1
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Khanal P, Patil VS, Bhattacharya K, Shrivastava AK, Bhandare VV. Exploring the globoid cell leukodystrophy protein network and therapeutic interventions. Sci Rep 2024; 14:18067. [PMID: 39103379 PMCID: PMC11300594 DOI: 10.1038/s41598-024-66437-8] [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: 02/25/2024] [Accepted: 07/01/2024] [Indexed: 08/07/2024] Open
Abstract
Globoid cell leukodystrophy is a severe rare disorder characterized by white matter degradation, resulting in a progressive loss of physical and mental abilities and has extremely limited therapeutic interventions. Therefore, this study aimed to delve into the Globoid cell leukodystrophy associated intricate network of differentially expressed genes (p < 0.05, |Fc|> 1) to identify potential druggable targets and possible therapeutic interventions using small molecules. The disease-associated neuronal protein circuit was constructed and analyzed, identifying 53 nodes (minimum edge cutoff 1), among which five (FOS, FOSB, GDNF, GFRA1, and JUN) were discerned as potential core protein nodes. Although our research enumerates the potential small molecules to target various protein nodes in the proposed disease network, we particularly underscore T-5224 to inhibit c-Jun activity as JUN was identified as one of the pivotal elements within the disease-associated neuronal protein circuit. The evaluation of T-5224 binding energy (- 11.0 kcal/mol) from docking study revealed that the compound to exhibit a notable affinity towards Jun/CRE complex. Moreover, the structural integrity of complex was affirmed through comprehensive molecular dynamics simulations, indicating a stable hydrophilic interaction between T-5224 and the Jun/CRE complex, thereby enhancing protein compactness and reducing solvent accessibility. This binding energy was further substantiated by free binding analysis, revealing a substantial thermodynamics complex state (- 448.00 ± 41.73 kJ/mol). Given that this investigation is confined to a computational framework, we additionally propose a hypothetical framework to ascertain the feasibility of inhibiting the Jun/CRE complex with T-5224 against Globoid cell leukodystrophy, employing a combination of in vitro and in vivo methodologies as a prospective avenue of this study.
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Affiliation(s)
- Pukar Khanal
- Department of Pharmacology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010, India.
- Silicon Script Sciences Private Limited, Bharatpur, Ghorahi, Dang, Nepal.
| | - Vishal S Patil
- Department of Pharmacology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010, India
| | - Kunal Bhattacharya
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, Assam, 781026, India
- Royal School of Pharmacy, The Assam Royal Global University, Guwahati, Assam, 781035, India
| | - Amit Kumar Shrivastava
- Department of Pharmacology, Universal College of Medical Sciences, Ranigaon, Bhairahawa, Rupandehi, Nepal
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2
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Pierce BG, Felbinger N, Metcalf M, Toth EA, Ofek G, Fuerst TR. Hepatitis C Virus E1E2 Structure, Diversity, and Implications for Vaccine Development. Viruses 2024; 16:803. [PMID: 38793684 PMCID: PMC11125608 DOI: 10.3390/v16050803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/02/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Hepatitis C virus (HCV) is a major medical health burden and the leading cause of chronic liver disease and cancer worldwide. More than 58 million people are chronically infected with HCV, with 1.5 million new infections occurring each year. An effective HCV vaccine is a major public health and medical need as recognized by the World Health Organization. However, due to the high variability of the virus and its ability to escape the immune response, HCV rapidly accumulates mutations, making vaccine development a formidable challenge. An effective vaccine must elicit broadly neutralizing antibodies (bnAbs) in a consistent fashion. After decades of studies from basic research through clinical development, the antigen of choice is considered the E1E2 envelope glycoprotein due to conserved, broadly neutralizing antigenic domains located in the constituent subunits of E1, E2, and the E1E2 heterodimeric complex itself. The challenge has been elicitation of robust humoral and cellular responses leading to broad virus neutralization due to the relatively low immunogenicity of this antigen. In view of this challenge, structure-based vaccine design approaches to stabilize key antigenic domains have been hampered due to the lack of E1E2 atomic-level resolution structures to guide them. Another challenge has been the development of a delivery platform in which a multivalent form of the antigen can be presented in order to elicit a more robust anti-HCV immune response. Recent nanoparticle vaccines are gaining prominence in the field due to their ability to facilitate a controlled multivalent presentation and trafficking to lymph nodes, where they can interact with both the cellular and humoral components of the immune system. This review focuses on recent advances in understanding the E1E2 heterodimeric structure to facilitate a rational design approach and the potential for development of a multivalent nanoparticle-based HCV E1E2 vaccine. Both aspects are considered important in the development of an effective HCV vaccine that can effectively address viral diversity and escape.
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Affiliation(s)
- Brian G. Pierce
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA; (B.G.P.); (N.F.); (M.M.); (E.A.T.); (G.O.)
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Nathaniel Felbinger
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA; (B.G.P.); (N.F.); (M.M.); (E.A.T.); (G.O.)
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Matthew Metcalf
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA; (B.G.P.); (N.F.); (M.M.); (E.A.T.); (G.O.)
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Eric A. Toth
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA; (B.G.P.); (N.F.); (M.M.); (E.A.T.); (G.O.)
| | - Gilad Ofek
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA; (B.G.P.); (N.F.); (M.M.); (E.A.T.); (G.O.)
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Thomas R. Fuerst
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA; (B.G.P.); (N.F.); (M.M.); (E.A.T.); (G.O.)
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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3
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Toth EA, Andrianov AK, Fuerst TR. Prospects for developing an Hepatitis C virus E1E2-based nanoparticle vaccine. Rev Med Virol 2023; 33:e2474. [PMID: 37565536 PMCID: PMC10626635 DOI: 10.1002/rmv.2474] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/12/2023]
Abstract
Globally, more than 58 million people are chronically infected with Hepatitis C virus (HCV) with 1.5 million new infections occurring each year. An effective vaccine for HCV is therefore a major unmet medical and public health need. Since HCV rapidly accumulates mutations, vaccines must elicit the production of broadly neutralising antibodies (bnAbs) in a reproducible fashion. Decades of research have generated a number of HCV vaccine candidates. Based on the available data and research through clinical development, a vaccine antigen based on the E1E2 glycoprotein complex appears to be the best choice, but robust induction of humoral and cellular responses leading to virus neutralisation has not yet been achieved. One issue that has arisen in developing an HCV vaccine (and many other vaccines as well) is the platform used for antigen delivery. The majority of viral vaccine trials have employed subunit vaccines. However, subunit vaccines often have limited immunogenicity, as seen for HCV, and thus multiple formats must be examined in order to elicit a robust anti-HCV immune response. Nanoparticle vaccines are gaining prominence in the field due to their ability to facilitate a controlled multivalent presentation and trafficking to lymph nodes, where they can interact with both arms of the immune system. This review discusses the potential for development of a nanoparticle-based HCV E1E2 vaccine, with an emphasis on the potential benefits of such an approach along with the major challenges facing the incorporation of E1E2 into nanoparticulate delivery systems and how those challenges can be addressed.
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Affiliation(s)
- Eric A. Toth
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Alexander K. Andrianov
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Thomas R. Fuerst
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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4
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Mosa A, Campo D, Khudyakov Y, AbouHaidar M, Gehring A, Zahoor A, Ball J, Urbanowicz R, Feld J. Polyvalent immunization elicits a synergistic broadly neutralizing immune response to hypervariable region 1 variants of hepatitis C virus. Proc Natl Acad Sci U S A 2023; 120:e2220294120. [PMID: 37276424 PMCID: PMC10268328 DOI: 10.1073/pnas.2220294120] [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: 11/29/2022] [Accepted: 04/29/2023] [Indexed: 06/07/2023] Open
Abstract
A hepatitis C virus (HCV) vaccine is urgently needed. Vaccine development has been hindered by HCV's genetic diversity, particularly within the immunodominant hypervariable region 1 (HVR1). Here, we developed a strategy to elicit broadly neutralizing antibodies to HVR1, which had previously been considered infeasible. We first applied a unique information theory-based measure of genetic distance to evaluate phenotypic relatedness between HVR1 variants. These distances were used to model the structure of HVR1's sequence space, which was found to have five major clusters. Variants from each cluster were used to immunize mice individually, and as a pentavalent mixture. Sera obtained following immunization neutralized every variant in a diverse HCVpp panel (n = 10), including those resistant to monovalent immunization, and at higher mean titers (1/ID50 = 435) than a glycoprotein E2 (1/ID50 = 205) vaccine. This synergistic immune response offers a unique approach to overcoming antigenic variability and may be applicable to other highly mutable viruses.
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Affiliation(s)
- Alexander I. Mosa
- Toronto Centre for Liver Disease, Toronto General Hospital, Toronto, M5G 2C4ON, Canada
| | - David S. Campo
- Molecular Epidemiology and Bioinformatics, Centers for Disease Control and Prevention, Atlanta30333, Georgia
| | - Yury Khudyakov
- Molecular Epidemiology and Bioinformatics, Centers for Disease Control and Prevention, Atlanta30333, Georgia
| | - Mounir G. AbouHaidar
- Department of Cell and Systems Biology, University of Toronto, Toronto, M5S 3G5ON, Canada
| | - Adam J. Gehring
- Department of Immunology, University of Toronto, Toronto, M5S 1A8ON, Canada
| | - Atif Zahoor
- Toronto Centre for Liver Disease, Toronto General Hospital, Toronto, M5G 2C4ON, Canada
| | - Jonathan K. Ball
- Wolfson Centre for Global Virus Infections, University of Nottingham, NottinghamNG8 1BB, United Kingdom
| | - Richard A. Urbanowicz
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, LiverpoolCH64 7TE, United Kingdom
| | - Jordan J. Feld
- Toronto Centre for Liver Disease, Toronto General Hospital, Toronto, M5G 2C4ON, Canada
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5
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Sliepen K, Radić L, Capella-Pujol J, Watanabe Y, Zon I, Chumbe A, Lee WH, de Gast M, Koopsen J, Koekkoek S, Del Moral-Sánchez I, Brouwer PJM, Ravichandran R, Ozorowski G, King NP, Ward AB, van Gils MJ, Crispin M, Schinkel J, Sanders RW. Induction of cross-neutralizing antibodies by a permuted hepatitis C virus glycoprotein nanoparticle vaccine candidate. Nat Commun 2022; 13:7271. [PMID: 36434005 PMCID: PMC9700739 DOI: 10.1038/s41467-022-34961-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022] Open
Abstract
Hepatitis C virus (HCV) infection affects approximately 58 million people and causes ~300,000 deaths yearly. The only target for HCV neutralizing antibodies is the highly sequence diverse E1E2 glycoprotein. Eliciting broadly neutralizing antibodies that recognize conserved cross-neutralizing epitopes is important for an effective HCV vaccine. However, most recombinant HCV glycoprotein vaccines, which usually include only E2, induce only weak neutralizing antibody responses. Here, we describe recombinant soluble E1E2 immunogens that were generated by permutation of the E1 and E2 subunits. We displayed the E2E1 immunogens on two-component nanoparticles and these nanoparticles induce significantly more potent neutralizing antibody responses than E2. Next, we generated mosaic nanoparticles co-displaying six different E2E1 immunogens. These mosaic E2E1 nanoparticles elicit significantly improved neutralization compared to monovalent E2E1 nanoparticles. These results provide a roadmap for the generation of an HCV vaccine that induces potent and broad neutralization.
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Affiliation(s)
- Kwinten Sliepen
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands.
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands.
| | - Laura Radić
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Joan Capella-Pujol
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Ian Zon
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Ana Chumbe
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Wen-Hsin Lee
- Department of Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marlon de Gast
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Jelle Koopsen
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Sylvie Koekkoek
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Iván Del Moral-Sánchez
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Philip J M Brouwer
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - Gabriel Ozorowski
- Department of Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, USA
- Institute for Protein Design, University of Washington, Seattle, USA
| | - Andrew B Ward
- Department of Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marit J van Gils
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Janke Schinkel
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Rogier W Sanders
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands.
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands.
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, USA.
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6
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Risueño C, Abrescia NGA, Coluzza I. Insights into Hepatitis C Virus E2 core Interactions with Human Cellular Receptor CD81 at Different pHs from Molecular Simulations. J Phys Chem B 2022; 126:8391-8403. [PMID: 36255318 DOI: 10.1021/acs.jpcb.2c04697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Hepatitis C virus (HCV) is the second viral agent that causes the majority of chronic hepatic infections worldwide, following Hepatitis B virus (HBV) infection. HCV infection comprises several steps, from the attachment to the receptors to the delivery of the viral genetic material and replication inside the cells. Tetraspanin CD81 is a key entry factor for HCV as it accompanies the virus during attachment and internalization through clathrin-mediated endocytosis. HCV-CD81 binding takes place through the viral glycoprotein E2. We performed full-atom molecular dynamics simulations reproducing the pH conditions that occur during the viral attachment to the hepatocytes (pH 7.4) and internalization (pH 6.2-4.6). We observed that changing the pH from 7.4 to 6.2 triggers a large conformational change in the binding orientation between E2core (E2core corresponds to residues 412-645 of the viral glycoprotein E2) and CD81LEL (CD81LEL corresponds to residues 112-204 of CD81) that occurs even more rapidly at low pH 4.6. This pH-induced switching mechanism has never been observed before and could allow the virus particles to sense the right moment during the maturation of the endosome to start fusion.
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Affiliation(s)
- Cristina Risueño
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio 48160, Spain.,Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, Donostia-San Sebastián 20014, Spain
| | - Nicola G A Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio 48160, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain.,Basque Foundation for Science, IKERBASQUE, Bilbao 48009, Spain
| | - Ivan Coluzza
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, Donostia-San Sebastián 20014, Spain.,Basque Foundation for Science, IKERBASQUE, Bilbao 48009, Spain.,Computational Biophysics Lab, Basque Center for Materials, Applications and Nanostructures (BCMaterials), Buil. Martina Casiano, Pl. 3 Parque Científico UPV/EHU Barrio Sarriena, Leioa 48940, Spain
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7
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de la Peña AT, Sliepen K, Eshun-Wilson L, Newby ML, Allen JD, Zon I, Koekkoek S, Chumbe A, Crispin M, Schinkel J, Lander GC, Sanders RW, Ward AB. Structure of the hepatitis C virus E1E2 glycoprotein complex. Science 2022; 378:263-269. [PMID: 36264808 PMCID: PMC10512783 DOI: 10.1126/science.abn9884] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Hepatitis C virus (HCV) infection is a leading cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma in humans and afflicts more than 58 million people worldwide. The HCV envelope E1 and E2 glycoproteins are essential for viral entry and comprise the primary antigenic target for neutralizing antibody responses. The molecular mechanisms of E1E2 assembly, as well as how the E1E2 heterodimer binds broadly neutralizing antibodies, remain elusive. Here, we present the cryo-electron microscopy structure of the membrane-extracted full-length E1E2 heterodimer in complex with three broadly neutralizing antibodies-AR4A, AT1209, and IGH505-at ~3.5-angstrom resolution. We resolve the interface between the E1 and E2 ectodomains and deliver a blueprint for the rational design of vaccine immunogens and antiviral drugs.
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Affiliation(s)
- Alba Torrents de la Peña
- Department of Integrative Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kwinten Sliepen
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Lisa Eshun-Wilson
- Department of Integrative Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maddy L. Newby
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Ian Zon
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Sylvie Koekkoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Ana Chumbe
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Janke Schinkel
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Gabriel C. Lander
- Department of Integrative Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
- Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Andrew B. Ward
- Department of Integrative Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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8
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Stejskal L, Kalemera MD, Lewis CB, Palor M, Walker L, Daviter T, Lees WD, Moss DS, Kremyda-Vlachou M, Kozlakidis Z, Gallo G, Bailey D, Rosenberg W, Illingworth CJR, Shepherd AJ, Grove J. An entropic safety catch controls hepatitis C virus entry and antibody resistance. eLife 2022; 11:e71854. [PMID: 35796426 PMCID: PMC9333995 DOI: 10.7554/elife.71854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 06/28/2022] [Indexed: 11/24/2022] Open
Abstract
E1 and E2 (E1E2), the fusion proteins of Hepatitis C Virus (HCV), are unlike that of any other virus yet described, and the detailed molecular mechanisms of HCV entry/fusion remain unknown. Hypervariable region-1 (HVR-1) of E2 is a putative intrinsically disordered protein tail. Here, we demonstrate that HVR-1 has an autoinhibitory function that suppresses the activity of E1E2 on free virions; this is dependent on its conformational entropy. Thus, HVR-1 is akin to a safety catch that prevents premature triggering of E1E2 activity. Crucially, this mechanism is turned off by host receptor interactions at the cell surface to allow entry. Mutations that reduce conformational entropy in HVR-1, or genetic deletion of HVR-1, turn off the safety catch to generate hyper-reactive HCV that exhibits enhanced virus entry but is thermally unstable and acutely sensitive to neutralising antibodies. Therefore, the HVR-1 safety catch controls the efficiency of virus entry and maintains resistance to neutralising antibodies. This discovery provides an explanation for the ability of HCV to persist in the face of continual immune assault and represents a novel regulatory mechanism that is likely to be found in other viral fusion machinery.
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Affiliation(s)
- Lenka Stejskal
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
| | - Mphatso D Kalemera
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Charlotte B Lewis
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Machaela Palor
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Lucas Walker
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Tina Daviter
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
- Shared Research Facilities, The Institute of Cancer ResearchLondonUnited Kingdom
| | - William D Lees
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
| | - David S Moss
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
| | | | - Zisis Kozlakidis
- International Agency for Research on Cancer, World Health OrganizationLyonFrance
| | | | | | - William Rosenberg
- Division of Medicine, Institute for Liver and Digestive Health, University College LondonLondonUnited Kingdom
| | - Christopher JR Illingworth
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Institut für Biologische Physik, Universität zu KölnCologneGermany
- MRC Biostatistics Unit, University of CambridgeCambridgeUnited Kingdom
| | - Adrian J Shepherd
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUnited Kingdom
| | - Joe Grove
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
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9
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Dos Santos VP, Rodrigues A, Dutra G, Bastos L, Mariano D, Mendonça JG, Lobo YJG, Mendes E, Maia G, Machado KDS, Werhli AV, Rocha G, de Lima LHF, de Melo-Minardi R. E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. PeerJ 2022; 10:e13099. [PMID: 35341044 PMCID: PMC8953562 DOI: 10.7717/peerj.13099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/21/2022] [Indexed: 01/12/2023] Open
Abstract
Background The SARS-CoV-2 pandemic reverberated, posing health and social hygiene obstacles throughout the globe. Mutant lineages of the virus have concerned scientists because of convergent amino acid alterations, mainly on the viral spike protein. Studies have shown that mutants have diminished activity of neutralizing antibodies and enhanced affinity with its human cell receptor, the ACE2 protein. Methods Hence, for real-time measuring of the impacts caused by variant strains in such complexes, we implemented E-Volve, a tool designed to model a structure with a list of mutations requested by users and return analyses of the variant protein. As a proof of concept, we scrutinized the spike-antibody and spike-ACE2 complexes formed in the variants of concern, B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma), by using contact maps depicting the interactions made amid them, along with heat maps to quantify these major interactions. Results The results found in this study depict the highly frequent interface changes made by the entire set of mutations, mainly conducted by N501Y and E484K. In the spike-Antibody complex, we have noticed alterations concerning electrostatic surface complementarity, breaching essential sites in the P17 and BD-368-2 antibodies. Alongside, the spike-ACE2 complex has presented new hydrophobic bonds. Discussion Molecular dynamics simulations followed by Poisson-Boltzmann calculations corroborate the higher complementarity to the receptor and lower to the antibodies for the K417T/E484K/N501Y (Gamma) mutant compared to the wild-type strain, as pointed by E-Volve, as well as an intensification of this effect by changes at the protein conformational equilibrium in solution. A local disorder of the loop α1'/β1', as well its possible effects on the affinity to the BD-368-2 antibody were also incorporated to the final conclusions after this analysis. Moreover, E-Volve can depict the main alterations in important biological structures, as shown in the SARS-CoV-2 complexes, marking a major step in the real-time tracking of the virus mutant lineages. E-Volve is available at http://bioinfo.dcc.ufmg.br/evolve.
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Affiliation(s)
- Vitor Pimentel Dos Santos
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - André Rodrigues
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gabriel Dutra
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luana Bastos
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Diego Mariano
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - José Gutembergue Mendonça
- Laboratory of Quantum and Computational Chemistry, Center of Exact and Natural Sciences, Department of Chemistry, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
| | - Yan Jerônimo Gomes Lobo
- Laboratory of Molecular Modeling and Bioinformatics, Campus Sete Lagoas, Department of Exact and Biological Sciences, Universidade Federal de São João del-Rei, Sete Lagoas, MG, Brazil
| | - Eduardo Mendes
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Giovana Maia
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Karina dos Santos Machado
- Computational Biology Laboratory (ComBi-Lab), Center for Computational Sciences-C3, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Adriano Velasque Werhli
- Computational Biology Laboratory (ComBi-Lab), Center for Computational Sciences-C3, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Gerd Rocha
- Laboratory of Quantum and Computational Chemistry, Center of Exact and Natural Sciences, Department of Chemistry, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
| | - Leonardo Henrique França de Lima
- Laboratory of Molecular Modeling and Bioinformatics, Campus Sete Lagoas, Department of Exact and Biological Sciences, Universidade Federal de São João del-Rei, Sete Lagoas, MG, Brazil
| | - Raquel de Melo-Minardi
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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10
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Conserved Residues Adjacent to ß-Barrel and Loop Intersection among Enterovirus VP1 Affect Viral Replication: Potential Target for Anti-Enteroviral Development. Viruses 2022; 14:v14020364. [PMID: 35215957 PMCID: PMC8877150 DOI: 10.3390/v14020364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 11/17/2022] Open
Abstract
Enterovirus genus has over one hundred genotypes and could cause several kinds of severe animal and human diseases. Understanding the role of conserved residues in the VP1 capsid protein among the enterovirus genus may lead to anti-enteroviral drug development. The highly conserved residues were found to be located at the loop and ß-barrel intersections. To elucidate the role of these VP1 residues among the enterovirus genus, alanine substitution reverse genetics (rg) variants were generated, and virus properties were investigated for their impact. Six highly conserved residues were identified as located near the inside of the canyon, and four of them were close to the ß-barrel and loop intersection. The variants rgVP1-R86A, rgVP1-P193A, rgVP1-G231A, and rgVP1-K256A were unable to be obtained, which may be due to disruption in the virus replication process. In contrast, rgVP1-E134A and rgVP1-P157A replicated well and rgVP1-P157A showed smaller plaque size, lower viral growth kinetics, and thermal instability at 39.5°C when compared to the rg wild type virus. These findings showed that the conserved residues located at the ß-barrel and loop junction play roles in modulating viral replication, which may provide a pivotal role for pan-enteroviral inhibitor candidate.
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11
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Gömer A, Brown RJP, Pfaender S, Deterding K, Reuter G, Orton R, Seitz S, Bock CT, Cavalleri JMV, Pietschmann T, Wedemeyer H, Steinmann E, Todt D. OUP accepted manuscript. Virus Evol 2022; 8:veac007. [PMID: 35242360 PMCID: PMC8887644 DOI: 10.1093/ve/veac007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Even 30 years after the discovery of the hepatitis C virus (HCV) in humans there is still no vaccine available. Reasons for this include the high mutation rate of HCV, which allows the virus to escape immune recognition and the absence of an immunocompetent animal model for vaccine development. Phylogenetically distinct hepaciviruses (genus Hepacivirus, family Flaviviridae) have been isolated from diverse species, each with a narrow host range: the equine hepacivirus (EqHV) is the closest known relative of HCV. In this study, we used amplicon-based deep-sequencing to investigate the viral intra-host population composition of the genomic regions encoding the surface glycoproteins E1 and E2. Patterns of E1E2 substitutional evolution were compared in longitudinally sampled EqHV-positive sera of naturally and experimentally infected horses and HCV-positive patients. Intra-host virus diversity was higher in chronically than in acutely infected horses, a pattern which was similar in the HCV-infected patients. However, overall glycoprotein variability was higher in HCV compared to EqHV. Additionally, selection pressure in HCV populations was higher, especially within the N-terminal region of E2, corresponding to the hypervariable region 1 (HVR1) in HCV. An alignment of glycoprotein sequences from diverse hepaciviruses identified the HVR1 as a unique characteristic of HCV: hepaciviruses from non-human species lack this region. Together, these data indicate that EqHV infection of horses could represent a powerful surrogate animal model to gain insights into hepaciviral evolution and HCVs HVR1-mediated immune evasion strategy.
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Affiliation(s)
| | | | - Stephanie Pfaender
- Department for Molecular and Medical Virology, Ruhr University Bochum, Universitätsstr. 150, Bochum 44801, Germany
| | - Katja Deterding
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Carl-Neuberg-Straße 1, Hannover 30625, Germany
- German Center for Infectious Disease Research (DZIF), HepNet Study-House, Hannover 30625, Germany
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs 7624, Hungary
| | | | - Stefan Seitz
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg 69120, Germany
| | - C- Thomas Bock
- Division of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute, Berlin 13353, Germany
| | - Jessika M V Cavalleri
- Clinical Unit of Equine Internal Medicine, University of Veterinary Medicine Vienna, Veterinärplatz 1, Vienna 1210, Austria
| | - Thomas Pietschmann
- Twincore, Centre for Experimental and Clinical Infection Research, Institute of Experimental Virology, Hannover 30625, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig Site, Hannover 30625, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover 30625, Germany
| | - Heiner Wedemeyer
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Carl-Neuberg-Straße 1, Hannover 30625, Germany
- German Center for Infectious Disease Research (DZIF), HepNet Study-House, Hannover 30625, Germany
| | - Eike Steinmann
- Department for Molecular and Medical Virology, Ruhr University Bochum, Universitätsstr. 150, Bochum 44801, Germany
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12
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Augestad EH, Bukh J, Prentoe J. Hepatitis C virus envelope protein dynamics and the link to hypervariable region 1. Curr Opin Virol 2021; 50:69-75. [PMID: 34403905 DOI: 10.1016/j.coviro.2021.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 12/11/2022]
Abstract
Conformational dynamics of viral envelope proteins seem to be involved in mediating evasion from neutralizing antibodies (NAbs) by mechanisms that limit exposure of conserved protein motifs. For hepatitis C virus (HCV), molecular studies have only recently begun to unveil how such dynamics of the envelope protein heterodimer, E1/E2, are linked to viral entry and NAb evasion. Here, we review data suggesting that E1/E2 exists in an equilibrium between theoretical 'open' (NAb-sensitive) and 'closed' (NAb-resistant) conformational states. We describe how this equilibrium is influenced by viral sequence polymorphisms and that it is critically dependent on the N-terminal region of E2, termed hypervariable region 1 (HVR1). Finally, we discuss how it appears that the virus binding site for the HCV entry co-receptor CD81 is less available in 'closed' E1/E2 states and that NAb-resistant viruses require a more intricate entry pathway involving also the entry co-receptor, SR-BI.
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Affiliation(s)
- Elias H Augestad
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark; Copenhagen Hepatitis C Program (CO-HEP), 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, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark; Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jannick Prentoe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark; Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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13
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Structural and Biophysical Characterization of the HCV E1E2 Heterodimer for Vaccine Development. Viruses 2021; 13:v13061027. [PMID: 34072451 PMCID: PMC8227786 DOI: 10.3390/v13061027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 02/07/2023] Open
Abstract
An effective vaccine for the hepatitis C virus (HCV) is a major unmet medical and public health need, and it requires an antigen that elicits immune responses to multiple key conserved epitopes. Decades of research have generated a number of vaccine candidates; based on these data and research through clinical development, a vaccine antigen based on the E1E2 glycoprotein complex appears to be the best choice. One bottleneck in the development of an E1E2-based vaccine is that the antigen is challenging to produce in large quantities and at high levels of purity and antigenic/functional integrity. This review describes the production and characterization of E1E2-based vaccine antigens, both membrane-associated and a novel secreted form of E1E2, with a particular emphasis on the major challenges facing the field and how those challenges can be addressed.
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14
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Kalemera MD, Capella-Pujol J, Chumbe A, Underwood A, Bull RA, Schinkel J, Sliepen K, Grove J. Optimized cell systems for the investigation of hepatitis C virus E1E2 glycoproteins. J Gen Virol 2021; 102. [PMID: 33147126 PMCID: PMC8116788 DOI: 10.1099/jgv.0.001512] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Great strides have been made in understanding and treating hepatitis C virus (HCV) thanks to the development of various experimental systems including cell-culture-proficient HCV, the HCV pseudoparticle system and soluble envelope glycoproteins. The HCV pseudoparticle (HCVpp) system is a platform used extensively in studies of cell entry, screening of novel entry inhibitors, assessing the phenotypes of clinically observed E1 and E2 glycoproteins and, most pertinently, in characterizing neutralizing antibody breadth induced upon vaccination and natural infection in patients. Nonetheless, some patient-derived clones produce pseudoparticles that are either non-infectious or exhibit infectivity too low for meaningful phenotyping. The mechanisms governing whether any particular clone produces infectious pseudoparticles are poorly understood. Here we show that endogenous expression of CD81, an HCV receptor and a cognate-binding partner of E2, in producer HEK 293T cells is detrimental to the infectivity of recovered HCVpp for most strains. Many HCVpp clones exhibited increased infectivity or had their infectivity rescued when they were produced in 293T cells CRISPR/Cas9 engineered to ablate CD81 expression (293TCD81KO). Clones made in 293TCD81KO cells were antigenically very similar to their matched counterparts made parental cells and appear to honour the accepted HCV entry pathway. Deletion of CD81 did not appreciably increase the recovered titres of soluble E2 (sE2). However, we did, unexpectedly, find that monomeric sE2 made in 293T cells and Freestyle 293-F (293-F) cells exhibit important differences. We found that 293-F-produced sE2 harbours mostly complex-type glycans whilst 293T-produced sE2 displays a heterogeneous mixture of both complex-type glycans and high-mannose or hybrid-type glycans. Moreover, sE2 produced in 293T cells is antigenically superior; exhibiting increased binding to conformational antibodies and the large extracellular loop of CD81. In summary, this work describes an optimal cell line for the production of HCVpp and reveals that sE2 made in 293T and 293-F cells are not antigenic equals. Our findings have implications for functional studies of E1E2 and the production of candidate immunogens.
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Affiliation(s)
- Mphatso D Kalemera
- Institute of Immunity and Transplantation, Division of Infection and Immunity, The Royal Free Hospital, University College London, London, UK
| | - Joan Capella-Pujol
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Ana Chumbe
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Alexander Underwood
- Viral Immunology Systems Program, The Kirby Institute, School of Medical Sciences, Faculty of Medicine, The University of New South Wales, Sydney, Australia
| | - Rowena A Bull
- Viral Immunology Systems Program, The Kirby Institute, School of Medical Sciences, Faculty of Medicine, The University of New South Wales, Sydney, Australia
| | - Janke Schinkel
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Joe Grove
- Institute of Immunity and Transplantation, Division of Infection and Immunity, The Royal Free Hospital, University College London, London, UK
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15
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Structure-Based and Rational Design of a Hepatitis C Virus Vaccine. Viruses 2021; 13:v13050837. [PMID: 34063143 PMCID: PMC8148096 DOI: 10.3390/v13050837] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/27/2021] [Accepted: 04/30/2021] [Indexed: 12/11/2022] Open
Abstract
A hepatitis C virus (HCV) vaccine is a critical yet unfulfilled step in addressing the global disease burden of HCV. While decades of research have led to numerous clinical and pre-clinical vaccine candidates, these efforts have been hindered by factors including HCV antigenic variability and immune evasion. Structure-based and rational vaccine design approaches have capitalized on insights regarding the immune response to HCV and the structures of antibody-bound envelope glycoproteins. Despite successes with other viruses, designing an immunogen based on HCV glycoproteins that can elicit broadly protective immunity against HCV infection is an ongoing challenge. Here, we describe HCV vaccine design approaches where immunogens were selected and optimized through analysis of available structures, identification of conserved epitopes targeted by neutralizing antibodies, or both. Several designs have elicited immune responses against HCV in vivo, revealing correlates of HCV antigen immunogenicity and breadth of induced responses. Recent studies have elucidated the functional, dynamic and immunological features of key regions of the viral envelope glycoproteins, which can inform next-generation immunogen design efforts. These insights and design strategies represent promising pathways to HCV vaccine development, which can be further informed by successful immunogen designs generated for other viruses.
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16
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From Structural Studies to HCV Vaccine Design. Viruses 2021; 13:v13050833. [PMID: 34064532 PMCID: PMC8147963 DOI: 10.3390/v13050833] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) is a serious and growing public health problem despite recent developments of antiviral therapeutics. To achieve global elimination of HCV, an effective cross-genotype vaccine is needed. The failure of previous vaccination trials to elicit an effective cross-reactive immune response demands better vaccine antigens to induce a potent cross-neutralizing response to improve vaccine efficacy. HCV E1 and E2 envelope (Env) glycoproteins are the main targets for neutralizing antibodies (nAbs), which aid in HCV clearance and protection. Therefore, a molecular-level understanding of the nAb responses against HCV is imperative for the rational design of cross-genotype vaccine antigens. Here we summarize the recent advances in structural studies of HCV Env and Env-nAb complexes and how they improve our understanding of immune recognition of HCV. We review the structural data defining HCV neutralization epitopes and conformational plasticity of the Env proteins, and the knowledge applicable to rational vaccine design.
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Velázquez-Moctezuma R, Augestad EH, Castelli M, Holmboe Olesen C, Clementi N, Clementi M, Mancini N, Prentoe J. Mechanisms of Hepatitis C Virus Escape from Vaccine-Relevant Neutralizing Antibodies. Vaccines (Basel) 2021; 9:291. [PMID: 33804732 PMCID: PMC8004074 DOI: 10.3390/vaccines9030291] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) is a major causative agent of acute and chronic hepatitis. It is estimated that 400,000 people die every year from chronic HCV infection, mostly from severe liver-related diseases such as cirrhosis and liver cancer. Although HCV was discovered more than 30 years ago, an efficient prophylactic vaccine is still missing. The HCV glycoprotein complex, E1/E2, is the principal target of neutralizing antibodies (NAbs) and, thus, is an attractive antigen for B-cell vaccine design. However, the high genetic variability of the virus necessitates the identification of conserved epitopes. Moreover, the high intrinsic mutational capacity of HCV allows the virus to continually escape broadly NAbs (bNAbs), which is likely to cause issues with vaccine-resistant variants. Several studies have assessed the barrier-to-resistance of vaccine-relevant bNAbs in vivo and in vitro. Interestingly, recent studies have suggested that escape substitutions can confer antibody resistance not only by direct modification of the epitope but indirectly through allosteric effects, which can be grouped based on the breadth of these effects on antibody susceptibility. In this review, we summarize the current understanding of HCV-specific NAbs, with a special focus on vaccine-relevant bNAbs and their targets. We highlight antibody escape studies pointing out the different methodologies and the escape mutations identified thus far. Finally, we analyze the antibody escape mechanisms of envelope protein escape substitutions and polymorphisms according to the most recent evidence in the HCV field. The accumulated knowledge in identifying bNAb epitopes as well as assessing barriers to resistance and elucidating relevant escape mechanisms may prove critical in the successful development of an HCV B-cell vaccine.
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Affiliation(s)
- Rodrigo Velázquez-Moctezuma
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (R.V.-M.); (E.H.A.); (C.H.O.)
- Department of Infectious Diseases, Hvidovre Hospital, 2650 Hvidovre, Denmark
| | - Elias H. Augestad
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (R.V.-M.); (E.H.A.); (C.H.O.)
- Department of Infectious Diseases, Hvidovre Hospital, 2650 Hvidovre, Denmark
| | - Matteo Castelli
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20132 Milano, Italy; (M.C.); (N.C.); (M.C.); (N.M.)
| | - Christina Holmboe Olesen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (R.V.-M.); (E.H.A.); (C.H.O.)
- Department of Infectious Diseases, Hvidovre Hospital, 2650 Hvidovre, Denmark
| | - Nicola Clementi
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20132 Milano, Italy; (M.C.); (N.C.); (M.C.); (N.M.)
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20132 Milano, Italy; (M.C.); (N.C.); (M.C.); (N.M.)
| | - Nicasio Mancini
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20132 Milano, Italy; (M.C.); (N.C.); (M.C.); (N.M.)
| | - Jannick Prentoe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (R.V.-M.); (E.H.A.); (C.H.O.)
- Department of Infectious Diseases, Hvidovre Hospital, 2650 Hvidovre, Denmark
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18
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Pierce BG, Keck ZY, Wang R, Lau P, Garagusi K, Elkholy K, Toth EA, Urbanowicz RA, Guest JD, Agnihotri P, Kerzic MC, Marin A, Andrianov AK, Ball JK, Mariuzza RA, Fuerst TR, Foung SKH. Structure-Based Design of Hepatitis C Virus E2 Glycoprotein Improves Serum Binding and Cross-Neutralization. J Virol 2020; 94:e00704-20. [PMID: 32878891 PMCID: PMC7592221 DOI: 10.1128/jvi.00704-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/20/2020] [Indexed: 12/22/2022] Open
Abstract
An effective vaccine for hepatitis C virus (HCV) is a major unmet need, and it requires an antigen that elicits immune responses to key conserved epitopes. Based on structures of antibodies targeting HCV envelope glycoprotein E2, we designed immunogens to modulate the structure and dynamics of E2 and favor induction of broadly neutralizing antibodies (bNAbs) in the context of a vaccine. These designs include a point mutation in a key conserved antigenic site to stabilize its conformation, as well as redesigns of an immunogenic region to add a new N-glycosylation site and mask it from antibody binding. Designs were experimentally characterized for binding to a panel of human monoclonal antibodies (HMAbs) and the coreceptor CD81 to confirm preservation of epitope structure and preferred antigenicity profile. Selected E2 designs were tested for immunogenicity in mice, with and without hypervariable region 1, which is an immunogenic region associated with viral escape. One of these designs showed improvement in polyclonal immune serum binding to HCV pseudoparticles and neutralization of isolates associated with antibody resistance. These results indicate that antigen optimization through structure-based design of the envelope glycoproteins is a promising route to an effective vaccine for HCV.IMPORTANCE Hepatitis C virus infects approximately 1% of the world's population, and no vaccine is currently available. Due to the high variability of HCV and its ability to actively escape the immune response, a goal of HCV vaccine design is to induce neutralizing antibodies that target conserved epitopes. Here, we performed structure-based design of several epitopes of the HCV E2 envelope glycoprotein to engineer its antigenic properties. Designs were tested in vitro and in vivo, demonstrating alteration of the E2 antigenic profile in several cases, and one design led to improvement of cross-neutralization of heterologous viruses. This represents a proof of concept that rational engineering of HCV envelope glycoproteins can be used to modulate E2 antigenicity and optimize a vaccine for this challenging viral target.
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Affiliation(s)
- Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Zhen-Yong Keck
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Ruixue Wang
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
| | - Patrick Lau
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Kyle Garagusi
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
| | - Khadija Elkholy
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
| | - Eric A Toth
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
| | - Richard A Urbanowicz
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Johnathan D Guest
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Pragati Agnihotri
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Melissa C Kerzic
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Alexander Marin
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
| | - Alexander K Andrianov
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
| | - Jonathan K Ball
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Roy A Mariuzza
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Thomas R Fuerst
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Steven K H Foung
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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19
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Ströh LJ, Krey T. HCV Glycoprotein Structure and Implications for B-Cell Vaccine Development. Int J Mol Sci 2020; 21:ijms21186781. [PMID: 32947858 PMCID: PMC7555785 DOI: 10.3390/ijms21186781] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/12/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023] Open
Abstract
Despite the approval of highly efficient direct-acting antivirals in the last decade Hepatitis C virus (HCV) remains a global health burden and the development of a vaccine would constitute an important step towards the control of HCV. The high genetic variability of the viral glycoproteins E1 and E2, which carry the main neutralizing determinants, together with their intrinsic structural flexibility, the high level of glycosylation that shields conserved neutralization epitopes and immune evasion using decoy epitopes renders the design of an efficient vaccine challenging. Recent structural and functional analyses have highlighted the role of the CD81 receptor binding site on E2, which overlaps with those neutralization epitopes within E2 that have been structurally characterized to date. This CD81 binding site consists of three distinct segments including “epitope I”, “epitope II” and the “CD81 binding loop”. In this review we summarize the structural features of the HCV glycoproteins that have been derived from X-ray structures of neutralizing and non-neutralizing antibody fragments complexed with either recombinant E2 or epitope-derived linear peptides. We focus on the current understanding how neutralizing antibodies interact with their cognate antigen, the structural features of the respective neutralization epitopes targeted by nAbs and discuss the implications for informed vaccine design.
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Affiliation(s)
- Luisa J. Ströh
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany;
| | - Thomas Krey
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany;
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, 23562 Luebeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 30625 Hannover, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Riems, 23562 Luebeck, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, 30625 Hannover, Germany
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany
- Correspondence: ; Tel.: +49-(0)451–3101-3101
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