. Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
- Correspondence: (N.S.A.); (A.H.A.); Tel.: +202-27590700 (ext. 3429) (N.S.A.); +202-27590700 (ext. 3400) (A.H.A.); Fax: +202-27581041 (N.S.A. & A.H.A.)
| |
Collapse
|
14
|
Ashraf MU, Salman HM, Khalid MF, Khan MHF, Anwar S, Afzal S, Idrees M, Chaudhary SU. CRISPR-Cas13a mediated targeting of hepatitis C virus internal-ribosomal entry site (IRES) as an effective antiviral strategy. Biomed Pharmacother 2021; 136:111239. [PMID: 33454599 DOI: 10.1016/j.biopha.2021.111239] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/28/2020] [Accepted: 12/31/2020] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C is an inflammatory liver disease caused by the single-stranded RNA (ssRNA) hepatitis C virus (HCV). The genetic diversity of the virus and quasispecies produced during replication have resulted in viral resistance to direct-acting antivirals (DAAs) as well as impediments in vaccine development. The recent adaptation of CRISPR-Cas as an alternative antiviral approach has demonstrated degradation of viral nucleic acids in eukaryotes. In particular, the CRISPR-effector Cas13 enzyme has been shown to target ssRNA viruses effectively. In this work, we have employed Cas13a to knockdown HCV in mammalian cells. Using a computational screen, we identified several potential Cas13a target sites within highly conserved regions of the HCV internal ribosomal entry site (IRES). Our results demonstrate significant inhibition of HCV replication as well as translation in huh-7.5 cells with minimal effects on cell viability. These findings were validated using a multi-modality approach involving qRT-PCR, luciferase assay, and MTT cell viability assay. In conclusion, the CRISPR-Cas13a system efficiently targets HCV in vitro, suggesting its potential as a programmable therapeutic antiviral strategy.
Collapse
Affiliation(s)
- Muhammad Usman Ashraf
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan; Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Hafiz Muhammad Salman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Farhan Khalid
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Haider Farooq Khan
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Saima Anwar
- Department of Biomedical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Samia Afzal
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Idrees
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.
| |
Collapse
|
15
|
Azzam R, Elboshi HA, Elgemeie GH. Novel Synthesis and Antiviral Evaluation of New Benzothiazole-Bearing N-Sulfonamide 2-Pyridone Derivatives as USP7 Enzyme Inhibitors. ACS OMEGA 2020; 5:30023-30036. [PMID: 33251438 PMCID: PMC7689895 DOI: 10.1021/acsomega.0c04424] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/29/2020] [Indexed: 05/10/2023]
Abstract
In this article, a series of benzothiazole-bearing N-sulfonamide 2-pyridone derivatives were synthesized via the reaction of benzothiazole sulfonylhydrazide with sodium salts of both (hydroxymethylene) cycloalkanones and unsaturated ketones, as well as ethoxymethylene derivatives. The structures of the resultant compounds were confirmed using IR, 1H NMR, 13C NMR, 1H-1H correlation spectroscopy (COSY), 1H-13C heteronuclear multiple bond coherence (HMBC), and 1H-13C heteronuclear multiple quantum coherence (HSQC) spectral analysis and elemental analysis. The newly synthesized compounds were evaluated in vitro for their antiviral activities against the HSV-1, HAV HM175, HCVcc genotype 4, CBV4, and HAdV7 viruses. Additionally, the compounds were examined for their cytotoxic effect on five normal cell lines. It was observed that five compounds were found to possess viral reduction of 50% or more against CBV4 with significant IC50, CC50, and SI values. In the case of HSV-1 and HAV HM175 viruses, three compounds have shown more than 50% reduction, while in the case of HCVcc genotype 4 and HAdV7 viruses, only two compounds demonstrated more than 50% reduction. Furthermore, the physicochemical properties of the most active compounds were evaluated. The two most potent compounds against HSV-1 virus, 7e and 13a, were evaluated for their inhibitory activity against USP7. Docking studies using Molecular Operating Environment (MOE) were used to identify the interactions between 7e and 13a compounds and the active site of the USP7 enzyme.
Collapse
|
16
|
Fernandes Campos GR, Ward J, Chen S, Bittar C, Vilela Rodrigues JP, Martinelli ADLC, Souza FF, Pereira LRL, Rahal P, Harris M. A novel substitution in NS5A enhances the resistance of hepatitis C virus genotype 3 to daclatasvir. J Gen Virol 2020; 102. [PMID: 33141008 PMCID: PMC8116786 DOI: 10.1099/jgv.0.001496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hepatitis C virus (HCV) genotype 3 presents a high level of both baseline and acquired resistance to direct-acting antivirals (DAAs), particularly those targeting the NS5A protein. To understand this resistance we studied a cohort of Brazilian patients treated with the NS5A DAA, daclatasvir and the nucleoside analogue, sofosbuvir. We observed a novel substitution at NS5A amino acid residue 98 [serine to glycine (S98G)] in patients who relapsed post-treatment. The effect of this substitution on both replication fitness and resistance to DAAs was evaluated using two genotype 3 subgenomic replicons. S98G had a modest effect on replication, but in combination with the previously characterized resistance-associated substitution (RAS), Y93H, resulted in a significant increase in daclatasvir resistance. This result suggests that combinations of substitutions may drive a high level of DAA resistance and provide some clues to the mechanism of action of the NS5A-targeting DAAs.
Collapse
Affiliation(s)
| | - Joseph Ward
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Shucheng Chen
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Cintia Bittar
- São Paulo State University, Institute of Biosciences, Languages and Exact Sciences, São José do Rio Preto, São Paulo State 15054-000, Brazil
| | | | | | - Fernanda Fernandes Souza
- University of São Paulo, Ribeirão Preto Faculty of Pharmaceutical Sciences, Ribeirão Preto, SP 14040-903, Brazil
| | - Leonardo Régis Leira Pereira
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Paula Rahal
- São Paulo State University, Institute of Biosciences, Languages and Exact Sciences, São José do Rio Preto, São Paulo State 15054-000, Brazil
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| |
Collapse
|
17
|
Ward JC, Bowyer S, Chen S, Fernandes Campos GR, Ramirez S, Bukh J, Harris M. Insights into the unique characteristics of hepatitis C virus genotype 3 revealed by development of a robust sub-genomic DBN3a replicon. J Gen Virol 2020; 101:1182-1190. [PMID: 32897181 PMCID: PMC7879556 DOI: 10.1099/jgv.0.001486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/03/2020] [Indexed: 12/14/2022] Open
Abstract
Hepatitis C virus (HCV) is an important human pathogen causing 400 000 chronic liver disease-related deaths annually. Until recently, the majority of laboratory-based investigations into the biology of HCV have focused on the genotype 2 isolate, JFH-1, involving replicons and infectious cell culture systems. However, genotype 2 is one of eight major genotypes of HCV and there is great sequence variation among these genotypes (>30 % nucleotide divergence). In this regard, genotype 3 is the second most common genotype and accounts for 30 % of global HCV cases. Further, genotype 3 is associated with both high levels of inherent resistance to direct-acting antiviral (DAA) therapy, and a more rapid progression to chronic liver diseases. Neither of these two attributes are fully understood, thus robust genotype 3 culture systems to unravel viral replication are required. Here we describe the generation of robust genotype 3 sub-genomic replicons (SGRs) based on the adapted HCV NS3-NS5B replicase from the DBN3a cell culture infectious clone. Such infectious cell culture-adaptive mutations could potentially promote the development of robust SGRs for other HCV strains and genotypes. The novel genotype 3 SGRs have been used both transiently and to establish stable SGR-harbouring cell lines. We show that these resources can be used to investigate aspects of genotype 3 biology, including NS5A function and DAA resistance. They will be useful tools for these studies, circumventing the need to work under the biosafety level 3 (BSL3) containment required in many countries.
Collapse
Affiliation(s)
- Joseph C. Ward
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sebastian Bowyer
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Shucheng Chen
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Guilherme Rodrigues Fernandes Campos
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- Present address: São Paulo State University, Institute of Biosciences, Languages and Exact Sciences, Cristóvão Colombo Street, 2265, Post Code 15054-000, São José do Rio Preto, São Paulo State, Brazil
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Kettegård Allé 30, DK-2650 Hvidovre, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Kettegård Allé 30, DK-2650 Hvidovre, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| |
Collapse
|
18
|
Azzam R, Elsayed RE, Elgemeie GH. Design and Synthesis of a New Class of Pyridine-Based N-Sulfonamides Exhibiting Antiviral, Antimicrobial, and Enzyme Inhibition Characteristics. ACS OMEGA 2020; 5:26182-26194. [PMID: 33073144 PMCID: PMC7557949 DOI: 10.1021/acsomega.0c03773] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/11/2020] [Indexed: 05/04/2023]
Abstract
A new strategy for designing and assembling a novel class of functionalized pyridine-based benzothiazole and benzimidazole incorporating sulfonamide moieties was developed. The synthesis was carried out by reacting N-cyanoacetoarylsulfonylhydrazide with various electrophiles such as 2-(benzo[d]thiazol-2-yl)-3,3-bis(alkylthio)acrylonitriles and 2-(benzo[d]imidazol-2-yl)-3,3-bis(methylthio)-acrylonitriles, as well as 2-ethoxyl acrylonitrile derivatives. The synthesized compounds were tested for their antiviral and antimicrobial potency. Two of the synthesized compounds, 15c and 15d, showed more than 50% viral reduction against HSV-1 and CBV4, with significant IC50 and CC50 values. The two potent compounds 15c and 15d have also shown inhibitory activity against Hsp90α protein with IC50 values of 10.24 and 4.48 μg/mL, respectively. A combination of 15c and 15d with acyclovir has led to IC50 values that are lower than that of acyclovir alone. Molecular modeling studies were used to identify the interactions between the 15c and 15d compounds and the active site of Hsp90α enzyme. The antimicrobial investigation of the new compounds has also shown that 8b and 15d exhibited a higher inhibition zone (IZ) than sulfadiazine and gentamicin against Klebsiella pneumonia, whereas 9a showed higher IZ than ampicillin against Staphylococcus aureus. According to the enzyme assay study on dihydrofolate reductase, 9a was shown to be the most potent compound among all examined compounds.
Collapse
|
19
|
ISGylation of Hepatitis C Virus NS5A Protein Promotes Viral RNA Replication via Recruitment of Cyclophilin A. J Virol 2020; 94:JVI.00532-20. [PMID: 32727878 DOI: 10.1128/jvi.00532-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/24/2020] [Indexed: 12/14/2022] Open
Abstract
Interferon-stimulated gene 15 (ISG15) is a ubiquitin-like protein that is covalently conjugated to many substrate proteins in order to modulate their functions; this conjugation is called ISGylation. Several groups reported that the ISGylation of hepatitis C virus (HCV) NS5A protein affects HCV replication. However, the ISG15 conjugation sites on NS5A are not well determined, and it is unclear whether the role of NS5A ISGylation in HCV replication is proviral or antiviral. Here, we investigated the role of NS5A ISGylation in HCV replication by using HCV RNA replicons that encode a mutation at each lysine (Lys) residue of the NS5A protein. Immunoblot analyses revealed that 5 Lys residues (K44, K68, K166, K215, and K308) of the 14 Lys residues within NS5A (genotype 1b, Con1) have the potential to accept ISGylation. We tested the NS5A ISGylation among different HCV genotypes and observed that the NS5A proteins of all of the HCV genotypes accept ISGylation at multiple Lys residues. Using an HCV luciferase reporter replicon assay revealed that residue K308 of NS5A is important for HCV (1b, Con1) RNA replication. We observed that K308, one of the Lys residues for NS5A ISGylation, is located within the binding region of cyclophilin A (CypA), which is the critical host factor for HCV replication. We obtained evidence derived from all of the HCV genotypes suggesting that NS5A ISGylation enhances the interaction between NS5A and CypA. Taken together, these results suggest that NS5A ISGylation functions as a proviral factor and promotes HCV replication via the recruitment of CypA.IMPORTANCE Host cells have evolved host defense machinery (such as innate immunity) to eliminate viral infections. Viruses have evolved several counteracting strategies for achieving an immune escape from host defense machinery, including type I interferons (IFNs) and inflammatory cytokines. ISG15 is an IFN-inducible ubiquitin-like protein that is covalently conjugated to the viral protein via specific Lys residues and suppresses viral functions and viral propagation. Here, we demonstrate that HCV NS5A protein accepts ISG15 conjugation at specific Lys residues and that the HERC5 E3 ligase specifically promotes NS5A ISGylation. We obtained evidence suggesting that NS5A ISGylation facilitates the recruitment of CypA, which is the critical host factor for HCV replication, thereby promoting HCV replication. These findings indicate that E3 ligase HERC5 is a potential therapeutic target for HCV infection. We propose that HCV hijacks an intracellular ISG15 function to escape the host defense machinery in order to establish a persistent infection.
Collapse
|
20
|
Lim SK, Othman R, Yusof R, Heh CH. Rational drug discovery: Ellagic acid as a potent dual-target inhibitor against hepatitis C virus genotype 3 (HCV G3) NS3 enzymes. Chem Biol Drug Des 2020; 97:28-40. [PMID: 32657543 DOI: 10.1111/cbdd.13756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 06/15/2020] [Accepted: 06/28/2020] [Indexed: 12/19/2022]
Abstract
Structure-based virtual screening (SBVS) has served as a popular strategy for rational drug discovery. In this study, we aimed to discover novel benzopyran-based inhibitors that targeted the NS3 enzymes (NS3/4A protease and NS3 helicase) of HCV G3 using a combination of in silico and in vitro approaches. With the aid of SBVS, six novel compounds were discovered to inhibit HCV G3 NS3/4A protease and two phytochemicals (ellagic acid and myricetin) were identified as dual-target inhibitors that inhibited both NS3/4A protease and NS3 helicase in vitro (IC50 = 40.37 ± 5.47 nm and 6.58 ± 0.99 µm, respectively). Inhibitory activities against the replication of HCV G3 replicons were further assessed in a cell-based system with four compounds showed dose-dependent inhibition. Compound P8 was determined to be the most potent compound from the cell-based assay with an EC50 of 19.05 µm. The dual-target inhibitor, ellagic acid, was determined as the second most potent (EC50 = 32.37 µm) and the most selective in its inhibitory activity against the replication of HCV replicons, without severely affecting the viability of the host cells (selectivity index > 6.18).
Collapse
Affiliation(s)
- See Khai Lim
- Drug Design and Development Research Group, University of Malaya, Kuala Lumpur, Malaysia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia
| | - Rozana Othman
- Drug Design and Development Research Group, University of Malaya, Kuala Lumpur, Malaysia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia.,Center for Natural Products Research and Drug Discovery (CENAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Rohana Yusof
- Drug Design and Development Research Group, University of Malaya, Kuala Lumpur, Malaysia.,Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Choon Han Heh
- Drug Design and Development Research Group, University of Malaya, Kuala Lumpur, Malaysia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
21
|
Abdel Karim SE, Youssef YH, Abdel-Halim M, Frakolaki E, Vassilaki N, Zoidis G, Ahmed NS, Abadi AH. Symmetric benzidine derivatives as anti-HCV agents: Insight into the nature, stereochemistry of the capping amino acid and the size of the terminal capping carbamates. Bioorg Chem 2020; 102:104089. [PMID: 32717691 DOI: 10.1016/j.bioorg.2020.104089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/30/2020] [Accepted: 07/07/2020] [Indexed: 12/22/2022]
Abstract
Novel symmetric molecules, bearing a benzidine prolinamide core, two terminal carbamate caps of variable sizes and nature, including natural and unnatural amino acids were developed. Several terminal N-carbamate substituents of the core structure, ranging from linear methyl, ethyl and butyl groups to branching isobutyl group; and an aromatic substituent were also synthesized. Series 1 has hydrophobic AA residues, namely S and R phenylglycine and a terminal carbamate capping group, whereas Series 2 bears sulphur containing amino acids, specifically S and R methionine and the natural R methylcysteine. The novel compounds were tested for their inhibitory activity (EC50) and their cytotoxicity (CC50), using an HCV 1b (Con1) reporter replicon cell line. Compound 4 with the unnatural capping residue, bearing d-Phenylglycine amino acid residue and N-isobutyloxycarbonyl capping group, was the most active within the two series, with EC50 = 0.0067 nM. Moreover, it showed high SI50 > 14788524 and was not cytotoxic at the highest tested concentration (100 μΜ), indicating its safety profile. Compound 4 also inhibited HCV genotypes 2a, 3a and 4a. Compared to the clinically approved NS5A inhibitor Daclatasvir, compound 4 shows higher activity against genotypes 1b and 3a, as well as improved safety profile.
Collapse
Affiliation(s)
- Shereen E Abdel Karim
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt
| | - Youssef H Youssef
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt
| | - Mohammad Abdel-Halim
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521 Athens, Greece
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521 Athens, Greece
| | - Grigoris Zoidis
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, GR-15771 Athens, Greece
| | - Nermin S Ahmed
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt
| | - Ashraf H Abadi
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt.
| |
Collapse
|
22
|
Khan S, Soni S, Veerapu NS. HCV Replicon Systems: Workhorses of Drug Discovery and Resistance. Front Cell Infect Microbiol 2020; 10:325. [PMID: 32714881 PMCID: PMC7344236 DOI: 10.3389/fcimb.2020.00325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/28/2020] [Indexed: 12/16/2022] Open
Abstract
The development of direct-acting antivirals (DAAs) has revolutionized the state-of-the art treatment of HCV infections, with sustained virologic response rates above 90%. However, viral variants harboring substitutions referred to as resistance-associated substitutions (RASs) may be present in baseline levels and confer resistance to DAAs, thereby posing a major challenge for HCV treatment. HCV replicons have been the primary tools for discovering and evaluating the inhibitory activity of DAAs against viral replication. Interest in replicon systems has further grown as they have become indispensable for discovering genotype-specific and cross-genotype RASs. Here, we review functional replicon systems for HCV, how these replicon systems have contributed to the development of DAAs, and the characteristics and distribution of RASs for DAAs.
Collapse
Affiliation(s)
- Shaheen Khan
- Virology Section, Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, India
| | - Shalini Soni
- Virology Section, Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, India
| | - Naga Suresh Veerapu
- Virology Section, Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, India
| |
Collapse
|
23
|
Abu-Zaied M, Hammad SF, Halaweish FT, Elgemeie GH. Sofosbuvir Thio-analogues: Synthesis and Antiviral Evaluation of the First Novel Pyridine- and Pyrimidine-Based Thioglycoside Phosphoramidates. ACS OMEGA 2020; 5:14645-14655. [PMID: 32596602 PMCID: PMC7315579 DOI: 10.1021/acsomega.0c01364] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/25/2020] [Indexed: 05/31/2023]
Abstract
The synthesis and antiviral screening of the first reported series of pyridine- and pyrimidine-based thioglycoside phosphoramidates are herein reported. They were prepared through two synthetic steps: The first step is via coupling of mercapto-derivatized heterocyclic bases with the appropriate α-bromo per-acetylated sugars. The second one is the hydrolysis of the acetate esters under basic conditions that were consequently conjugated with the phosphoramidating reagent to afford the desired thioglycoside protides. Eight compounds were evaluated for their antiviral activities against different viral cell lines, namely, adenovirus 7, HAV (hepatitis A) HM175, Coxsackievirus B4, and HSV-1 (herpes simplex virus type 1), in addition to the antiviral bioassay against ED-43/SG-Feo (VYG) replicon of HCV (hepatitis C virus) genotype 4a. Both compounds 5b and 11 showed notable antiviral activity against Coxsackie virus B4, reflected from the CC50 values of 17 and 20 μg/100 μL and IC50 values of 4.5 and 6.0 μg/100 μL, respectively. Same two compounds elicited remarkable activities toward herpes simplex virus type 1, represented by CC50 values of 17 and 16 μg/100 μL and IC50 values of 6.3 and 6.6 μg/100 μL, respectively. Combination of 11 with acyclovir elicited a notable synergistic activity in comparison with acyclovir alone, as inferred from herpes simplex polymerase enzyme inhibitory assay values of 2.64 and 4.78 μg/100 mL, respectively. Only compound 11 elicited a remarkable activity against HCV. Potential promising activities of compound 11 have been shown with respect to CC50, IC50, and enzyme assay inhibitory activities.
Collapse
Affiliation(s)
| | - Sherif F. Hammad
- Pharmaceutical
Chemistry Department, Faculty of Pharmacy, Helwan University, Helwan, Cairo 11795, Egypt
- Basic
and Applied Sciences Institute, Egypt-Japan
University of Science and Technology (E-JUST), P.O Box 179, New Borg El-Arab City, Alexandria 21934, Egypt
| | - Fathi T. Halaweish
- Department
of Chemistry & Biochemistry, South Dakota
State University, Brookings, South Dakota 57007, United States
| | - Galal Hamza Elgemeie
- Chemistry
Department, Faculty of Science, Helwan University, Helwan, Cairo 11795, Egypt
| |
Collapse
|
24
|
Hannemann H. Viral replicons as valuable tools for drug discovery. Drug Discov Today 2020; 25:1026-1033. [PMID: 32272194 PMCID: PMC7136885 DOI: 10.1016/j.drudis.2020.03.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/28/2020] [Accepted: 03/13/2020] [Indexed: 12/15/2022]
Abstract
RNA viruses can cause severe diseases such as dengue, Lassa, chikungunya and Ebola. Many of these viruses can only be propagated under high containment levels, necessitating the development of low containment surrogate systems such as subgenomic replicons and minigenome systems. Replicons are self-amplifying recombinant RNA molecules expressing proteins sufficient for their own replication but which do not produce infectious virions. Replicons can persist in cells and are passed on during cell division, enabling quick, efficient and high-throughput testing of drug candidates that act on viral transcription, translation and replication. This review will explore the history and potential for drug discovery of hepatitis C virus, dengue virus, respiratory syncytial virus, Ebola virus and norovirus replicon and minigenome systems.
Collapse
Affiliation(s)
- Holger Hannemann
- The Native Antigen Company, Langford Locks, Kidlington OX5 1LH, UK.
| |
Collapse
|
25
|
Cell Culture Studies of the Efficacy and Barrier to Resistance of Sofosbuvir-Velpatasvir and Glecaprevir-Pibrentasvir against Hepatitis C Virus Genotypes 2a, 2b, and 2c. Antimicrob Agents Chemother 2020; 64:AAC.01888-19. [PMID: 31818814 DOI: 10.1128/aac.01888-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
The introduction of highly efficient therapies with direct-acting antivirals (DAA) for patients with chronic hepatitis C virus (HCV) infection offers exceptional opportunities to globally control this deadly disease. For achieving this ambitious goal, it is essential to prevent antiviral resistance against the most optimal first-line and retreatment DAA choices. We performed independent comparisons of the efficacy and barrier to resistance of pangenotypic DAA regimens for HCV genotype 2 infections, using previously and newly developed efficient cell culture-adapted strains of subtypes 2a, 2b, and 2c. With the applied experimental cell culture conditions, combination treatment with the sofosbuvir-velpatasvir or glecaprevir-pibrentasvir DAA regimen was efficient in eradicating HCV infections; in contrast, single-drug treatments frequently led to viral escape. Sequence analysis of drug targets from recovered viruses revealed known resistance-associated substitutions (RAS) emerging in the NS3 protease or NS5A after treatment failure. These RAS were genetically stable after viral passage, and viruses with these RAS exhibited significant phenotypic resistance. After sofosbuvir treatment failure, only a genotype 2a virus harbored NS5B RAS S282T and thus had decreased susceptibility to nucleotide analogs (nucs). However, in most cases, viral escape from sofosbuvir led to other NS5B substitutions but drug susceptibility was maintained, and in one case, no changes in NS5B were detected. For a genotype 2b virus, after treatment failure with sofosbuvir-velpatasvir, the efficacy of retreatment with glecaprevir-pibrentasvir was maintained due to the high barrier to resistance and low cross-resistance of pibrentasvir. Our findings suggest the slight superiority of glecaprevir-pibrentasvir against genotype 2b in culture, which could have potential therapeutic interest meriting more definitive investigations in the clinic.
Collapse
|
26
|
Azzam RA, Elgemeie GH, Osman RR. Synthesis of novel pyrido[2,1-b]benzothiazole and N-substituted 2-pyridylbenzothiazole derivatives showing remarkable fluorescence and biological activities. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
27
|
Azzam RA, Osman RR, Elgemeie GH. Efficient Synthesis and Docking Studies of Novel Benzothiazole-Based Pyrimidinesulfonamide Scaffolds as New Antiviral Agents and Hsp90α Inhibitors. ACS OMEGA 2020; 5:1640-1655. [PMID: 32010839 PMCID: PMC6990646 DOI: 10.1021/acsomega.9b03706] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/20/2019] [Indexed: 05/04/2023]
Abstract
A series of novel substituted 2-pyrimidylbenzothiazoles incorporating either sulfonamide moieties or the amino group at C2 of the pyrimidine ring were synthesized and evaluated for its antiviral potency. The novel synthesis of the ring system was carried out by reacting guanidine or N-arylsulfonated guanidine with different derivatives of ylidene benzothiazole based on Michael addition pathways. The antiviral activity of the newly synthesized compounds was examined by a plaque reduction assay against HSV-1, CBV4, HAV HM 175, HCVcc genotype 4 viruses, and HAdV7. In the case of HSV-1, it was determined that 5 out of the 21 synthesized compounds exhibited superior viral reduction in the range of 70-90% with significant IC50, CC50, and SI values as compared with acyclovir. In the case of CBV4, nine compounds have shown more than 50% reduction. Comparable results were obtained for seven of these synthesized compounds when evaluated against HAV with only a couple of them showing 50% reduction or more against HCVcc genotype 4. Remarkably, one compound, 9a, has shown broad action against all five examined viruses, rendering it as potentially an effective antiviral agent. The five potent compounds 9a, 9b, 14b, 14g, and 14h against HSV-1 have also presented inhibitory activity against the Hsp90α protein with IC50 in the range of 4.87-10.47 μg/mL. Interestingly, a combination of the potent synthesized compounds with acyclovir led to IC50 values lower than that of acyclovir alone. The potent compounds 9a, 9b, 14b, 14g, and 14h were also docked inside the active site of Hsp90α to assess the interaction pattern between the tested compounds and the active site of the protein.
Collapse
|
28
|
Watanabe N, Suzuki T, Date T, Hussan HA, Hmwe SS, Aizaki H, Sugiyama M, Mizokami M, Delaney Iv W, Cheng G, Muramatsu M, Wakita T. Establishment of infectious genotype 4 cell culture-derived hepatitis C virus. J Gen Virol 2019; 101:188-197. [PMID: 31859613 DOI: 10.1099/jgv.0.001378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
To establish infectious genotype 4a (GT4a) cell culture-derived hepatitis C virus (HCVcc), we constructed full-length ED43 and 12 mutants possessing single or double mutations that increase ED43 replicon replication, and performed cell culture after RNA transfection. Sequential long-term culture of full-length ED43 RNA-transfected cells showed increased viral production in two ED43 mutants named ED43 QK/SI and TR/SI among the tested clones. These ED43 mutants possessed a common mutation, R1405G, in the NS3 helicase region and another mutation, D2413G or V2414A, in the NS5a-NS5b cleavage site. Furthermore, serial reinfection of naïve Huh7.5.1 cells accelerated peak HCV production at an earlier time point after every infection. After the fourth infection, we found a common mutation, R1405G, and six additional mutations in both ED43 QK/SI and TR/SI mutants. All seven mutations supported continuous viral production for more than 40 days in both ED43 QS-7M (QK/SI with seven mutations) and ED43 TS-7M (TR/SI with seven mutations). In addition, ED43 TS-7M did not require additional mutations for continuous virus culture up to 124 days. Both ED43 QS-7M and TS-7M were sensitive to the neutralizing E2 antibodies HCV1 and AR3A and the direct-acting antivirals, simeprevir, ledipasvir and sofosbuvir. In conclusion, we established an infectious ED43 strain containing adaptive mutations, which is important for the analysis of HCV genotype-specific pathogenesis, development of pan-genotypic agents and analysis of drug resistance.
Collapse
Affiliation(s)
- Noriyuki Watanabe
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takaya Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoko Date
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hussein Aly Hussan
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Su Su Hmwe
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideki Aizaki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masaya Sugiyama
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba, Japan
| | - Masashi Mizokami
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba, Japan
| | | | | | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
29
|
Structure-activity relationships of fluorene compounds inhibiting HCV variants. Antiviral Res 2019; 174:104678. [PMID: 31862501 DOI: 10.1016/j.antiviral.2019.104678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023]
Abstract
Approximately 71 million people suffer from hepatitis C virus (HCV) infection worldwide. Persistent HCV infection causes liver diseases such as chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma, resulting in approximately 400,000 deaths annually. Effective direct-acting antiviral agents (DAAs) have been developed and are currently used for HCV treatment targeting the following three proteins: NS3/4A proteinase that cleaves the HCV polyprotein into various functional proteins, RNA-dependent RNA polymerase (designated as NS5B), and NS5A, which is required for the formation of double membrane vesicles serving as RNA replication organelles. At least one compound inhibiting NS5A is included in current HCV treatment regimens due to the high efficacy and low toxicity of drugs targeting NS5A. Here we report fluorene compounds showing strong inhibitory effects on GT 1b and 3a of HCV. Moreover, some compounds were effective against resistance-associated variants to DAAs. The structure-activity relationships of the compounds were analyzed. Furthermore, we investigated the molecular bases of the inhibitory activities of some compounds by the molecular docking method.
Collapse
|
30
|
Kuchay S, Saeed M, Giorgi C, Li J, Hoffmann HH, Pinton P, Rice CM, Pagano M. NS5A Promotes Constitutive Degradation of IP3R3 to Counteract Apoptosis Induced by Hepatitis C Virus. Cell Rep 2019; 25:833-840.e3. [PMID: 30355490 DOI: 10.1016/j.celrep.2018.09.088] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/17/2018] [Accepted: 09/26/2018] [Indexed: 01/28/2023] Open
Abstract
FBXL2 targets IP3R3 for ubiquitin-mediated degradation to limit Ca2+ flux to mitochondria and, consequently, apoptosis. Efficient replication of hepatitis C virus (HCV) requires geranylgeranylation of FBXL2. Here, we show that the viral protein NS5A forms a trimeric complex with IP3R3 and FBXL2, unmasking IP3R3's degron in the absence of inositol 1,4,5-trisphosphate (IP3) stimulation. FBXL2 knockdown or expression of a stable IP3R3 mutant causes persistent Ca2+ flux and sensitizes cells to apoptosis, resulting in the inhibition of viral replication. Importantly, the effect of FBXL2 silencing is rescued by depleting IP3R3, but not p85β, another established FBXL2 substrate, indicating that the anti-HCV effect of FBXL2 knockdown is largely due to IP3R3 stabilization. Finally, disruption of the FBXL2-NS5A-IP3R3 complex using somatic cell genetics or pharmacologic inhibition results in IP3R3 stabilization and suppression of HCV replication. This study reveals an IP3-independent molecular mechanism through which HCV promotes IP3R3 degradation, thereby inhibiting virus-induced apoptosis and establishing chronic infection.
Collapse
Affiliation(s)
- Shafi Kuchay
- Department of Biochemistry and Molecular Pharmacology, Laura and Isaac Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Howard Hughes Medical Institute, 522 First Avenue, SRB 1107, New York, NY 10016, USA.
| | - Mohsan Saeed
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065, USA
| | - Carlotta Giorgi
- Department of Biochemistry and Molecular Pharmacology, Laura and Isaac Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Ferrara, Italy
| | - Jie Li
- Department of Biochemistry and Molecular Pharmacology, Laura and Isaac Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065, USA
| | - Paolo Pinton
- Department of Morphology, Surgery and Experimental Medicine, Section of Pathology, Oncology and Experimental Biology, Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Ferrara, Italy
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065, USA.
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, Laura and Isaac Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Howard Hughes Medical Institute, 522 First Avenue, SRB 1107, New York, NY 10016, USA.
| |
Collapse
|
31
|
Replicons of a Rodent Hepatitis C Model Virus Permit Selection of Highly Permissive Cells. J Virol 2019; 93:JVI.00733-19. [PMID: 31292246 DOI: 10.1128/jvi.00733-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/04/2019] [Indexed: 12/20/2022] Open
Abstract
Animal hepaciviruses represent promising surrogate models for hepatitis C virus (HCV), for which there are no efficient immunocompetent animal models. Experimental infection of laboratory rats with rodent hepacivirus isolated from feral Rattus norvegicus (RHV-rn1) mirrors key aspects of HCV infection in humans, including chronicity, hepatitis, and steatosis. Moreover, RHV has been adapted to infect immunocompetent laboratory mice. RHV in vitro systems have not been developed but would enable detailed studies of the virus life cycle crucial for designing animal experiments to model HCV infection. Here, we established efficient RHV-rn1 selectable subgenomic replicons with and without reporter genes. Rat and mouse liver-derived cells did not readily support the complete RHV life cycle, but replicon-containing cell clones could be selected with and without acquired mutations. Replication was significantly enhanced by mutations in NS4B and NS5A and in cell clones cured of replicon RNA. These mutations increased RHV replication of both mono- and bicistronic constructs, and CpG/UpA-dinucleotide optimization of reporter genes allowed replication. Using the replicon system, we show that the RHV-rn1 NS3-4A protease cleaves a human mitochondrial antiviral signaling protein reporter, providing a sensitive readout for virus replication. RHV-rn1 replication was inhibited by the HCV polymerase inhibitor sofosbuvir and high concentrations of HCV NS5A antivirals but not by NS3 protease inhibitors. The microRNA-122 antagonist miravirsen inhibited RHV-rn1 replication, demonstrating the importance of this HCV host factor for RHV. These novel RHV in vitro systems will be useful for studies of tropism, molecular virology, and characterization of virus-host interactions, thereby providing important complements to in vivo systems.IMPORTANCE A vaccine against hepatitis C virus (HCV) is crucial for global control of this important pathogen, which induces fatal human liver diseases. Vaccine development has been hampered by the lack of immunocompetent animal models. Discovery of rodent hepacivirus (RHV) enabled establishment of novel surrogate animal models. These allow robust infection and reverse genetic and immunization studies of laboratory animals, which develop HCV-like chronicity. Currently, there are no RHV in vitro systems available to study tropism and molecular virology. Here, we established the first culture systems for RHV, recapitulating the intracellular phase of the virus life cycle in vitro These replicon systems enabled identification of replication-enhancing mutations and selection of cells highly permissive to RHV replication, which allow study of virus-host interactions. HCV antivirals targeting NS5A, NS5B, and microRNA-122 efficiently inhibited RHV replication. Hence, several important aspects of HCV replication are shared by the rodent virus system, reinforcing its utility as an HCV model.
Collapse
|
32
|
Wing PA, Jones M, Cheung M, DaSilva S, Bamford C, Jason Lee WY, Aranday-Cortes E, Da Silva Filipe A, McLauchlan J, Smith D, Irving W, Cunningham M, Ansari A, Barnes E, Foster GR. Amino Acid Substitutions in Genotype 3a Hepatitis C Virus Polymerase Protein Affect Responses to Sofosbuvir. Gastroenterology 2019; 157:692-704.e9. [PMID: 31078622 PMCID: PMC6739484 DOI: 10.1053/j.gastro.2019.05.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 04/25/2019] [Accepted: 05/07/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Sofosbuvir is a frequently used pan-genotype inhibitor of hepatitis C virus (HCV) polymerase. This drug eliminates most chronic HCV infections, and resistance-associated substitutions in the polymerase are rare. However, HCV genotype 3 responds slightly less well to sofosbuvir-based therapies than other genotypes. We collected data from England's National Health Service Early Access Program to search for virus factors associated with sofosbuvir treatment failure. METHODS We collected patient serum samples and used the capture-fusion assay to assess viral sensitivity to sofosbuvir in 14 HCV genotype 3 samples. We identified polymorphisms associated with reduced response and created modified forms of HCV and replicons containing the substitutions of interest and tested their sensitivity to sofosbuvir and ribavirin. We examined the effects of these polymorphisms by performing logistic regression multivariate analysis on their association with sustained virologic response in a separate cohort of 411 patients with chronic HCV genotype 3 infection who had been treated with sofosbuvir and ribavirin, with or without pegylated interferon. RESULTS We identified a substitution in the HCV genotype 3a NS5b polymerase at amino acid 150 (alanine [A] to valine [V]), V at position 150 was observed in 42% of patients) with a reduced response to sofosbuvir in virus replication assays. In patients treated with sofosbuvir-containing regimens, the A150V variant was associated with a reduced response to treatment with sofosbuvir and ribavirin, with or without pegylated interferon. In 326 patients with V at position 150, 71% achieved an sustained virologic response compared to 88% with A at position 150. In cells, V at position 150 reduced the response to sofosbuvir 7-fold. We found that another rare substitution, glutamic acid (E) at position 206, significantly reduced the response to sofosbuvir (8.34-fold reduction); the combinations of V at position 150 and E at position 206 reduced the virus response to sofosbuvir 35.77-fold. Additionally, in a single patient, we identified 5 rare polymorphisms that reduced sensitivity to sofosbuvir our cell system. CONCLUSIONS A common polymorphism, V at position 150 in the HCV genotype 3a NS5b polymerase, combined with other variants, reduces the virus response to sofosbuvir. Clinically, infection with HCV genotype 3 containing this variant reduces odds of sustained virologic response. In addition, we identified rare combinations of variants in HCV genotype 3 that reduce response to sofosbuvir.
Collapse
Affiliation(s)
- Peter A.C. Wing
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Meleri Jones
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Michelle Cheung
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Sampath DaSilva
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Connor Bamford
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Wing-Yiu Jason Lee
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Elihu Aranday-Cortes
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Ana Da Silva Filipe
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK
| | - John McLauchlan
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK
| | - David Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University National Health Service Trust, Oxford, UK
| | - William Irving
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, UK,University of Nottingham, Nottingham, UK
| | - Morven Cunningham
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Azim Ansari
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University National Health Service Trust, Oxford, UK
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University National Health Service Trust, Oxford, UK
| | - Graham R. Foster
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK,Reprint requests Address requests for reprints to: Graham R. Foster, PhD, Barts Liver Centre, Blizard Institute, 4 Newark Street, London E1 2AT, UK.
| |
Collapse
|
33
|
Leila AR, Mousa MHA, Frakolaki E, Vassilaki N, Bartenschlager R, Zoidis G, Abdel-Halim M, Abadi AH. Symmetric Anti-HCV Agents: Synthesis, Antiviral Properties, and Conformational Aspects of Core Scaffolds. ACS OMEGA 2019; 4:11440-11454. [PMID: 31460249 PMCID: PMC6682128 DOI: 10.1021/acsomega.9b01242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/04/2019] [Indexed: 05/17/2023]
Abstract
As hepatitis C virus (HCV) is one of the major health problems in many countries, interest has been aroused in the design, synthesis, and optimization of novel NS5A inhibitors, outside the chemical space of currently available direct acting antivirals (DAAs). Two series of symmetric molecules with core scaffold 3,3'-(buta-1,3-diyne-1,4-diyl)dianiline or 4,4'-(buta-1,3-diyne-1,4-diyl)dianiline, coupled on its nitrogen as amide with different end caps, were synthesized and tested for their activities against HCV by using cell-based antiviral assays. Molecules with the 3,3'-(buta-1,3-diyne-1,4-diyl)dianiline core were more active than their 4,4'-congeners. Only the 3,3'-derivatives showed noncoplanarity of core phenyls that mostly led to a better interaction with the target protein and appears to be a crucial element for efficient inhibition of HCV replication. Compounds 2f and 2q exhibited potent inhibition of genotype (GT) 1b HCV replication with EC50 values in the picomolar range and selectivity index greater than 6 orders of magnitude. The compounds seem more selective toward GT 1b and 4a. In conclusion, novel symmetric molecules with a 3,3'-(buta-1,3-diyne-1,4-diyl)dianiline core are potent and selective inhibitors that provide new extension to explore the structure-activity relationship of NS5A targeting DAAs.
Collapse
Affiliation(s)
- Alaa R.
S. Leila
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Mai H. A. Mousa
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Efseveia Frakolaki
- Molecular
Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521 Athens, Greece
| | - Niki Vassilaki
- Molecular
Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521 Athens, Greece
| | - Ralf Bartenschlager
- Department
of Infectious Diseases, Molecular Virology, University of Heidelberg, 69117 Heidelberg, Germany
- German
Center for Infection Research, Heidelberg
Partner Site, 69120 Heidelberg, Germany
| | - Grigoris Zoidis
- School
of Health Sciences, Faculty of Pharmacy, Department of Pharmaceutical
Chemistry, University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece
| | - Mohammad Abdel-Halim
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Ashraf H. Abadi
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| |
Collapse
|
34
|
Giannakopoulou E, Pardali V, Frakolaki E, Siozos V, Myrianthopoulos V, Mikros E, Taylor MC, Kelly JM, Vassilaki N, Zoidis G. Scaffold hybridization strategy towards potent hydroxamate-based inhibitors of Flaviviridae viruses and Trypanosoma species. MEDCHEMCOMM 2019; 10:991-1006. [PMID: 31303998 DOI: 10.1039/c9md00200f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/15/2019] [Indexed: 12/14/2022]
Abstract
Infections with Flaviviridae viruses, such as hepatitis C virus (HCV) and dengue virus (DENV) pose global health threats. Infected individuals are at risk of developing chronic liver failure or haemorrhagic fever respectively, often with a fatal outcome if left untreated. Diseases caused by tropical parasites of the Trypanosoma species, T. brucei and T. cruzi, constitute significant socioeconomic burden in sub-Saharan Africa and continental Latin America, yet drug development is under-funded. Anti-HCV chemotherapy is associated with severe side effects and high cost, while dengue has no clinically approved therapy and antiparasitic drugs are outdated and difficult to administer. Moreover, drug resistance is an emerging concern. Consequently, the need for new revolutionary chemotherapies is urgent. By utilizing a molecular framework combination approach, we combined two distinct chemical entities with proven antiviral and trypanocidal activity into a novel hybrid scaffold attached by an acetohydroxamic acid group (CH2CONHOH), aiming at derivatives with dual activity. The novel spiro-carbocyclic substituted hydantoin analogues were rationally designed, synthesized and evaluated for their potency against three HCV genotypes (1b, 3a, 4a), DENV and two Trypanosoma species (T. brucei, T. cruzi). They exhibited significant EC50 values and remarkable selectivity indices. Several modifications were undertaken to further explore the structure activity relationships (SARs) and confirm the pivotal role of the acetohydroxamic acid metal binding group.
Collapse
Affiliation(s)
- Erofili Giannakopoulou
- School of Health Sciences , Faculty of Pharmacy , Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , GR-15771 Athens , Greece .
| | - Vasiliki Pardali
- School of Health Sciences , Faculty of Pharmacy , Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , GR-15771 Athens , Greece .
| | - Efseveia Frakolaki
- Molecular Virology Laboratory , Hellenic Pasteur Institute , Vas. Sofias Avenue , GR-11521 , Athens , Greece
| | - Vasileios Siozos
- Molecular Virology Laboratory , Hellenic Pasteur Institute , Vas. Sofias Avenue , GR-11521 , Athens , Greece
| | - Vassilios Myrianthopoulos
- School of Health Sciences , Faculty of Pharmacy , Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , GR-15771 Athens , Greece .
| | - Emmanuel Mikros
- School of Health Sciences , Faculty of Pharmacy , Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , GR-15771 Athens , Greece .
| | - Martin C Taylor
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street , London WC1E 7HT , UK
| | - John M Kelly
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street , London WC1E 7HT , UK
| | - Niki Vassilaki
- Molecular Virology Laboratory , Hellenic Pasteur Institute , Vas. Sofias Avenue , GR-11521 , Athens , Greece
| | - Grigoris Zoidis
- School of Health Sciences , Faculty of Pharmacy , Department of Pharmaceutical Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , GR-15771 Athens , Greece .
| |
Collapse
|
35
|
Smith D, Magri A, Bonsall D, Ip CL, Trebes A, Brown A, Piazza P, Bowden R, Nguyen D, Ansari MA, Simmonds P, Barnes E. Resistance analysis of genotype 3 hepatitis C virus indicates subtypes inherently resistant to nonstructural protein 5A inhibitors. Hepatology 2019; 69:1861-1872. [PMID: 29425396 PMCID: PMC6492296 DOI: 10.1002/hep.29837] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/03/2018] [Indexed: 12/12/2022]
Abstract
Hepatitis C virus (HCV) genotype (gt) 3 is highly prevalent globally, with non-gt3a subtypes common in Southeast Asia. Resistance-associated substitutions (RASs) have been shown to play a role in treatment failure. However, the role of RASs in gt3 is not well understood. We report the prevalence of RASs in a cohort of direct-acting antiviral treatment-naive, gt3-infected patients, including those with rarer subtypes, and evaluate the effect of these RASs on direct-acting antivirals in vitro. Baseline samples from 496 gt3 patients enrolled in the BOSON clinical trial were analyzed by next-generation sequencing after probe-based enrichment for HCV. Whole viral genomes were analyzed for the presence of RASs to approved direct-acting antivirals. The resistance phenotype of RASs in combination with daclatasvir, velpatasvir, pibrentasvir, elbasvir, and sofosbuvir was measured using the S52 ΔN gt3a replicon model. The nonstructural protein 5A A30K and Y93H substitutions were the most common at 8.9% (n = 44) and 12.3% (n = 61), respectively, and showed a 10-fold and 11-fold increase in 50% effect concentration for daclatasvir compared to the unmodified replicon. Paired RASs (A30K + L31M and A30K + Y93H) were identified in 18 patients (9 of each pair); these combinations were shown to be highly resistant to daclatasvir, velpatasvir, elbasvir, and pibrentasvir. The A30K + L31M combination was found in all gt3b and gt3g samples. Conclusion: Our study reveals high frequencies of RASs to nonstructural protein 5A inhibitors in gt3 HCV; the paired A30K + L31M substitutions occur in all patients with gt3b and gt3g virus, and in vitro analysis suggests that these subtypes may be inherently resistant to all approved nonstructural protein 5A inhibitors for gt3 HCV. (Hepatology 2018).
Collapse
Affiliation(s)
- David Smith
- Nuffield Department of Medicine and the Oxford NIHR BRCUniversity of OxfordOxfordUK
| | - Andrea Magri
- Nuffield Department of Medicine and the Oxford NIHR BRCUniversity of OxfordOxfordUK
- Oxford Martin SchoolUniversity of OxfordOxfordUK
| | - David Bonsall
- Nuffield Department of Medicine and the Oxford NIHR BRCUniversity of OxfordOxfordUK
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Camilla L.C. Ip
- Nuffield Department of Medicine and the Oxford NIHR BRCUniversity of OxfordOxfordUK
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Amy Trebes
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Anthony Brown
- Nuffield Department of Medicine and the Oxford NIHR BRCUniversity of OxfordOxfordUK
| | - Palo Piazza
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Rory Bowden
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Dung Nguyen
- Nuffield Department of Medicine and the Oxford NIHR BRCUniversity of OxfordOxfordUK
| | - M. Azim Ansari
- Nuffield Department of Medicine and the Oxford NIHR BRCUniversity of OxfordOxfordUK
- Oxford Martin SchoolUniversity of OxfordOxfordUK
| | - Peter Simmonds
- Nuffield Department of Medicine and the Oxford NIHR BRCUniversity of OxfordOxfordUK
| | - Eleanor Barnes
- Nuffield Department of Medicine and the Oxford NIHR BRCUniversity of OxfordOxfordUK
| | | |
Collapse
|
36
|
Matloub AA, Gomaa EZ, Hassan AA, Elbatanony MM, El-Senousy WM. Comparative Chemical and Bioactivity Studies of Intra- and Extracellular Metabolites of Endophytic Bacteria, Bacillus subtilis NCIB 3610. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09856-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
37
|
Costa R, Todt D, Zapatero-Belinchón F, Schenk C, Anastasiou OE, Walker A, Hertel B, Timmer L, Bojkova D, Ruckert M, Sarrazin C, Timm J, Lohmann V, Manns MP, Steinmann E, von Hahn T, Ciesek S. SEC14L2, a lipid-binding protein, regulates HCV replication in culture with inter- and intra-genotype variations. J Hepatol 2019; 70:603-614. [PMID: 30472319 DOI: 10.1016/j.jhep.2018.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND & AIMS The lipid-binding protein, SEC14L2, is crucial for the efficient viral replication of clinical hepatitis C virus (HCV) isolates in cell culture. Given the role of SEC14L2 in HCV replication, we aimed to study a large number of HCV positive sera carrying genotypes 1-4, to identify viral factors associated with efficient replication in culture. Additionally, we investigated whether 13 single nucleotide polymorphisms (SNPs) of SEC14L2 have an impact on RNA replication of naturally occurring HCV isolates. METHODS We generated Huh-7.5 cell lines overexpressing SEC14L2 or 13 coding SNPs and tested 73 different HCV positive sera for in vitro replication. Furthermore, we genotyped a cohort of 262 patients with chronic HCV for the common SNP (rs757660) and investigated its effect on the clinical phenotype. RESULTS HCV isolates from genotype 1, 2, 3 and 4 replicate in Huh-7.5 cells overexpressing SEC14L2. Interestingly, only subgenomic replicons from genotypes 1 and 3 showed enhanced replication whereas genotypes 2 and 4 remained unaffected. Furthermore, replication was independent of viral load. Importantly, all tested SNPs supported HCV RNA replication in vitro, while 1 SNP was associated with decreased SEC1L2 expression and viral RNA. All SNPs exhibited comparable cellular cholesterol and vitamin E abundance in naïve Huh-7.5 cells. CONCLUSIONS This large screen of natural HCV isolates of 4 genotypes underscores the relevance of SEC14L2 as an in vitro HCV host factor. Additionally, SEC14L2 variants appear to recapitulate the wild-type enhancement of HCV replication. Variant rs191341134 showed a decreased effect due to lowered stability, whereas variant rs757660, a high prevalence mutant, showed a similar phenotype to the wild-type. LAY SUMMARY Until the year 2015, consistent replication of patient-derived isolates of hepatitis C virus (HCV) in an in vitro model remained a limitation in HCV research. In 2015 a group of authors identified a protein named SEC14L2 that enabled the replication of HCV isolates in cell culture. We performed a large screen encompassing 73 isolates of 4 different HCV genotypes. Additionally, we replaced the natural SEC14L2 with 13 different mutants to test if the protein variation significantly altered its HCV replication enhancing functions. We showed that different genotypes of HCV react differently to the presence of this protein and the variants of the protein mimic the behavior of the wild-type.
Collapse
Affiliation(s)
- Rui Costa
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; Institute for Molecular Biology, Hannover Medical School, Hannover, Germany; Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Daniel Todt
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany; Institute of Experimental Virology, Twincore, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Francisco Zapatero-Belinchón
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; Institute for Molecular Biology, Hannover Medical School, Hannover, Germany
| | - Christian Schenk
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Olympia E Anastasiou
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Andreas Walker
- Institute of Virology, University Hospital Düsseldorf, Faculty of Medicine, University Düsseldorf, Düsseldorf, Germany
| | - Barbara Hertel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; Institute for Molecular Biology, Hannover Medical School, Hannover, Germany
| | - Lejla Timmer
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Denisa Bojkova
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Maren Ruckert
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; Institute for Molecular Biology, Hannover Medical School, Hannover, Germany
| | - Christoph Sarrazin
- University Hospital Frankfurt, Department of Gastroenterology and Hepatology, Frankfurt am Main, Germany; German Center for Infection Research, DZIF, Germany
| | - Jörg Timm
- Institute of Virology, University Hospital Düsseldorf, Faculty of Medicine, University Düsseldorf, Düsseldorf, Germany
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Michael P Manns
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; German Center for Infection Research, DZIF, Germany
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany; Institute of Experimental Virology, Twincore, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Thomas von Hahn
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; Institute for Molecular Biology, Hannover Medical School, Hannover, Germany; German Center for Infection Research, DZIF, Germany
| | - Sandra Ciesek
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany; German Center for Infection Research, DZIF, Germany.
| |
Collapse
|
38
|
Schenk C, Meyrath M, Warnken U, Schnölzer M, Mier W, Harak C, Lohmann V. Characterization of a Threonine-Rich Cluster in Hepatitis C Virus Nonstructural Protein 5A and Its Contribution to Hyperphosphorylation. J Virol 2018; 92:JVI.00737-18. [PMID: 30258001 PMCID: PMC6258934 DOI: 10.1128/jvi.00737-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/20/2018] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is a phosphoprotein with key functions in regulating viral RNA replication and assembly. Two phosphoisoforms are discriminated by their different apparent molecular weights: a basally phosphorylated (p56) and a hyperphosphorylated (p58) variant. The precise mechanisms governing p58 synthesis and specific functions of the isoforms are poorly understood. Our study aimed at a deeper understanding of determinants involved in p58 synthesis. We analyzed two variants of p56 and p58 of isolate JFH-1 separately by mass spectrometry using an expression model and thereby identified a threonine-rich phosphopeptide exclusively found in the hyperphosphorylated variant. Individual exchange of possible phosphoacceptor sites to phosphoablatant or -mimetic residues had little impact on HCV replication or assembly in cell culture. A phosphospecific antibody recognizing pT242 revealed that this position was indeed phosphorylated only in p58 and depended on casein kinase Iα. Importantly, phosphoablative mutations at positions T244 and S247 abrogated pT242 detection without substantial effects on global p58 levels, whereas mutations in the preceding serine-rich cluster dramatically reduced total p58 levels but had minor impact on pT242 levels, suggesting the existence of distinct subspecies of hyperphosphorylated NS5A. Mass spectrometry analyses of different genotypes showed variable phosphorylation patterns across NS5A and suggested that the threonine-rich region is also phosphorylated at T242 in gt4a and at S249 in gt1a, gt1b, and gt4a. Our data therefore indicate that p58 is not a single homogenously phosphorylated protein species but rather a population of various phosphoisoforms, with high variability between genotypes.IMPORTANCE Hepatitis C virus infections affect 71 million people worldwide and cause severe chronic liver disease. Recently, efficient antiviral therapies have been established, with inhibitors of nonstructural protein NS5A as a cornerstone. NS5A is a central regulator of HCV replication and assembly but is still enigmatic in its molecular functions. It exists in two phosphoisoforms, p56 and p58. We identified a phosphopeptide exclusively found in p58 and analyzed the determinants involved in phosphorylation of this region. We found evidence for very different phosphorylation patterns resulting in p58. These results challenge the concept of p58 being a homogenous species of NS5A molecules phosphorylated at the same positions and argues for at least two independently phosphorylated variants showing the same electrophoretic mobility, likely serving different functions.
Collapse
Affiliation(s)
- Christian Schenk
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Max Meyrath
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Walter Mier
- Department of Nuclear Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Harak
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| |
Collapse
|
39
|
Ashraf MU, Iman K, Khalid MF, Salman HM, Shafi T, Rafi M, Javaid N, Hussain R, Ahmad F, Shahzad-Ul-Hussan S, Mirza S, Shafiq M, Afzal S, Hamera S, Anwar S, Qazi R, Idrees M, Qureshi SA, Chaudhary SU. Evolution of efficacious pangenotypic hepatitis C virus therapies. Med Res Rev 2018; 39:1091-1136. [PMID: 30506705 DOI: 10.1002/med.21554] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022]
Abstract
Hepatitis C compromises the quality of life of more than 350 million individuals worldwide. Over the last decade, therapeutic regimens for treating hepatitis C virus (HCV) infections have undergone rapid advancements. Initially, structure-based drug design was used to develop molecules that inhibit viral enzymes. Subsequently, establishment of cell-based replicon systems enabled investigations into various stages of HCV life cycle including its entry, replication, translation, and assembly, as well as role of host proteins. Collectively, these approaches have facilitated identification of important molecules that are deemed essential for HCV life cycle. The expanded set of putative virus and host-encoded targets has brought us one step closer to developing robust strategies for efficacious, pangenotypic, and well-tolerated medicines against HCV. Herein, we provide an overview of the development of various classes of virus and host-directed therapies that are currently in use along with others that are undergoing clinical evaluation.
Collapse
Affiliation(s)
- Muhammad Usman Ashraf
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Kanzal Iman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Farhan Khalid
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Department of Biomedical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Hafiz Muhammad Salman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Plant Biotechnology Laboratory, Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Talha Shafi
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Momal Rafi
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | - Nida Javaid
- Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Rashid Hussain
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Fayyaz Ahmad
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | | | - Shaper Mirza
- Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Shafiq
- Plant Biotechnology Laboratory, Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Samia Afzal
- Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sadia Hamera
- Department of Plant Genetics, Institute of Life Sciences, University of Rostock, Germany
| | - Saima Anwar
- Department of Biomedical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Romena Qazi
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital & Research Centre, Lahore, Pakistan
| | - Muhammad Idrees
- Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.,Hazara University, Mansehra, Pakistan
| | - Sohail A Qureshi
- Institute of Integrative Biosciences, CECOS-University of Information Technology and Emerging Sciences, Peshawar, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| |
Collapse
|
40
|
Asante-Appiah E, Liu R, Curry S, McMonagle P, Agrawal S, Carr D, Rokosz L, Lahser F, Bystol K, Chase R, Black S, Ferrari E, Ingravallo P, Tong L, Yu W, Kozlowski J. In Vitro Antiviral Profile of Ruzasvir, a Potent and Pangenotype Inhibitor of Hepatitis C Virus NS5A. Antimicrob Agents Chemother 2018; 62:e01280-18. [PMID: 30150466 PMCID: PMC6201069 DOI: 10.1128/aac.01280-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/13/2018] [Indexed: 12/13/2022] Open
Abstract
Inhibition of NS5A has emerged as an attractive strategy to intervene in hepatitis C virus (HCV) replication. Ruzasvir (formerly MK-8408) was developed as a novel NS5A inhibitor to improve upon the potency and barrier to resistance of early compounds. Ruzasvir inhibited HCV RNA replication with 50% effective concentrations (EC50s) of 1 to 4 pM in Huh7 or Huh7.5 cells bearing replicons for HCV genotype 1 (GT1) to GT7. The antiviral activity was modestly (10-fold) reduced in the presence of 40% normal human serum. The picomolar potency in replicon cells extended to sequences of clinical isolates available in public databases that were synthesized and tested as replicons. In GT1a, ruzasvir inhibited common NS5A resistance-associated substitutions (RASs), with the exception of M28G. De novo resistance selection studies identified pathways with certain amino acid substitutions at residues 28, 30, 31, and 93 across genotypes. Substitutions at position 93 were more common in GT1 to -4, while changes at position 31 emerged frequently in GT5 and -6. With the exception of GT4, the reintroduction of selected RASs conferred a ≥100-fold potency reduction in the antiviral activity of ruzasvir. Common RASs from other classes of direct-acting antiviral agents (DAAs) did not confer cross-resistance to ruzasvir. The interaction of ruzasvir with an NS3/4A protease inhibitor (grazoprevir) and an NS5B polymerase prodrug (uprifosbuvir) was additive to synergistic, with no evidence of antagonism or cytotoxicity. The antiviral profile of ruzasvir supported its further evaluation in human trials in combination with grazoprevir and uprifosbuvir.
Collapse
Affiliation(s)
- Ernest Asante-Appiah
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Rong Liu
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Stephanie Curry
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Patricia McMonagle
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Sony Agrawal
- Department of In Vitro Pharmacology, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Donna Carr
- Department of In Vitro Pharmacology, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Laura Rokosz
- Department of In Vitro Pharmacology, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Frederick Lahser
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Karin Bystol
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Robert Chase
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Stuart Black
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Eric Ferrari
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Paul Ingravallo
- Department of Infectious Diseases, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Ling Tong
- Department of Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Wensheng Yu
- Department of Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Joseph Kozlowski
- Department of Medicinal Chemistry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| |
Collapse
|
41
|
Hepatitis C virus cell culture models: an encomium on basic research paving the road to therapy development. Med Microbiol Immunol 2018; 208:3-24. [PMID: 30298360 DOI: 10.1007/s00430-018-0566-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/01/2018] [Indexed: 12/17/2022]
Abstract
Chronic hepatitis C virus (HCV) infections affect 71 million people worldwide, often resulting in severe liver damage. Since 2014 highly efficient therapies based on directly acting antivirals (DAAs) are available, offering cure rates of almost 100%, if the infection is diagnosed in time. It took more than a decade to discover HCV in 1989 and another decade to establish a cell culture model. This review provides a personal view on the importance of HCV cell culture models, particularly the replicon system, in the process of therapy development, from drug screening to understanding of mode of action and resistance, with a special emphasis on the contributions of Ralf Bartenschlager's group. It summarizes the tremendous efforts of scientists in academia and industry required to achieve efficient DAAs, focusing on the main targets, protease, polymerase and NS5A. It furthermore underpins the importance of strong basic research laying the ground for translational medicine.
Collapse
|
42
|
Batista MN, Sanches PRDS, Carneiro BM, Braga ACS, Campos GRF, Cilli EM, Rahal P. GA-Hecate antiviral properties on HCV whole cycle represent a new antiviral class and open the door for the development of broad spectrum antivirals. Sci Rep 2018; 8:14329. [PMID: 30254334 PMCID: PMC6156508 DOI: 10.1038/s41598-018-32176-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 08/02/2018] [Indexed: 12/14/2022] Open
Abstract
In recent years, synthetic peptides have been considered promising targets for drug development that possess low side-effects, are cost-effective and are susceptible to rational design. Hecate was initially described as a potent bacterial inhibitor and subsequently as an anticancer drug with functions related to its lipid interaction property. Viruses, such as hepatitis C virus (HCV), have a lipid-dependent life cycle and could be affected by Hecate in many ways. Here, we assessed modifications on Hecate’s N-terminus region and its effects on HCV and hepatotoxicity. Gallic acid-conjugated Hecate was the most efficient Hecate-derivative, presenting high potential as an antiviral and inhibiting between 50 to 99% of all major steps within the HCV infectious cycle. However, the most promising aspect was GA-Hecate’s mechanism of action, which was associated with a balanced lipid interaction with the viral envelope and lipid droplets, as well as dsRNA intercalation, allowing for the possibility to affect other ssRNA viruses and those with a lipid-dependent cycle.
Collapse
Affiliation(s)
- Mariana Nogueira Batista
- Institute of Bioscience, Language and Exact Science, UNESP - São Paulo State University, São José do Rio Preto, SP, Brazil
| | | | - Bruno Moreira Carneiro
- Institute of Bioscience, Language and Exact Science, UNESP - São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Ana Cláudia Silva Braga
- Institute of Bioscience, Language and Exact Science, UNESP - São Paulo State University, São José do Rio Preto, SP, Brazil
| | | | - Eduardo Maffud Cilli
- Institute of Chemistry, UNESP - São Paulo State University, Araraquara, SP, Brazil.
| | - Paula Rahal
- Institute of Bioscience, Language and Exact Science, UNESP - São Paulo State University, São José do Rio Preto, SP, Brazil.
| |
Collapse
|
43
|
Ramirez S, Bukh J. Current status and future development of infectious cell-culture models for the major genotypes of hepatitis C virus: Essential tools in testing of antivirals and emerging vaccine strategies. Antiviral Res 2018; 158:264-287. [PMID: 30059723 DOI: 10.1016/j.antiviral.2018.07.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 02/08/2023]
Abstract
In this review, we summarize the relevant scientific advances that led to the development of infectious cell culture systems for hepatitis C virus (HCV) with the corresponding challenges and successes. We also provide an overview of how these systems have contributed to the study of antiviral compounds and their relevance for the development of a much-needed vaccine against this major human pathogen. An efficient infectious system to study HCV in vitro, using human hepatoma derived cells, has only been available since 2005, and was limited to a single isolate, named JFH1, until 2012. Successive developments have been slow and cumbersome, as each available system has been the result of a systematic effort for discovering adaptive mutations conferring culture replication and propagation to patient consensus clones that are inherently non-viable in vitro. High genetic heterogeneity is a paramount characteristic of this virus, and as such, it should preferably be reflected in basic, translational, and clinical studies. The limited number of efficient viral culture systems, in the context of the vast genetic diversity of HCV, continues to represent a major hindrance for the study of this virus, posing a significant barrier towards studies of antivirals (particularly of resistance) and for advancing vaccine development. Intensive research efforts, driven by isolate-specific culture adaptation, have only led to efficient full-length infectious culture systems for a few strains of HCV genotypes 1, 2, 3, and 6. Hence research aimed at identifying novel strategies that will permit universal culture of HCV will be needed to further our understanding of this unique virus causing 400 thousand deaths annually.
Collapse
Affiliation(s)
- 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, 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, Denmark.
| |
Collapse
|
44
|
Humes D, Ramirez S, Jensen TB, Li YP, Gottwein JM, Bukh J. Recombinant hepatitis C virus genotype 5a infectious cell culture systems expressing minimal JFH1 NS5B sequences permit polymerase inhibitor studies. Virology 2018; 522:177-192. [PMID: 30032031 DOI: 10.1016/j.virol.2018.05.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 02/07/2023]
Abstract
The six major epidemiologically important hepatitis C virus (HCV) genotypes differ in global distribution and antiviral responses. Full-length infectious cell-culture adapted clones, the gold standard for HCV studies in vitro, are missing for genotypes 4 and 5. To address this challenge for genotype 5, we constructed a consensus full-length clone of strain SA13 (SA13fl), which was found non-viable in Huh7.5 cells. Step-wise adaptation of SA13fl-based recombinants, beginning with a virus encoding the NS5B-thumb domain and 3´UTR of JFH1 (SA13/JF372-X), resulted in a high-titer SA13 virus with only 41 JFH1-encoded NS5B-thumb residues (SA13/JF470-510cc); this required sixteen cell-culture adaptive substitutions within the SA13fl polyprotein and two 3´UTR-changes. SA13/JF372-X and SA13/JF470-510cc were equally sensitive to nucleoside polymerase inhibitors, including sofosbuvir, but showed differential sensitivity to inhibitors targeting the NS5B palm or thumb. SA13/JF470-510cc represents a model to elucidate the influence of HCV RNA elements on viral replication and map determinants of sensitivity to polymerase inhibitors.
Collapse
Affiliation(s)
- Daryl Humes
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Tanja B Jensen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Yi-Ping Li
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Judith M Gottwein
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| |
Collapse
|
45
|
Characterization of the Anti-Hepatitis C Virus Activity of New Nonpeptidic Small-Molecule Cyclophilin Inhibitors with the Potential for Broad Anti-Flaviviridae Activity. Antimicrob Agents Chemother 2018; 62:AAC.00126-18. [PMID: 29760125 PMCID: PMC6021681 DOI: 10.1128/aac.00126-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/19/2018] [Indexed: 12/17/2022] Open
Abstract
Although members of the Flaviviridae display high incidence, morbidity, and mortality rates, the development of specific antiviral drugs for each virus is unlikely. Cyclophilins, a family of host peptidyl-prolyl cis-trans isomerases (PPIases), play a pivotal role in the life cycles of many viruses and therefore represent an attractive target for broad-spectrum antiviral development. We report here the pangenotypic anti-hepatitis C virus (HCV) activity of a small-molecule cyclophilin inhibitor (SMCypI). Mechanistic and modeling studies revealed that the SMCypI bound to cyclophilin A in competition with cyclosporine (CsA), inhibited its PPIase activity, and disrupted the CypA-nonstructural protein 5A (NS5A) interaction. Resistance selection showed that the lead SMCypI hardly selected amino acid substitutions conferring low-level or no resistance in vitro. Interestingly, the SMCypI selected D320E and Y321H substitutions, located in domain II of the NS5A protein. These substitutions were previously associated with low-level resistance to cyclophilin inhibitors such as alisporivir. Finally, the SMCypI inhibited the replication of other members of the Flaviviridae family with higher 50% effective concentrations (EC50s) than for HCV. Thus, because of its chemical plasticity and simplicity of synthesis, our new family of SMCypIs represents a promising new class of drugs with the potential for broad-spectrum anti-Flaviviridae activity as well as an invaluable tool to explore the role of cyclophilins in viral life cycles.
Collapse
|
46
|
Gottwein JM, Pham LV, Mikkelsen LS, Ghanem L, Ramirez S, Scheel TKH, Carlsen THR, Bukh J. Efficacy of NS5A Inhibitors Against Hepatitis C Virus Genotypes 1-7 and Escape Variants. Gastroenterology 2018; 154:1435-1448. [PMID: 29274866 DOI: 10.1053/j.gastro.2017.12.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 11/26/2017] [Accepted: 12/18/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Inhibitors of the hepatitis C virus (HCV) NS5A protein are a key component of effective treatment regimens, but the genetic heterogeneity of HCV has limited the efficacy of these agents and mutations lead to resistance. We directly compared the efficacy of all clinically relevant NS5A inhibitors against HCV genotype 1-7 prototype isolates and resistant escape variants, and investigated the effects of pre-existing resistance-associated substitutions (RAS) on HCV escape from treatment. METHODS We measured the efficacy of different concentrations of daclatasvir, ledipasvir, ombitasvir, elbasvir, ruzasvir, velpatasvir, and pibrentasvir in cultured cells infected with HCV recombinants expressing genotype 1-7 NS5A proteins with or without RAS. We engineered HCV variants that included RAS identified in escape experiments, using recombinants with or without T/Y93H and daclatasvir, or that contained RAS previously reported from patients. RESULTS NS5A inhibitors had varying levels of efficacy against original and resistant viruses. Only velpatasvir and pibrentasvir had uniform high activity against all HCV genotypes tested. RAS hotspots in NS5A were found at amino acids 28, 30, 31, and 93. Engineered escape variants had high levels of fitness. Pibrentasvir had the highest level of efficacy against variants; viruses with RAS at amino acids 28, 30, or 31 had no apparent resistance to pibrentasvir, and HCV with RAS at amino acid 93 had a low level of resistance to this drug. However, specific combinations of RAS and deletion of amino acid 32 led to significant resistance to pibrentasvir. For the remaining NS5A inhibitors tested, RAS at amino acids 28 and 93 led to high levels of resistance. Among these inhibitors, velpatasvir was more effective against variants with RAS at amino acid 30 and some variants with RAS at amino acid 31 than the other agents. Variants with the pre-existing RAS T/Y93H acquired additional NS5A changes during escape experiments, resulting in HCV variants with specific combinations of RAS, showing high fitness and high resistance. CONCLUSIONS We performed a comprehensive comparison of the efficacy of the 7 clinically relevant inhibitors of HCV NS5A and identified variants associated with resistance to each agent. These findings could improve treatment of patients with HCV infection.
Collapse
Affiliation(s)
- Judith M Gottwein
- Copenhagen Hepatitis C Program, Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - Long V Pham
- Copenhagen Hepatitis C Program, Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Lotte S Mikkelsen
- Copenhagen Hepatitis C Program, Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Lubna Ghanem
- Copenhagen Hepatitis C Program, Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program, Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Troels K H Scheel
- Copenhagen Hepatitis C Program, Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thomas H R Carlsen
- Copenhagen Hepatitis C Program, Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program, Department of Infectious Diseases and Clinical Research Centre, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| |
Collapse
|
47
|
Schöbel A, Rösch K, Herker E. Functional innate immunity restricts Hepatitis C Virus infection in induced pluripotent stem cell-derived hepatocytes. Sci Rep 2018; 8:3893. [PMID: 29497123 PMCID: PMC5832748 DOI: 10.1038/s41598-018-22243-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 02/20/2018] [Indexed: 12/15/2022] Open
Abstract
Knowledge of activation and interplay between the hepatitis C virus (HCV) and the hosts’ innate immunity is essential to understanding the establishment of chronic HCV infection. Human hepatoma cell lines, widely used as HCV cell culture system, display numerous metabolic alterations and a defective innate immunity, hindering the detailed study of virus-host interactions. Here, we analysed the suitability of induced pluripotent stem cell (iPSC)-derived hepatocyte-like cells (iHLCs) as a physiologically relevant model to study HCV replication in vitro. Density gradients and triglyceride analysis revealed that iHLCs secreted very-low density lipoprotein (VLDL)-like lipoproteins, providing a putative platform for bona fide lipoviroparticles. iHLCs supported the full HCV life cycle, but in contrast to Huh7 and Huh7.5 cells, replication and viral RNA levels decreased continuously. Following HCV infection, interferon-stimulated gene (ISG)-expression significantly increased in iHLCs, whereas induction was almost absent in Huh7/7.5 cells. However, IFNα-stimulation equally induced ISGs in iHLCs and hepatoma cells. JAK-STAT pathway inhibition increased HCV replication in mature iHLCs, but not in Huh7 cells. Additionally, HCV replication levels where higher in STAT2-, but not STAT1-knockdown iHLCs. Our findings support iHLCs as a suitable model for HCV-host interaction regarding a functional innate immunity and lipoprotein synthesis.
Collapse
Affiliation(s)
- Anja Schöbel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Kathrin Rösch
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Eva Herker
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.
| |
Collapse
|
48
|
Frey A, Piras-Straub K, Walker A, Timm J, Gerken G, Herzer K. The influence of immunosuppressants on direct-acting antiviral therapy is dependent on the hepatitis C virus genotype. Transpl Infect Dis 2017; 20. [PMID: 29111569 DOI: 10.1111/tid.12803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/05/2017] [Accepted: 07/13/2017] [Indexed: 01/20/2023]
Abstract
BACKGROUND Direct-acting antivirals (DAAs) have substantially increased sustained virological response rates after liver transplantation, with improved tolerance compared to interferon-based therapy. The influence of immunosuppressive agents on the efficacy of DAAs has not been clarified. METHODS Subgenomic hepatitis C virus (HCV) replicons for genotype (GT) 1b, 2b, 3a, and 4a were treated with the mammalian target of rapamycin (mTOR) inhibitors everolimus and sirolimus or with the calcineurin inhibitors (CNIs) cyclosporine or tacrolimus, either alone or in combination with selected DAAs. Cell proliferation-related effects were excluded with MTT assays. HCV replication activity was quantified by quantitative real-time polymerase chain reaction or luciferase assay. RESULTS Addition of either mTOR inhibitor to the DAA daclatasvir (DAC) resulted in a 30% increase in antiviral activity compared to DAC alone for HCV GT2a, GT3a, and GT4a (all P ≤ .01). Similar results were obtained using sofosbuvir and ledipasvir. In contrast, addition of either mTOR inhibitor to DAC induced a 30% reduction in antiviral activity in GT1b cells (P ≤ .01 vs DAC alone). Neither CNI affects the antiviral activity of the DAAs in any HCV GT. CONCLUSION For patients with HCV GT2a, GT3a, or GT4a infection, mTOR-based immunosuppressive therapy may be beneficial. CNI-based therapy may be more efficacious in GT1b patients, as mTOR inhibitors seem to impair antiviral efficacy of DAAs in HCV GT1b infection.
Collapse
Affiliation(s)
- Alexandra Frey
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Katja Piras-Straub
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Andreas Walker
- Department of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Jörg Timm
- Department of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Guido Gerken
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Kerstin Herzer
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| |
Collapse
|
49
|
Hepatitis C Virus Replication Depends on Endosomal Cholesterol Homeostasis. J Virol 2017; 92:JVI.01196-17. [PMID: 29046459 DOI: 10.1128/jvi.01196-17] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/28/2017] [Indexed: 01/16/2023] Open
Abstract
Similar to other positive-strand RNA viruses, hepatitis C virus (HCV) causes massive rearrangements of intracellular membranes, resulting in a membranous web (MW) composed of predominantly double-membrane vesicles (DMVs), the presumed sites of RNA replication. DMVs are enriched for cholesterol, but mechanistic details on the source and recruitment of cholesterol to the viral replication organelle are only partially known. Here we focused on selected lipid transfer proteins implicated in direct lipid transfer at various endoplasmic reticulum (ER)-membrane contact sites. RNA interference (RNAi)-mediated knockdown identified several hitherto unknown HCV dependency factors, such as steroidogenic acute regulatory protein-related lipid transfer domain protein 3 (STARD3), oxysterol-binding protein-related protein 1A and -B (OSBPL1A and -B), and Niemann-Pick-type C1 (NPC1), all residing at late endosome and lysosome membranes and required for efficient HCV RNA replication but not for replication of the closely related dengue virus. Focusing on NPC1, we found that knockdown or pharmacological inhibition caused cholesterol entrapment in lysosomal vesicles concomitant with decreased cholesterol abundance at sites containing the viral replicase factor NS5A. In untreated HCV-infected cells, unesterified cholesterol accumulated at the perinuclear region, partially colocalizing with NS5A at DMVs, arguing for NPC1-mediated endosomal cholesterol transport to the viral replication organelle. Consistent with cholesterol being an important structural component of DMVs, reducing NPC1-dependent endosomal cholesterol transport impaired MW integrity. This suggests that HCV usurps lipid transfer proteins, such as NPC1, at ER-late endosome/lysosome membrane contact sites to recruit cholesterol to the viral replication organelle, where it contributes to MW functionality.IMPORTANCE A key feature of the replication of positive-strand RNA viruses is the rearrangement of the host cell endomembrane system to produce a membranous replication organelle (RO). The underlying mechanisms are far from being elucidated fully. In this report, we provide evidence that HCV RNA replication depends on functional lipid transport along the endosomal-lysosomal pathway that is mediated by several lipid transfer proteins, such as the Niemann-Pick type C1 (NPC1) protein. Pharmacological inhibition of NPC1 function reduced viral replication, impaired the transport of cholesterol to the viral replication organelle, and altered organelle morphology. Besides NPC1, our study reports the importance of additional endosomal and lysosomal lipid transfer proteins required for viral replication, thus contributing to our understanding of how HCV manipulates their function in order to generate a membranous replication organelle. These results might have implications for the biogenesis of replication organelles of other positive-strand RNA viruses.
Collapse
|
50
|
Braga ACS, Carneiro BM, Batista MN, Akinaga MM, Bittar C, Rahal P. Heat shock proteins HSPB8 and DNAJC5B have HCV antiviral activity. PLoS One 2017; 12:e0188467. [PMID: 29182667 PMCID: PMC5705118 DOI: 10.1371/journal.pone.0188467] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/07/2017] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C is a disease caused by the hepatitis C virus (HCV), and an estimated 3% of the world population is infected with the virus. During replication, HCV interacts with several cellular proteins. Studies have shown that several heat shock proteins (HSPs) have an altered expression profile in the presence of the virus, and some HSPs interact directly with HCV proteins. In the present study, we evaluated the expression levels of heat shock proteins in vitro in the presence and absence of HCV. The differential expression of 84 HSPs and chaperones was observed using a qPCR array, comparing HCV uninfected and infected Huh7.5 cells. To validate qPCR array, the differentially expressed genes were tested by real-time PCR in three different HCV models: subgenomic HCV replicon cells (SGR-JFH-1), JFH-1 infected cells (both genotype 2a) and subgenomic S52 cells (genotype 3). The HSPB8 gene showed increased expression in all three viral models. We silenced HSPB8 expression and observed an increase in viral replication. In contrast, when we increased the expression of HSPB8, a decrease in the HCV replication rate was observed. The same procedure was adopted for DNAJC5B, and HCV showed a similar replication pattern as that observed for HSPB8. These results suggest that HSPB8 may act as an intracellular factor against hepatitis C virus replication and that DNAJC5B has the same function, with more relevant results for genotype 3. We also evaluated the direct interactions between HCV and HSP proteins, and the IP experiments showed that the HCV NS4B protein interacts with HSPB8. These results contribute to a better understanding of the mechanisms involved in HCV replication.
Collapse
Affiliation(s)
- Ana Claudia Silva Braga
- Laboratório de Estudos Genômicos, UNESP/IBILCE, São José do Rio Preto, São Paulo, Brazil
- * E-mail:
| | - Bruno Moreira Carneiro
- Laboratório de Estudos Genômicos, UNESP/IBILCE, São José do Rio Preto, São Paulo, Brazil
- Instituto de Ciências Exatas e Naturais, UFMT/CUR, Rondonópolis, Mato Grosso, Brazil
| | | | - Mônica Mayumi Akinaga
- Laboratório de Estudos Genômicos, UNESP/IBILCE, São José do Rio Preto, São Paulo, Brazil
| | - Cíntia Bittar
- Laboratório de Estudos Genômicos, UNESP/IBILCE, São José do Rio Preto, São Paulo, Brazil
| | - Paula Rahal
- Laboratório de Estudos Genômicos, UNESP/IBILCE, São José do Rio Preto, São Paulo, Brazil
| |
Collapse
|