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Tortorici MA, Addetia A, Seo AJ, Brown J, Sprouse K, Logue J, Clark E, Franko N, Chu H, Veesler D. Persistent immune imprinting occurs after vaccination with the COVID-19 XBB.1.5 mRNA booster in humans. Immunity 2024; 57:904-911.e4. [PMID: 38490197 DOI: 10.1016/j.immuni.2024.02.016] [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: 12/01/2023] [Revised: 01/25/2024] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
Immune imprinting describes how the first exposure to a virus shapes immunological outcomes of subsequent exposures to antigenically related strains. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron breakthrough infections and bivalent COVID-19 vaccination primarily recall cross-reactive memory B cells induced by prior Wuhan-Hu-1 spike mRNA vaccination rather than priming Omicron-specific naive B cells. These findings indicate that immune imprinting occurs after repeated Wuhan-Hu-1 spike exposures, but whether it can be overcome remains unclear. To understand the persistence of immune imprinting, we investigated memory and plasma antibody responses after administration of the updated XBB.1.5 COVID-19 mRNA vaccine booster. We showed that the XBB.1.5 booster elicited neutralizing antibody responses against current variants that were dominated by recall of pre-existing memory B cells previously induced by the Wuhan-Hu-1 spike. Therefore, immune imprinting persists after multiple exposures to Omicron spikes through vaccination and infection, including post XBB.1.5 booster vaccination, which will need to be considered to guide future vaccination.
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Affiliation(s)
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Albert J Seo
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Kaiti Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jenni Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Erica Clark
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Helen Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Predicting Functional Conformational Ensembles and Binding Mechanisms of Convergent Evolution for SARS-CoV-2 Spike Omicron Variants Using AlphaFold2 Sequence Scanning Adaptations and Molecular Dynamics Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587850. [PMID: 38617283 PMCID: PMC11014522 DOI: 10.1101/2024.04.02.587850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
In this study, we combined AlphaFold-based approaches for atomistic modeling of multiple protein states and microsecond molecular simulations to accurately characterize conformational ensembles and binding mechanisms of convergent evolution for the SARS-CoV-2 Spike Omicron variants BA.1, BA.2, BA.2.75, BA.3, BA.4/BA.5 and BQ.1.1. We employed and validated several different adaptations of the AlphaFold methodology for modeling of conformational ensembles including the introduced randomized full sequence scanning for manipulation of sequence variations to systematically explore conformational dynamics of Omicron Spike protein complexes with the ACE2 receptor. Microsecond atomistic molecular dynamic simulations provide a detailed characterization of the conformational landscapes and thermodynamic stability of the Omicron variant complexes. By integrating the predictions of conformational ensembles from different AlphaFold adaptations and applying statistical confidence metrics we can expand characterization of the conformational ensembles and identify functional protein conformations that determine the equilibrium dynamics for the Omicron Spike complexes with the ACE2. Conformational ensembles of the Omicron RBD-ACE2 complexes obtained using AlphaFold-based approaches for modeling protein states and molecular dynamics simulations are employed for accurate comparative prediction of the binding energetics revealing an excellent agreement with the experimental data. In particular, the results demonstrated that AlphaFold-generated extended conformational ensembles can produce accurate binding energies for the Omicron RBD-ACE2 complexes. The results of this study suggested complementarities and potential synergies between AlphaFold predictions of protein conformational ensembles and molecular dynamics simulations showing that integrating information from both methods can potentially yield a more adequate characterization of the conformational landscapes for the Omicron RBD-ACE2 complexes. This study provides insights in the interplay between conformational dynamics and binding, showing that evolution of Omicron variants through acquisition of convergent mutational sites may leverage conformational adaptability and dynamic couplings between key binding energy hotspots to optimize ACE2 binding affinity and enable immune evasion.
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Hannula L, Kuivanen S, Lasham J, Kant R, Kareinen L, Bogacheva M, Strandin T, Sironen T, Hepojoki J, Sharma V, Saviranta P, Kipar A, Vapalahti O, Huiskonen JT, Rissanen I. Nanobody engineering for SARS-CoV-2 neutralization and detection. Microbiol Spectr 2024; 12:e0419922. [PMID: 38363137 PMCID: PMC10986514 DOI: 10.1128/spectrum.04199-22] [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: 10/17/2022] [Accepted: 01/03/2024] [Indexed: 02/17/2024] Open
Abstract
In response to the ongoing COVID-19 pandemic, the quest for coronavirus inhibitors has inspired research on a variety of small proteins beyond conventional antibodies, including robust single-domain antibody fragments, i.e., "nanobodies." Here, we explore the potential of nanobody engineering in the development of antivirals and diagnostic tools. Through fusion of nanobody domains that target distinct binding sites, we engineered multimodular nanobody constructs that neutralize wild-type SARS-CoV-2 and the Alpha and Delta variants at high potency, with IC50 values as low as 50 pM. Despite simultaneous binding to distinct epitopes, Beta and Omicron variants were more resistant to neutralization by the multimodular nanobodies, which highlights the importance of accounting for antigenic drift in the design of biologics. To further explore the applications of nanobody engineering in outbreak management, we present an assay based on fusions of nanobodies with fragments of NanoLuc luciferase that can detect sub-nanomolar quantities of the SARS-CoV-2 spike protein in a single step. Our work showcases the potential of nanobody engineering to combat emerging infectious diseases. IMPORTANCE Nanobodies, small protein binders derived from the camelid antibody, are highly potent inhibitors of respiratory viruses that offer several advantages over conventional antibodies as candidates for specific therapies, including high stability and low production costs. In this work, we leverage the unique properties of nanobodies and apply them as building blocks for new therapeutic and diagnostic tools. We report ultra-potent SARS-CoV-2 inhibition by engineered nanobodies comprising multiple modules in structure-guided combinations and develop nanobodies that carry signal molecules, allowing rapid detection of the SARS-CoV-2 spike protein. Our results highlight the potential of engineered nanobodies in the development of effective countermeasures, both therapeutic and diagnostic, to manage outbreaks of emerging viruses.
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Affiliation(s)
- Liina Hannula
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Suvi Kuivanen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdynia, Poland
| | - Lauri Kareinen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Mariia Bogacheva
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tomas Strandin
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jussi Hepojoki
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Petri Saviranta
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Anja Kipar
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Olli Vapalahti
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Juha T. Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Ilona Rissanen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
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Zhu C, Pang S, Liu J, Duan Q. Current Progress, Challenges and Prospects in the Development of COVID-19 Vaccines. Drugs 2024; 84:403-423. [PMID: 38652356 DOI: 10.1007/s40265-024-02013-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2024] [Indexed: 04/25/2024]
Abstract
The COVID-19 pandemic has resulted in over 772 million confirmed cases, including nearly 7 million deaths, according to the World Health Organization (WHO). Leveraging rapid development, accelerated vaccine approval processes, and large-scale production of various COVID-19 vaccines using different technical platforms, the WHO declared an end to the global health emergency of COVID-19 on May 5, 2023. Current COVID-19 vaccines encompass inactivated, live attenuated, viral vector, protein subunit, nucleic acid (DNA and RNA), and virus-like particle (VLP) vaccines. However, the efficacy of these vaccines is diminishing due to the constant mutation of SARS-CoV-2 and the heightened immune evasion abilities of emerging variants. This review examines the impact of the COVID-19 pandemic, the biological characteristics of the virus, and its diverse variants. Moreover, the review underscores the effectiveness, advantages, and disadvantages of authorized COVID-19 vaccines. Additionally, it analyzes the challenges, strategies, and future prospects of developing a safe, broad-spectrum vaccine that confers sufficient and sustainable immune protection against new variants of SARS-CoV-2. These discussions not only offer insight for the development of next-generation COVID-19 vaccines but also summarize experiences for combating future emerging viruses.
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Affiliation(s)
- Congrui Zhu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510000, China
| | - Shengmei Pang
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Jiaqi Liu
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Qiangde Duan
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
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Ávila-Nieto C, Vergara-Alert J, Amengual-Rigo P, Ainsua-Enrich E, Brustolin M, Rodríguez de la Concepción ML, Pedreño-Lopez N, Rodon J, Urrea V, Pradenas E, Marfil S, Ballana E, Riveira-Muñoz E, Pérez M, Roca N, Tarrés-Freixas F, Cantero G, Pons-Grífols A, Rovirosa C, Aguilar-Gurrieri C, Ortiz R, Barajas A, Trinité B, Lepore R, Muñoz-Basagoiti J, Perez-Zsolt D, Izquierdo-Useros N, Valencia A, Blanco J, Guallar V, Clotet B, Segalés J, Carrillo J. Immunization with V987H-stabilized Spike glycoprotein protects K18-hACE2 mice and golden Syrian hamsters upon SARS-CoV-2 infection. Nat Commun 2024; 15:2349. [PMID: 38514609 PMCID: PMC10957958 DOI: 10.1038/s41467-024-46714-w] [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: 04/21/2023] [Accepted: 02/27/2024] [Indexed: 03/23/2024] Open
Abstract
Safe and effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are crucial to fight against the coronavirus disease 2019 pandemic. Most vaccines are based on a mutated version of the Spike glycoprotein [K986P/V987P (S-2P)] with improved stability, yield and immunogenicity. However, S-2P is still produced at low levels. Here, we describe the V987H mutation that increases by two-fold the production of the recombinant Spike and the exposure of the receptor binding domain (RBD). S-V987H immunogenicity is similar to S-2P in mice and golden Syrian hamsters (GSH), and superior to a monomeric RBD. S-V987H immunization confer full protection against severe disease in K18-hACE2 mice and GSH upon SARS-CoV-2 challenge (D614G or B.1.351 variants). Furthermore, S-V987H immunized K18-hACE2 mice show a faster tissue viral clearance than RBD- or S-2P-vaccinated animals challenged with D614G, B.1.351 or Omicron BQ1.1 variants. Thus, S-V987H protein might be considered for future SARS-CoV-2 vaccines development.
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Affiliation(s)
| | - Júlia Vergara-Alert
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Pep Amengual-Rigo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Marco Brustolin
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Jordi Rodon
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Victor Urrea
- IrsiCaixa AIDS Research Institute, Campus Can Ruti, Badalona, Spain
| | - Edwards Pradenas
- IrsiCaixa AIDS Research Institute, Campus Can Ruti, Badalona, Spain
| | - Silvia Marfil
- IrsiCaixa AIDS Research Institute, Campus Can Ruti, Badalona, Spain
| | - Ester Ballana
- IrsiCaixa AIDS Research Institute, Campus Can Ruti, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruit, Badalona, Spain
- CIBERINFEC. ISCIII, Madrid, Spain
| | | | - Mònica Pérez
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Núria Roca
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Ferran Tarrés-Freixas
- IrsiCaixa AIDS Research Institute, Campus Can Ruti, Badalona, Spain
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Guillermo Cantero
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain
| | | | - Carla Rovirosa
- IrsiCaixa AIDS Research Institute, Campus Can Ruti, Badalona, Spain
| | | | - Raquel Ortiz
- IrsiCaixa AIDS Research Institute, Campus Can Ruti, Badalona, Spain
| | - Ana Barajas
- IrsiCaixa AIDS Research Institute, Campus Can Ruti, Badalona, Spain
| | - Benjamin Trinité
- IrsiCaixa AIDS Research Institute, Campus Can Ruti, Badalona, Spain
| | - Rosalba Lepore
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | | | - Nuria Izquierdo-Useros
- IrsiCaixa AIDS Research Institute, Campus Can Ruti, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruit, Badalona, Spain
- CIBERINFEC. ISCIII, Madrid, Spain
| | - Alfonso Valencia
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine. University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Campus Can Ruti, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruit, Badalona, Spain
- CIBERINFEC. ISCIII, Madrid, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine. University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain
| | - Victor Guallar
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Campus Can Ruti, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruit, Badalona, Spain
- CIBERINFEC. ISCIII, Madrid, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine. University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain
- Fundaciò Lluita contra les infeccions. Hospital Germans Trias i Pujol, Badalona, Catalonia, Spain
- Universitat Autonoma de Barcelona. Bellaterra, Cerdanyola del Vallès, Catalonia, Spain
| | - Joaquim Segalés
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Catalonia, Spain.
- Universitat Autonoma de Barcelona. Bellaterra, Cerdanyola del Vallès, Catalonia, Spain.
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, Bellaterra, Cerdanyola del Vallès, Spain.
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Campus Can Ruti, Badalona, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruit, Badalona, Spain.
- CIBERINFEC. ISCIII, Madrid, Spain.
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Inchauste L, Nurtop E, Brisbarre N, Ninove L, Gallian P, de Lamballerie X, Priet S. Exploring cell-free assays for COVID-19 serosurvey. Sci Rep 2024; 14:6096. [PMID: 38480769 PMCID: PMC10938000 DOI: 10.1038/s41598-024-55852-6] [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: 02/14/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Serosurveys to monitor immunity toward COVID-19 in the population are primarily performed using an ELISA to screen samples for SARS-CoV-2 antibodies, followed by confirmation by a virus neutralization test, which is considered the Gold Standard. However, virus neutralization test may not be feasible for some laboratories because of the requirement for specific facilities and trained personnel. In an attempt to address this limitation, we evaluated three cell-free methods as potential alternatives for assessing SARS-CoV-2 seroprevalence in human population from plasma. We report the establishment of two inhibition ELISAs designed to detect anti-Spike RBD IgG antibodies and a microsphere quantitative suspension array technology assay, based on the Luminex xMAP platform, to measure the presence of antibodies against various SARS-CoV-2 antigens, including anti-RBD. These methods were also compared to a commercial chemiluminescent immunoassay designed for anti-RBD antibodies detection and to the combined ELISA + virus neutralization test strategy. These cell-free assays performed equally to estimate the percentage of positive and negative samples and could be used to determine the prevalence of SARS-CoV-2 antibodies in human population, at least in cohort with high-expected prevalence, without the use of seroneutralization assay.
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Affiliation(s)
- Lucia Inchauste
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Elif Nurtop
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Nadège Brisbarre
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Établissement Français du Sang Provence Alpes Côte d'Azur et Corse, Marseille, France
| | - Laetitia Ninove
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Pierre Gallian
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Établissement Français du Sang, La Plaine Saint-Denis, Saint-Denis, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Stéphane Priet
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France.
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape. J Chem Inf Model 2024; 64:1657-1681. [PMID: 38373700 DOI: 10.1021/acs.jcim.3c01857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
The latest wave of SARS-CoV-2 Omicron variants displayed a growth advantage and increased viral fitness through convergent evolution of functional hotspots that work synchronously to balance fitness requirements for productive receptor binding and efficient immune evasion. In this study, we combined AlphaFold2-based structural modeling approaches with atomistic simulations and mutational profiling of binding energetics and stability for prediction and comprehensive analysis of the structure, dynamics, and binding of the SARS-CoV-2 Omicron BA.2.86 spike variant with ACE2 host receptor and distinct classes of antibodies. We adapted several AlphaFold2 approaches to predict both the structure and conformational ensembles of the Omicron BA.2.86 spike protein in the complex with the host receptor. The results showed that the AlphaFold2-predicted structural ensemble of the BA.2.86 spike protein complex with ACE2 can accurately capture the main conformational states of the Omicron variant. Complementary to AlphaFold2 structural predictions, microsecond molecular dynamics simulations reveal the details of the conformational landscape and produced equilibrium ensembles of the BA.2.86 structures that are used to perform mutational scanning of spike residues and characterize structural stability and binding energy hotspots. The ensemble-based mutational profiling of the receptor binding domain residues in the BA.2 and BA.2.86 spike complexes with ACE2 revealed a group of conserved hydrophobic hotspots and critical variant-specific contributions of the BA.2.86 convergent mutational hotspots R403K, F486P, and R493Q. To examine the immune evasion properties of BA.2.86 in atomistic detail, we performed structure-based mutational profiling of the spike protein binding interfaces with distinct classes of antibodies that displayed significantly reduced neutralization against the BA.2.86 variant. The results revealed the molecular basis of compensatory functional effects of the binding hotspots, showing that BA.2.86 lineage may have evolved to outcompete other Omicron subvariants by improving immune evasion while preserving binding affinity with ACE2 via through a compensatory effect of R493Q and F486P convergent mutational hotspots. This study demonstrated that an integrative approach combining AlphaFold2 predictions with complementary atomistic molecular dynamics simulations and robust ensemble-based mutational profiling of spike residues can enable accurate and comprehensive characterization of structure, dynamics, and binding mechanisms of newly emerging Omicron variants.
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Affiliation(s)
- Nishank Raisinghani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States of America
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States of America
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States of America
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Kumar S, Dasgupta S, Sajadi MM, Snyder GA, DeVico AL, Ray K. Discordant Antigenic Properties of Soluble and Virion SARS-CoV-2 Spike Proteins. Viruses 2024; 16:407. [PMID: 38543772 PMCID: PMC10974403 DOI: 10.3390/v16030407] [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: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 04/01/2024] Open
Abstract
Efforts to develop vaccine and immunotherapeutic countermeasures against the COVID-19 pandemic focus on targeting the trimeric spike (S) proteins of SARS-CoV-2. Vaccines and therapeutic design strategies must impart the characteristics of virion S from historical and emerging variants onto practical constructs such as soluble, stabilized trimers. The virus spike is a heterotrimer of two subunits: S1, which includes the receptor binding domain (RBD) that binds the cell surface receptor ACE2, and S2, which mediates membrane fusion. Previous studies suggest that the antigenic, structural, and functional characteristics of virion S may differ from current soluble surrogates. For example, it was reported that certain anti-glycan, HIV-1 neutralizing monoclonal antibodies bind soluble SARS-CoV-2 S but do not neutralize SARS-CoV-2 virions. In this study, we used single-molecule fluorescence correlation spectroscopy (FCS) under physiologically relevant conditions to examine the reactivity of broadly neutralizing and non-neutralizing anti-S human monoclonal antibodies (mAbs) isolated in 2020. Binding efficiency was assessed by FCS with soluble S trimers, pseudoviruses and inactivated wild-type virions representing variants emerging from 2020 to date. Anti-glycan mAbs were tested and compared. We find that both anti-S specific and anti-glycan mAbs exhibit variable but efficient binding to a range of stabilized, soluble trimers. Across mAbs, the efficiencies of soluble S binding were positively correlated with reactivity against inactivated virions but not pseudoviruses. Binding efficiencies with pseudoviruses were generally lower than with soluble S or inactivated virions. Among neutralizing mAbs, potency did not correlate with binding efficiencies on any target. No neutralizing activity was detected with anti-glycan antibodies. Notably, the virion S released from membranes by detergent treatment gained more efficient reactivity with anti-glycan, HIV-neutralizing antibodies but lost reactivity with all anti-S mAbs. Collectively, the FCS binding data suggest that virion surfaces present appreciable amounts of both functional and nonfunctional trimers, with neutralizing anti-S favoring the former structures and non-neutralizing anti-glycan mAbs binding the latter. S released from solubilized virions represents a nonfunctional structure bound by anti-glycan mAbs, while engineered soluble trimers present a composite structure that is broadly reactive with both mAb types. The detection of disparate antigenicity and immunoreactivity profiles in engineered and virion-associated S highlight the value of single-virus analyses in designing future antiviral strategies against SARS-CoV-2.
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Affiliation(s)
- Sameer Kumar
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Souradip Dasgupta
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Mohammad M. Sajadi
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Division of Clinical Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Greg A. Snyder
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Anthony L. DeVico
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
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59
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Reiter L, Greffrath J, Zidel B, Ostrowski M, Gommerman J, Madhi SA, Tran R, Martin-Orozco N, Panicker RKG, Cooper C, Pastrak A. Comparable safety and non-inferior immunogenicity of the SARS-CoV-2 mRNA vaccine candidate PTX-COVID19-B and BNT162b2 in a phase 2 randomized, observer-blinded study. Sci Rep 2024; 14:5365. [PMID: 38438427 PMCID: PMC10912344 DOI: 10.1038/s41598-024-55320-1] [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: 12/20/2023] [Accepted: 02/22/2024] [Indexed: 03/06/2024] Open
Abstract
In the aftermath of the COVID-19 pandemic, the evolution of the SARS-CoV-2 into a seasonal pathogen along with the emergence of new variants, underscores the need for dynamic and adaptable responses, emphasizing the importance of sustained vaccination strategies. This observer-blind, double-dummy, randomized immunobridging phase 2 study (NCT05175742) aimed to compare the immunogenicity induced by two doses of 40 μg PTX-COVID19-B vaccine candidate administered 28 days apart, with the response induced by two doses of 30 µg Pfizer-BioNTech COVID-19 vaccine (BNT162b2), administered 21 days apart, in Nucleocapsid-protein seronegative adults 18-64 years of age. Both vaccines were administrated via intramuscular injection in the deltoid muscle. Two weeks after the second dose, the neutralizing antibody (NAb) geometric mean titer ratio and seroconversion rate met the non-inferiority criteria, successfully achieving the primary immunogenicity endpoints of the study. PTX-COVID19-B demonstrated similar safety and tolerability profile to BNT162b2 vaccine. The lowest NAb response was observed in subjects with low-to-undetectable NAb at baseline or no reported breakthrough infection. Conversely, participants who experienced breakthrough infections during the study exhibited higher NAb titers. This study also shows induction of cell-mediated immune (CMI) responses by PTX-COVID19-B. In conclusion, the vaccine candidate PTX-COVID19-B demonstrated favourable safety profile along with immunogenicity similar to the active comparator BNT162b2 vaccine.
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Affiliation(s)
- Lawrence Reiter
- Providence Therapeutics Holdings Inc., 120-8832 Blackfoot Trail SE, Calgary, AB, T2J 3J1, Canada
| | - Johann Greffrath
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bian Zidel
- Malton Medical Center, 6870 Goreway Dr., Mississauga, ON, L4V 1P1, Canada
| | - Mario Ostrowski
- Department of Medicine, Immunology, University of Toronto, Medical Sciences Building, Rm 6271. 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Jennifer Gommerman
- Department of Immunology, Temerty Faculty of Medicine, 1 King's College Circle, Rm. 7233, Toronto, ON, M5S 1A8, Canada
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard Tran
- Providence Therapeutics Holdings Inc., 120-8832 Blackfoot Trail SE, Calgary, AB, T2J 3J1, Canada
| | - Natalia Martin-Orozco
- Providence Therapeutics Holdings Inc., 120-8832 Blackfoot Trail SE, Calgary, AB, T2J 3J1, Canada
| | | | - Curtis Cooper
- The Ottawa Hospital Viral Hepatitis Program, Division of Infectious Diseases, Department of Medicine, The Ottawa Hospital, University of Ottawa, 75 Laurier Ave. East, Ottawa, ON, K1N 6N5, Canada
| | - Aleksandra Pastrak
- Providence Therapeutics Holdings Inc., 120-8832 Blackfoot Trail SE, Calgary, AB, T2J 3J1, Canada.
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60
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Polo-Megías D, Cano-Muñoz M, Berruezo AG, Laumond G, Moog C, Conejero-Lara F. Investigating vulnerability of the conserved SARS-CoV-2 spike's heptad repeat 2 as target for fusion inhibitors using chimeric miniproteins. Int J Biol Macromol 2024; 262:130132. [PMID: 38354919 DOI: 10.1016/j.ijbiomac.2024.130132] [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: 01/01/2024] [Revised: 02/09/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Inhibition of SARS-CoV-2 membrane fusion is a highly desired target to combat COVID-19. The interaction between the spike's heptad repeat (HR) regions 1 (HR1) and 2 (HR2) is a crucial step during the fusion process and these highly conserved HR regions constitute attractive targets for fusion inhibitors. However, the relative importance of each subregion of the long HR1-HR2 interface for viral inhibition remains unclear. Here, we designed, produced, and characterized a series of chimeric miniproteins that mimic two different half subdomains of HR1. The proteins were designed as single polypeptide chains that spontaneously fold into antiparallel trimeric helical bundles aimed at structurally imitate the molecular surface of each HR1 half subregion. All the miniproteins folded stably as helical structures and could bind complementary HR2 peptides with moderate affinity. However, only the miniproteins mimicking the N-terminal HR1 half subdomain, but not those imitating C-terminal one, could inhibit cell infection by SARS-COV-2 real viruses in cell cultures. Most interestingly, the inhibitory activity of the miniproteins correlated with their structural stability, but not with their relative binding affinity for HR2 peptides. These results are highly relevant for designing more focused and active fusion inhibitors targeting the highly conserved HR2 region of the Spike.
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Affiliation(s)
- Daniel Polo-Megías
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Mario Cano-Muñoz
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Alberto G Berruezo
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Géraldine Laumond
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, F-67000 Strasbourg, France
| | - Christiane Moog
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, F-67000 Strasbourg, France; Vaccine Research Institute (VRI), F-94000 Créteil, France
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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61
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Winiger RR, Perez L. Therapeutic antibodies and alternative formats against SARS-CoV-2. Antiviral Res 2024; 223:105820. [PMID: 38307147 DOI: 10.1016/j.antiviral.2024.105820] [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: 10/30/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
The COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) heavily burdened the entire world. Despite a prompt generation of vaccines and therapeutics to confront infection, the virus remains a threat. The ancestor viral strain has evolved into several variants of concern, with the Omicron variant now having many distinct sublineages. Consequently, most available antibodies targeting the spike went obsolete and thus new therapies or therapeutic formats are needed. In this review we focus on antibody targets, provide an overview of the therapeutic progress made so far, describe novel formats being explored, and lessons learned from therapeutic antibodies that can enhance pandemic preparedness.
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Affiliation(s)
- Rahel R Winiger
- University of Lausanne (UNIL), Lausanne University Hospital (CHUV), Service of Immunology and Allergy, and Center for Human Immunology Lausanne (CHIL), Switzerland.
| | - Laurent Perez
- University of Lausanne (UNIL), Lausanne University Hospital (CHUV), Service of Immunology and Allergy, and Center for Human Immunology Lausanne (CHIL), Switzerland.
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62
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Yao Z, Zhang L, Duan Y, Tang X, Lu J. Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein. J Infect 2024; 88:106121. [PMID: 38367704 DOI: 10.1016/j.jinf.2024.106121] [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: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/19/2024]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has substantially damaged the global economy and human health. The spike (S) protein of coronaviruses plays a pivotal role in viral entry by binding to host cell receptors. Additionally, it acts as the primary target for neutralizing antibodies in those infected and is the central focus for currently utilized or researched vaccines. During the virus's adaptation to the human host, the S protein of SARS-CoV-2 has undergone significant evolution. As the COVID-19 pandemic has unfolded, new mutations have arisen and vanished, giving rise to distinctive amino acid profiles within variant of concern strains of SARS-CoV-2. Notably, many of these changes in the S protein have been positively selected, leading to substantial alterations in viral characteristics, such as heightened transmissibility and immune evasion capabilities. This review aims to provide an overview of our current understanding of the structural implications associated with key amino acid changes in the S protein of SARS-CoV-2. These research findings shed light on the intricate and dynamic nature of viral evolution, underscoring the importance of continuous monitoring and analysis of viral genomes. Through these molecular-level investigations, we can attain deeper insights into the virus's adaptive evolution, offering valuable guidance for designing vaccines and developing antiviral drugs to combat the ever-evolving viral threats.
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Affiliation(s)
- Zhuocheng Yao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lin Zhang
- College of Fishery, Ocean University of China, Qingdao 266003, China
| | - Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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63
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Katte RH, Ao Y, Xu W, Han Y, Zhong G, Ghimire D, Florence J, Tucker TA, Lu M. Differentiating Cell Entry Potentials of SARS-CoV-2 Omicron Subvariants on Human Lung Epithelium Cells. Viruses 2024; 16:391. [PMID: 38543757 PMCID: PMC10975267 DOI: 10.3390/v16030391] [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: 01/11/2024] [Revised: 02/25/2024] [Accepted: 02/28/2024] [Indexed: 04/01/2024] Open
Abstract
The surface spike (S) glycoprotein mediates cell entry of SARS-CoV-2 into the host through fusion at the plasma membrane or endocytosis. Omicron lineages/sublineages have acquired extensive mutations in S to gain transmissibility advantages and altered antigenicity. The fusogenicity, antigenicity, and evasion of Omicron subvariants have been extensively investigated at unprecedented speed to align with the mutation rate of S. Cells that overexpress receptors/cofactors are mostly used as hosts to amplify infection sensitivity to tested variants. However, systematic cell entry comparisons of most prior dominant Omicron subvariants using human lung epithelium cells are yet to be well-studied. Here, with human bronchial epithelium BEAS-2B cells as the host, we compared single-round virus-to-cell entry and cell-to-cell fusion of Omicron BA.1, BA.5, BQ.1.1, CH.1.1, XBB.1.5, and XBB.1.16 based upon split NanoLuc fusion readout assays and the S-pseudotyped lentivirus system. Virus-to-cell entry of tested S variants exhibited cell-type dependence. The parental Omicron BA.1 required more time to develop full entry to HEK293T-ACE2-TMPRSS2 than BEAS-2B cells. Compared to unchanged P681, S-cleavage constructs of P681H/R did not have any noticeable advantages in cell entry. Omicron BA.1 and its descendants entered BEAS-2B cells more efficiently than D614G, and it was slightly less or comparable to that of Delta. Serine protease-pretreated Omicron subvariants enhanced virus-to-cell entry in a dose-dependent manner, suggesting fusion at the plasma membrane persists as a productive cell entry route. Spike-mediated cell-to-cell fusion and total S1/S2 processing of Omicron descendants were similar. Our results indicate no obvious entry or fusion advantages of recent Omicron descendants over preceding variants since Delta, thus supporting immune evasion conferred by antigenicity shifts due to altered S sequences as probably the primary viral fitness driver.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Maolin Lu
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA; (R.H.K.); (Y.H.); (T.A.T.)
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64
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Chan CWF, Wang B, Nan L, Huang X, Mao T, Chu HY, Luo C, Chu H, Choi GCG, Shum HC, Wong ASL. High-throughput screening of genetic and cellular drivers of syncytium formation induced by the spike protein of SARS-CoV-2. Nat Biomed Eng 2024; 8:291-309. [PMID: 37996617 DOI: 10.1038/s41551-023-01140-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 10/18/2023] [Indexed: 11/25/2023]
Abstract
Mapping mutations and discovering cellular determinants that cause the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to induce infected cells to form syncytia would facilitate the development of strategies for blocking the formation of such cell-cell fusion. Here we describe high-throughput screening methods based on droplet microfluidics and the size-exclusion selection of syncytia, coupled with large-scale mutagenesis and genome-wide knockout screening via clustered regularly interspaced short palindromic repeats (CRISPR), for the large-scale identification of determinants of cell-cell fusion. We used the methods to perform deep mutational scans in spike-presenting cells to pinpoint mutable syncytium-enhancing substitutions in two regions of the spike protein (the fusion peptide proximal region and the furin-cleavage site). We also used a genome-wide CRISPR screen in cells expressing the receptor angiotensin-converting enzyme 2 to identify inhibitors of clathrin-mediated endocytosis that impede syncytium formation, which we validated in hamsters infected with SARS-CoV-2. Finding genetic and cellular determinants of the formation of syncytia may reveal insights into the physiological and pathological consequences of cell-cell fusion.
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Affiliation(s)
- Charles W F Chan
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Bei Wang
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Lang Nan
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Xiner Huang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tianjiao Mao
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Hoi Yee Chu
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Cuiting Luo
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People's Republic of China.
| | - Gigi C G Choi
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
| | - Alan S L Wong
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
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65
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Pasala C, Sharma S, Roychowdhury T, Moroni E, Colombo G, Chiosis G. N-Glycosylation as a Modulator of Protein Conformation and Assembly in Disease. Biomolecules 2024; 14:282. [PMID: 38540703 PMCID: PMC10968129 DOI: 10.3390/biom14030282] [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: 01/29/2024] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 05/01/2024] Open
Abstract
Glycosylation, a prevalent post-translational modification, plays a pivotal role in regulating intricate cellular processes by covalently attaching glycans to macromolecules. Dysregulated glycosylation is linked to a spectrum of diseases, encompassing cancer, neurodegenerative disorders, congenital disorders, infections, and inflammation. This review delves into the intricate interplay between glycosylation and protein conformation, with a specific focus on the profound impact of N-glycans on the selection of distinct protein conformations characterized by distinct interactomes-namely, protein assemblies-under normal and pathological conditions across various diseases. We begin by examining the spike protein of the SARS virus, illustrating how N-glycans regulate the infectivity of pathogenic agents. Subsequently, we utilize the prion protein and the chaperone glucose-regulated protein 94 as examples, exploring instances where N-glycosylation transforms physiological protein structures into disease-associated forms. Unraveling these connections provides valuable insights into potential therapeutic avenues and a deeper comprehension of the molecular intricacies that underlie disease conditions. This exploration of glycosylation's influence on protein conformation effectively bridges the gap between the glycome and disease, offering a comprehensive perspective on the therapeutic implications of targeting conformational mutants and their pathologic assemblies in various diseases. The goal is to unravel the nuances of these post-translational modifications, shedding light on how they contribute to the intricate interplay between protein conformation, assembly, and disease.
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Affiliation(s)
- Chiranjeevi Pasala
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (C.P.); (S.S.); (T.R.)
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (C.P.); (S.S.); (T.R.)
| | - Tanaya Roychowdhury
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (C.P.); (S.S.); (T.R.)
| | - Elisabetta Moroni
- The Institute of Chemical Sciences and Technologies (SCITEC), Italian National Research Council (CNR), 20131 Milano, Italy; (E.M.); (G.C.)
| | - Giorgio Colombo
- The Institute of Chemical Sciences and Technologies (SCITEC), Italian National Research Council (CNR), 20131 Milano, Italy; (E.M.); (G.C.)
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (C.P.); (S.S.); (T.R.)
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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66
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Gentile D, Chiummiento L, Santarsiere A, Funicello M, Lupattelli P, Rescifina A, Venuti A, Piperno A, Sciortino MT, Pennisi R. Targeting Viral and Cellular Cysteine Proteases for Treatment of New Variants of SARS-CoV-2. Viruses 2024; 16:338. [PMID: 38543704 PMCID: PMC10976049 DOI: 10.3390/v16030338] [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: 12/19/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 04/21/2024] Open
Abstract
The continuous emergence of SARS-CoV-2 variants caused the persistence of the COVID-19 epidemic and challenged the effectiveness of the existing vaccines. The viral proteases are the most attractive targets for developing antiviral drugs. In this scenario, our study explores the use of HIV-1 protease inhibitors against SARS-CoV-2. An in silico screening of a library of HIV-1 proteases identified four anti-HIV compounds able to interact with the 3CLpro of SARS-CoV-2. Thus, in vitro studies were designed to evaluate their potential antiviral effectiveness against SARS-CoV-2. We employed pseudovirus technology to simulate, in a highly safe manner, the adsorption of the alpha (α-SARS-CoV-2) and omicron (ο-SARS-CoV-2) variants of SARS-CoV-2 and study the inhibitory mechanism of the selected compounds for cell-virus interaction. The results reported a mild activity against the viral proteases 3CLpro and PLpro, but efficient inhibitory effects on the internalization of both variants mediated by cathepsin B/L. Our findings provide insights into the feasibility of using drugs exhibiting antiviral effects for other viruses against the viral and host SARS-CoV-2 proteases required for entry.
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Affiliation(s)
- Davide Gentile
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy
| | - Lucia Chiummiento
- Department of Scienze, University of Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Alessandro Santarsiere
- Department of Scienze, University of Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Maria Funicello
- Department of Scienze, University of Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Paolo Lupattelli
- Department of Chimica, Sapienza University of Roma, p. le Aldo Moro 5, 00185 Roma, Italy
| | - Antonio Rescifina
- Department of Drug and Health Sciences, University of Catania, V. le A. Doria, 95125 Catania, Italy
| | - Assunta Venuti
- International Agency for Research on Cancer (IARC), World Health Organization, 69366 LYON CEDEX 07, France
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Maria Teresa Sciortino
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Rosamaria Pennisi
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
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Dulin H, Barre RS, Xu D, Neal A, Vizcarra E, Chavez J, Ulu A, Yang MS, Khan SR, Wuang K, Bhakta N, Chea C, Wilson EH, Martinez-Sobrido L, Hai R. Harnessing preexisting influenza virus-specific immunity increases antibody responses against SARS-CoV-2. J Virol 2024; 98:e0157123. [PMID: 38206036 PMCID: PMC10878257 DOI: 10.1128/jvi.01571-23] [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: 10/09/2023] [Accepted: 11/13/2023] [Indexed: 01/12/2024] Open
Abstract
In pandemic scenarios involving novel human pathogenic viruses, it is highly desirable that vaccines induce strong neutralizing antibodies as quickly as possible. However, current vaccine strategies require multiple immunization doses to produce high titers of neutralizing antibodies and are poorly protective after a single vaccination. We therefore wished to design a vaccine candidate that would induce increased protective immune responses following the first vaccine dose. We hypothesized that antibodies against the receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein could be increased by drawing upon immunity to a previous infection. We generated a fusion protein containing the influenza H1N1 PR8 virus nucleoprotein (NP) and the SARS-CoV-2 spike RBD. Mice with or without preexisting immunity to PR8 were then vaccinated with NP/RBD. We observed significantly increased SARS-CoV-2 neutralizing antibodies in mice with PR8 immunity compared to mice without preexisting PR8 immunity. Vaccination with NP/RBD protected mice from SARS-CoV-2-induced morbidity and mortality after a single dose. Additionally, we compared SARS-CoV-2 virus titers in the lungs and nasal turbinates 4 days post-challenge of mice vaccinated with NP/RBD. SARS-CoV-2 virus was detectable in the lungs and nasal turbinate of mice without preexisting PR8 immunity, while SARS-CoV-2 virus was completely undetectable in mice with preexisting PR8 immunity. We also found that CD4-positive T cells in mice with preexisting immunity to PR8 play an essential role in producing the increased antibody response against RBD. This vaccine strategy potentially can be modified to target other pathogens of concern and offers extra value in future pandemic scenarios.IMPORTANCEIncreased globalization and changes in human interactions with wild animals has increased the likelihood of the emergence of novel viruses with pandemic potential. Vaccines can be effective in preventing severe disease caused by pandemic viruses. However, it takes time to develop protective immunity via prime-boost vaccination. More effective vaccine designs should quickly induce protective immunity. We propose leveraging preexisting immunity to a different pathogen to boost protection against emerging viruses. We targeted SARS-CoV-2 as a representative pandemic virus and generated a fusion protein vaccine that combines the nucleoprotein from influenza A virus and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Our vaccine design significantly increased the production of RBD-specific antibodies in mice that had previously been exposed to influenza virus, compared to those without previous exposure. This enhanced immunity reduced SARS-CoV-2 replication in mice. Our results offer a vaccine design that could be valuable in a future pandemic setting.
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Affiliation(s)
- Harrison Dulin
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
- Cell, Molecular, and Developmental Biology Graduate Program, University of California, Riverside, California, USA
| | - Ramya S. Barre
- Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Duo Xu
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
| | - Arrmund Neal
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
| | - Edward Vizcarra
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California, USA
| | - Jerald Chavez
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
| | - Arzu Ulu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California, USA
| | - Myeon-Sik Yang
- Texas Biomedical Research Institute, San Antonio, Texas, USA
| | | | - Keidy Wuang
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
| | - Nikhil Bhakta
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
| | - Chanvoraboth Chea
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
| | - Emma H. Wilson
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California, USA
| | | | - Rong Hai
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
- Cell, Molecular, and Developmental Biology Graduate Program, University of California, Riverside, California, USA
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68
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Gonzalez KJ, Huang J, Criado MF, Banerjee A, Tompkins SM, Mousa JJ, Strauch EM. A general computational design strategy for stabilizing viral class I fusion proteins. Nat Commun 2024; 15:1335. [PMID: 38351001 PMCID: PMC10864359 DOI: 10.1038/s41467-024-45480-z] [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: 04/04/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
Many pathogenic viruses rely on class I fusion proteins to fuse their viral membrane with the host cell membrane. To drive the fusion process, class I fusion proteins undergo an irreversible conformational change from a metastable prefusion state to an energetically more stable postfusion state. Mounting evidence underscores that antibodies targeting the prefusion conformation are the most potent, making it a compelling vaccine candidate. Here, we establish a computational design protocol that stabilizes the prefusion state while destabilizing the postfusion conformation. With this protocol, we stabilize the fusion proteins of the RSV, hMPV, and SARS-CoV-2 viruses, testing fewer than a handful of designs. The solved structures of these designed proteins from all three viruses evidence the atomic accuracy of our approach. Furthermore, the humoral response of the redesigned RSV F protein compares to that of the recently approved vaccine in a mouse model. While the parallel design of two conformations allows the identification of energetically sub-optimal positions for one conformation, our protocol also reveals diverse molecular strategies for stabilization. Given the clinical significance of viruses using class I fusion proteins, our algorithm can substantially contribute to vaccine development by reducing the time and resources needed to optimize these immunogens.
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Affiliation(s)
- Karen J Gonzalez
- Institute of Bioinformatics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Jiachen Huang
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Miria F Criado
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, 36849, USA
| | - Avik Banerjee
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Stephen M Tompkins
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Jarrod J Mousa
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Eva-Maria Strauch
- Institute of Bioinformatics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, 30602, USA.
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, 30602, USA.
- Department of Medicine, School of Medicine, Washington University, St. Louis, MO, 63110, USA.
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Carten JD, Khelashvili G, Bidon MK, Straus MR, Tang T, Jaimes JA, Whittaker GR, Weinstein H, Daniel S. A Mechanistic Understanding of the Modes of Ca 2+ Ion Binding to the SARS-CoV-1 Fusion Peptide and Their Role in the Dynamics of Host Membrane Penetration. ACS Infect Dis 2024; 10:398-411. [PMID: 38270149 DOI: 10.1021/acsinfecdis.3c00260] [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] [Indexed: 01/26/2024]
Abstract
The SARS-CoV-1 spike glycoprotein contains a fusion peptide (FP) segment that mediates the fusion of the viral and host cell membranes. Calcium ions are thought to position the FP optimally for membrane insertion by interacting with negatively charged residues in this segment (E801, D802, D812, E821, D825, and D830); however, which residues bind to calcium and in what combinations supportive of membrane insertion are unknown. Using biological assays and molecular dynamics studies, we have determined the functional configurations of FP-Ca2+ binding that likely promote membrane insertion. We first individually mutated the negatively charged residues in the SARS CoV-1 FP to assay their roles in cell entry and syncytia formation, finding that charge loss in the D802A or D830A mutants greatly reduced syncytia formation and pseudoparticle transduction of VeroE6 cells. Interestingly, one mutation (D812A) led to a modest increase in cell transduction, further indicating that FP function likely depends on calcium binding at specific residues and in specific combinations. To interpret these results mechanistically and identify specific modes of FP-Ca2+ binding that modulate membrane insertion, we performed molecular dynamics simulations of the SARS-CoV-1 FP and Ca2+ions. The preferred residue pairs for Ca2+ binding we identified (E801/D802, E801/D830, and D812/E821) include the two residues found to be essential for S function in our biological studies (D802 and D830). The three preferred Ca2+ binding pairs were also predicted to promote FP membrane insertion. We also identified a Ca2+ binding pair (E821/D825) predicted to inhibit FP membrane insertion. We then carried out simulations in the presence of membranes and found that binding of Ca2+ to SARS-CoV-1 FP residue pairs E801/D802 and D812/E821 facilitates membrane insertion by enabling the peptide to adopt conformations that shield the negative charges of the FP to reduce repulsion by the membrane phospholipid headgroups. This calcium binding mode also optimally positions the hydrophobic LLF region of the FP for membrane penetration. Conversely, Ca2+ binding to the FP E801/D802 and D821/D825 pairs eliminates the negative charge screening and instead creates a repulsive negative charge that hinders membrane penetration of the LLF motif. These computational results, taken together with our biological studies, provide an improved and nuanced mechanistic understanding of the dymanics of SARS-CoV-1 calcium binding and their potential effects on host cell entry.
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Affiliation(s)
- Juliana Debrito Carten
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - George Khelashvili
- Department of Physiology & Biophysics, Weill Cornell Medicine, New York, New York 10065, United States
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10065, United States
| | - Miya K Bidon
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Marco R Straus
- Departments of Microbiology & Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Javier A Jaimes
- Departments of Microbiology & Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Gary R Whittaker
- Departments of Microbiology & Immunology, Cornell University, Ithaca, New York 14853, United States
- Public & Ecosystem Health, Cornell University, Ithaca, New York 14853, United States
| | - Harel Weinstein
- Department of Physiology & Biophysics, Weill Cornell Medicine, New York, New York 10065, United States
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10065, United States
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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Suzuki S, Kuroda M, Aoki K, Kawaji K, Hiramatsu Y, Sasano M, Nishiyama A, Murayama K, Kodama EN, Oishi S, Hayashi H. Helix-based screening with structure prediction using artificial intelligence has potential for the rapid development of peptide inhibitors targeting class I viral fusion. RSC Chem Biol 2024; 5:131-140. [PMID: 38333196 PMCID: PMC10849125 DOI: 10.1039/d3cb00166k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/04/2023] [Indexed: 02/10/2024] Open
Abstract
The rapid development of drugs against emerging and re-emerging viruses is required to prevent future pandemics. However, inhibitors usually take a long time to optimize. Here, to improve the optimization step, we used two heptad repeats (HR) in the spike protein (S protein) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a model and established a screening system for peptide-based inhibitors containing an α-helix region (SPICA). SPICA can be used to identify critical amino acid regions and evaluate the inhibitory effects of peptides as decoys. We further employed an artificial intelligence structure-prediction system (AlphaFold2) for the rapid analysis of structure-activity relationships. Here, we identified that critical amino acid regions, DVDLGD (amino acids 1163-1168 in the S protein), IQKEIDRLNE (1179-1188), and NLNESLIDL (1192-1200), played a pivotal role in SARS-CoV-2 fusion. Peptides containing these critical amino acid regions efficiently blocked viral replication. We also demonstrated that AlphaFold2 could successfully predict structures similar to the reported crystal and cryo-electron microscopy structures of the post-fusion form of the SARS-CoV-2 S protein. Notably, the predicted structures of the HR1 region and the peptide-based fusion inhibitors corresponded well with the antiviral effects of each fusion inhibitor. Thus, the combination of SPICA and AlphaFold2 is a powerful tool to design viral fusion inhibitors using only the amino-acid sequence of the fusion protein.
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Affiliation(s)
- Satoshi Suzuki
- Department of Infectious Diseases, Tohoku University Graduate School of Medicine 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Mio Kuroda
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University 1, Misasagi-Shichono-cho, Yamashina-ku Kyoto 607-8412 Japan
| | - Keisuke Aoki
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University 1, Misasagi-Shichono-cho, Yamashina-ku Kyoto 607-8412 Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku Kyoto 606-8501 Japan
| | - Kumi Kawaji
- Division of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Yoshiki Hiramatsu
- Department of Infectious Diseases, Tohoku University Graduate School of Medicine 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Mina Sasano
- Division of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Akie Nishiyama
- Department of Infectious Diseases, Tohoku University Graduate School of Medicine 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Kazutaka Murayama
- Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Eiichi N Kodama
- Department of Infectious Diseases, Tohoku University Graduate School of Medicine 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
- Division of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
- Department of Infectious Disease, Graduate School of Medicine and Tohoku Medical Megabank Organization, Tohoku University 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Shinya Oishi
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University 1, Misasagi-Shichono-cho, Yamashina-ku Kyoto 607-8412 Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku Kyoto 606-8501 Japan
| | - Hironori Hayashi
- Division of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
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71
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Zhang L, Kempf A, Nehlmeier I, Cossmann A, Richter A, Bdeir N, Graichen L, Moldenhauer AS, Dopfer-Jablonka A, Stankov MV, Simon-Loriere E, Schulz SR, Jäck HM, Čičin-Šain L, Behrens GMN, Drosten C, Hoffmann M, Pöhlmann S. SARS-CoV-2 BA.2.86 enters lung cells and evades neutralizing antibodies with high efficiency. Cell 2024; 187:596-608.e17. [PMID: 38194966 PMCID: PMC11317634 DOI: 10.1016/j.cell.2023.12.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/03/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
BA.2.86, a recently identified descendant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 sublineage, contains ∼35 mutations in the spike (S) protein and spreads in multiple countries. Here, we investigated whether the virus exhibits altered biological traits, focusing on S protein-driven viral entry. Employing pseudotyped particles, we show that BA.2.86, unlike other Omicron sublineages, enters Calu-3 lung cells with high efficiency and in a serine- but not cysteine-protease-dependent manner. Robust lung cell infection was confirmed with authentic BA.2.86, but the virus exhibited low specific infectivity. Further, BA.2.86 was highly resistant against all therapeutic antibodies tested, efficiently evading neutralization by antibodies induced by non-adapted vaccines. In contrast, BA.2.86 and the currently circulating EG.5.1 sublineage were appreciably neutralized by antibodies induced by the XBB.1.5-adapted vaccine. Collectively, BA.2.86 has regained a trait characteristic of early SARS-CoV-2 lineages, robust lung cell entry, and evades neutralizing antibodies. However, BA.2.86 exhibits low specific infectivity, which might limit transmissibility.
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Affiliation(s)
- Lu Zhang
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany
| | - Anne Cossmann
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Anja Richter
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Najat Bdeir
- Department of Viral Immunology, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | | | - Alexandra Dopfer-Jablonka
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany
| | - Metodi V Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Etienne Simon-Loriere
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, 75015 Paris, France; National Reference Center for Viruses of respiratory Infections, Institut Pasteur, 75015 Paris, France
| | - Sebastian R Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Zentrum für Infektionsforschung, 38124 Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany; Center for Individualized Infection Medicine, a joint venture of HZI and MHH, 30625 Hannover, Germany
| | - Georg M N Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 30625 Hannover, Germany; Center for Individualized Infection Medicine, a joint venture of HZI and MHH, 30625 Hannover, Germany
| | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany.
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany.
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72
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Lapuente D, Winkler TH, Tenbusch M. B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity. Cell Mol Immunol 2024; 21:144-158. [PMID: 37945737 PMCID: PMC10805925 DOI: 10.1038/s41423-023-01095-w] [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: 09/17/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 prompted scientific, medical, and biotech communities to investigate infection- and vaccine-induced immune responses in the context of this pathogen. B-cell and antibody responses are at the center of these investigations, as neutralizing antibodies (nAbs) are an important correlate of protection (COP) from infection and the primary target of SARS-CoV-2 vaccine modalities. In addition to absolute levels, nAb longevity, neutralization breadth, immunoglobulin isotype and subtype composition, and presence at mucosal sites have become important topics for scientists and health policy makers. The recent pandemic was and still is a unique setting in which to study de novo and memory B-cell (MBC) and antibody responses in the dynamic interplay of infection- and vaccine-induced immunity. It also provided an opportunity to explore new vaccine platforms, such as mRNA or adenoviral vector vaccines, in unprecedented cohort sizes. Combined with the technological advances of recent years, this situation has provided detailed mechanistic insights into the development of B-cell and antibody responses but also revealed some unexpected findings. In this review, we summarize the key findings of the last 2.5 years regarding infection- and vaccine-induced B-cell immunity, which we believe are of significant value not only in the context of SARS-CoV-2 but also for future vaccination approaches in endemic and pandemic settings.
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Affiliation(s)
- Dennis Lapuente
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
| | - Thomas H Winkler
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany.
| | - Matthias Tenbusch
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany
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Zan F, Zhou Y, Chen T, Chen Y, Mu Z, Qian Z, Ou X. Stabilization of the Metastable Pre-Fusion Conformation of the SARS-CoV-2 Spike Glycoprotein through N-Linked Glycosylation of the S2 Subunit. Viruses 2024; 16:223. [PMID: 38399999 PMCID: PMC10891965 DOI: 10.3390/v16020223] [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: 12/15/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus responsible for the coronavirus disease 2019 (COVID-19) pandemic, represents a serious threat to public health. The spike (S) glycoprotein of SARS-CoV-2 mediates viral entry into host cells and is heavily glycosylated. In this study, we systemically analyzed the roles of 22 putative N-linked glycans in SARS-CoV-2 S protein expression, membrane fusion, viral entry, and stability. Using the α-glycosidase inhibitors castanospermine and NB-DNJ, we confirmed that disruption of N-linked glycosylation blocked the maturation of the S protein, leading to the impairment of S protein-mediated membrane fusion. Single-amino-acid substitution of each of the 22 N-linked glycosylation sites with glutamine revealed that 9 out of the 22 N-linked glycosylation sites were critical for S protein folding and maturation. Thus, substitution at these sites resulted in reduced S protein-mediated cell-cell fusion and viral entry. Notably, the N1074Q mutation markedly affected S protein stability and induced significant receptor-independent syncytium (RIS) formation in HEK293T/hACE2-KO cells. Additionally, the removal of the furin cleavage site partially compensated for the instability induced by the N1074Q mutation. Although the corresponding mutation in the SARS-CoV S protein (N1056Q) did not induce RIS in HEK293T cells, the N669Q and N1080Q mutants exhibited increased fusogenic activity and did induce syncytium formation in HEK293T cells. Therefore, N-glycans on the SARS-CoV and SARS-CoV-2 S2 subunits are highly important for maintaining the pre-fusion state of the S protein. This study revealed the critical roles of N-glycans in S protein maturation and stability, information that has implications for the design of vaccines and antiviral strategies.
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Affiliation(s)
- Fuwen Zan
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Yao Zhou
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Ting Chen
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Yahan Chen
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Zhixia Mu
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
- State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Zhaohui Qian
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
- State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Xiuyuan Ou
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
- State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
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74
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Ketaren NE, Mast FD, Fridy PC, Olivier JP, Sanyal T, Sali A, Chait BT, Rout MP, Aitchison JD. Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.14.549041. [PMID: 37503298 PMCID: PMC10369967 DOI: 10.1101/2023.07.14.549041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
To date, all major modes of monoclonal antibody therapy targeting SARS-CoV-2 have lost significant efficacy against the latest circulating variants. As SARS-CoV-2 omicron sublineages account for over 90% of COVID-19 infections, evasion of immune responses generated by vaccination or exposure to previous variants poses a significant challenge. A compelling new therapeutic strategy against SARS-CoV-2 is that of single domain antibodies, termed nanobodies, which address certain limitations of monoclonal antibodies. Here we demonstrate that our high-affinity nanobody repertoire, generated against wild-type SARS-CoV-2 spike protein (Mast, Fridy et al. 2021), remains effective against variants of concern, including omicron BA.4/BA.5; a subset is predicted to counter resistance in emerging XBB and BQ.1.1 sublineages. Furthermore, we reveal the synergistic potential of nanobody cocktails in neutralizing emerging variants. Our study highlights the power of nanobody technology as a versatile therapeutic and diagnostic tool to combat rapidly evolving infectious diseases such as SARS-CoV-2.
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Affiliation(s)
- Natalia E. Ketaren
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Fred D. Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, USA
| | - Peter C. Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Jean Paul Olivier
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, USA
| | - Tanmoy Sanyal
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94143, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94143, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - John D. Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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75
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Bruch EM, Zhu S, Szymkowicz L, Blake T, Kiss T, James DA, Rak A, Narayan K, Balmer MT, Chicz RM. Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2. Sci Rep 2024; 14:2038. [PMID: 38263191 PMCID: PMC10805794 DOI: 10.1038/s41598-024-52499-1] [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: 09/11/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, uses a surface expressed trimeric spike glycoprotein for cell entry. This trimer is the primary target for neutralizing antibodies making it a key candidate for vaccine development. During the global pandemic circulating variants of concern (VOC) caused several waves of infection, severe disease, and death. The reduced efficacy of the ancestral trimer-based vaccines against emerging VOC led to the need for booster vaccines. Here we present a detailed characterization of the Sanofi Beta trimer, utilizing cryo-EM for structural elucidation. We investigate the conformational dynamics and stabilizing features using orthogonal SPR, SEC, nanoDSF, and HDX-MS techniques to better understand how this antigen elicits superior broad neutralizing antibodies as a variant booster vaccine. This structural analysis confirms the Beta trimer preference for canonical quaternary structure with two RBD in the up position and the reversible equilibrium between the canonical spike and open trimer conformations. Moreover, this report provides a better understanding of structural differences between spike antigens contributing to differential vaccine efficacy.
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76
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Xu K, Li J, Lu X, Ge X, Wang K, Wang J, Qiao Z, Quan Y, Li C. The Immunogenicity of CpG, MF59-like, and Alum Adjuvant Delta Strain Inactivated SARS-CoV-2 Vaccines in Mice. Vaccines (Basel) 2024; 12:60. [PMID: 38250873 PMCID: PMC10819607 DOI: 10.3390/vaccines12010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/23/2024] Open
Abstract
The continuous evolution and mutation of SARS-CoV-2 have highlighted the need for more effective vaccines. In this study, CpG, MF59-like, and Alum adjuvant Delta strain inactivated SARS-CoV-2 vaccines were prepared, and the immunogenicity of these vaccines in mice was evaluated. The Delta + MF59-like vaccine group produced the highest levels of S- and RBD-binding antibodies and live Delta virus neutralization levels after one shot of immunization, while mice in the Delta + Alum vaccine group had the highest levels of these antibodies after two doses, and the Delta + MF59-like and Delta + Alum vaccine groups produced high levels of cross-neutralization antibodies against prototype, Beta, and Gamma strain SARS-CoV-2 viruses. There was no significant decrease in neutralizing antibody levels in any vaccine group during the observation period. CpG, MF59-like, and Alum adjuvant Delta strain inactivated SARS-CoV-2 vaccines excited different antibody subtypes compared with unadjuvanted vaccines; the Delta + CpG vaccine group had a higher proportion of IgG2b antibodies, indicating bias towards Th1 immunity. The proportions of IgG1 and IgG2b in the Delta + MF59-like vaccine group were similar to those of the unadjuvanted vaccine. However, the Delta + Alum vaccine group had a higher proportion of IgG1 antibodies, indicating bias towards Th2 immunity. Antigen-specific cytokine secretion CD4/8+ T cells were analyzed. In conclusion, the results of this study show differences in the immune efficacy of CpG, MF59-like, and Alum adjuvant Delta strain inactivated SARS-CoV-2 vaccines in mice, which have significant implications for the selection strategy for vaccine adjuvants.
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Affiliation(s)
- Kangwei Xu
- National Institutes for Food and Drug Control, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China; (K.X.)
| | - Jing Li
- Sinovac Life Sciences Co., Ltd., No. 21, Tianfu St., Daxing Biomedicine Industrial Base of Zhongguancun Science Park, Daxing District, Beijing 100050, China
| | - Xu Lu
- National Institutes for Food and Drug Control, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China; (K.X.)
| | - Xiaoqin Ge
- Sinovac Life Sciences Co., Ltd., No. 21, Tianfu St., Daxing Biomedicine Industrial Base of Zhongguancun Science Park, Daxing District, Beijing 100050, China
| | - Kaiqin Wang
- National Institutes for Food and Drug Control, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China; (K.X.)
| | - Jiahao Wang
- Sinovac Life Sciences Co., Ltd., No. 21, Tianfu St., Daxing Biomedicine Industrial Base of Zhongguancun Science Park, Daxing District, Beijing 100050, China
| | - Zhizhong Qiao
- National Institutes for Food and Drug Control, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China; (K.X.)
| | - Yaru Quan
- National Institutes for Food and Drug Control, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China; (K.X.)
| | - Changgui Li
- National Institutes for Food and Drug Control, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China; (K.X.)
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77
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Biskupek I, Gieldon A. Two-Stage Recognition Mechanism of the SARS-CoV-2 Receptor-Binding Domain to Angiotensin-Converting Enzyme-2 (ACE2). Int J Mol Sci 2024; 25:679. [PMID: 38203850 PMCID: PMC10779479 DOI: 10.3390/ijms25010679] [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: 11/02/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
The SARS-CoV-2 virus, commonly known as COVID-19, occurred in 2019. It is a highly contagious illness with effects ranging from mild symptoms to severe illness. It is also one of the best-known pathogens since more than 200,000 scientific papers occurred in the last few years. With the publication of the SARS-CoV-2 (SARS-CoV-2-CTD) spike (S) protein in a complex with human ACE2 (hACE2) (PDB (6LZG)), the molecular analysis of one of the most crucial steps on the infection pathway was possible. The aim of this manuscript is to simulate the most widely spread mutants of SARS-CoV-2, namely Alpha, Beta, Gamma, Delta, Omicron, and the first recognized variant (natural wild type). With the wide search of the hypersurface of the potential energy performed using the UNRES force field, the intermediate state of the ACE2-RBD complex was found. R403, K/N/T417, L455, F486, Y489, F495, Y501, and Y505 played a crucial role in the protein recognition mechanism. The intermediate state cannot be very stable since it will prevent the infection cascade.
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Affiliation(s)
| | - Artur Gieldon
- Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308 Gdansk, Poland;
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78
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Zaidi AK, Dawoodi S. Structural biology of SARS-CoV-2. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 202:31-43. [PMID: 38237989 DOI: 10.1016/bs.pmbts.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This chapter provides a comprehensive overview of the techniques employed to unravel the structural biology of SARS-CoV-2, facilitating a deeper understanding of the virus for developing future therapeutic strategies. Various techniques such as Electron microscopy (EM) for capturing high-resolution images of the virus and X-ray crystallography used for determining atomic-level structures of viral proteins are discussed. Cryo-electron microscopy (cryo-EM) imaging is also examined as a powerful tool for visualizing the virus's structure in its native state. Intracellular detection and tracking of SARS-CoV-2 are discussed, highlighting the techniques employed to study the virus's behavior within host cells. The chapter further explores how cryo-EM has been instrumental in delivering high-quality structural information on SARS-CoV-2, enabling researchers to better understand its mechanisms of infection and replication. The structural visualization of SARS-CoV-2 is then presented, focusing on key components such as the spike protein structure, RNA polymerase structure, and the visualization of intact and in-situ virions using cryo-electron tomography (cryo-ET). Lastly, the chapter touches upon the application of nuclear magnetic resonance (NMR) spectroscopy for studying the dynamics and interactions of viral proteins.
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Affiliation(s)
| | - Sunny Dawoodi
- Anaesthesiologist, University Hospitals Birmingham and NHS Foundation Trust, United Kingdom.
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79
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Krammer F. The role of vaccines in the COVID-19 pandemic: what have we learned? Semin Immunopathol 2024; 45:451-468. [PMID: 37436465 PMCID: PMC11136744 DOI: 10.1007/s00281-023-00996-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/24/2023] [Indexed: 07/13/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged late in 2019 and caused the coronavirus disease 2019 (COVID-19) pandemic that has so far claimed approximately 20 million lives. Vaccines were developed quickly, became available in the end of 2020, and had a tremendous impact on protection from SARS-CoV-2 mortality but with emerging variants the impact on morbidity was diminished. Here I review what we learned from COVID-19 from a vaccinologist's perspective.
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Affiliation(s)
- Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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80
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Yamamoto Y, Inoue T. Current Status and Perspectives of Therapeutic Antibodies Targeting the Spike Protein S2 Subunit against SARS-CoV-2. Biol Pharm Bull 2024; 47:917-923. [PMID: 38692869 DOI: 10.1248/bpb.b23-00639] [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] [Indexed: 05/03/2024]
Abstract
The global coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has devastated public health and the global economy. New variants are continually emerging because of amino acid mutations within the SARS-CoV-2 spike protein. Existing neutralizing antibodies (nAbs) that target the receptor-binding domain (RBD) within the spike protein have been shown to have reduced neutralizing activity against these variants. In particular, the recently expanding omicron subvariants BQ 1.1 and XBB are resistant to nAbs approved for emergency use by the United States Food and Drug Administration. Therefore, it is essential to develop broad nAbs to combat emerging variants. In contrast to the massive accumulation of mutations within the RBD, the S2 subunit remains highly conserved among variants. Therefore, nAbs targeting the S2 region may provide effective cross-protection against novel SARS-CoV-2 variants. Here, we provide a detailed summary of nAbs targeting the S2 subunit: the fusion peptide, stem helix, and heptad repeats 1 and 2. In addition, we provide prospects to solve problems such as the weak neutralizing potency of nAbs targeting the S2 subunit.
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Affiliation(s)
- Yuichiro Yamamoto
- Laboratory of Molecular Targeted Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science
| | - Tetsuya Inoue
- Laboratory of Molecular Targeted Therapy, Faculty of Pharmaceutical Sciences, Tokyo University of Science
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81
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Jia J, Garbarino E, Wang Y, Li J, Song M, Zhang X, Wang X, Li L, Chi J, Cui L, Tang H. Generation of SARS-CoV-2 spike receptor binding domain mutants and functional screening for immune evaders using a novel lentivirus-based system. J Med Virol 2024; 96:e29425. [PMID: 38258313 DOI: 10.1002/jmv.29425] [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: 08/17/2023] [Revised: 12/19/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024]
Abstract
The emergence of rapid and continuous mutations of severe acute respiratory syndrome 2 (SARS-CoV-2) spike glycoprotein that increased with the Omicron variant points out the necessity to anticipate such mutations for conceiving specific and adaptable therapies to avoid another pandemic. The crucial target for the antibody treatment and vaccine design is the receptor binding domain (RBD) of the SARS-CoV-2 spike. It is also the site where the virus has shown its high ability to mutate and consequently escape immune response. We developed a robust and simple method for generating a large number of functional SARS-CoV-2 spike RBD mutants by error-prone PCR and a novel nonreplicative lentivirus-based system. We prepared anti-RBD wild type (WT) polyclonal antibodies and used them to screen and select for mutant libraries that escape inhibition of virion entry into recipient cells expressing human angiotensin-converting enzyme 2 and transmembrane serine protease 2. We isolated, cloned, and sequenced six mutants totally bearing nine mutation sites. Eight mutations were found in successive WT variants, including Omicron and other recombinants, whereas one is novel. These results, together with the detailed functional analyses of two mutants provided the proof of concept for our approach.
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Affiliation(s)
- Junli Jia
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Emanuela Garbarino
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yuhang Wang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
- Department of Blood Transfusion, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jiaming Li
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Minmin Song
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xin Zhang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xinjie Wang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Lingyun Li
- Department of Medical Genetics, Nanjing Medical University, Nanjing, China
| | - Jing Chi
- Department of Microbiological Laboratory, Baoan District Center for Disease Control and Prevention, Shenzhen, China
| | - Lunbiao Cui
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Huamin Tang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
- The Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing, China
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82
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Jin L, Mao Z. Living virus-based nanohybrids for biomedical applications. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1923. [PMID: 37619605 DOI: 10.1002/wnan.1923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
Living viruses characterized by distinctive biological functions including specific targeting, gene invasion, immune modulation, and so forth have been receiving intensive attention from researchers worldwide owing to their promising potential for producing numerous theranostic modalities against diverse pathological conditions. Nevertheless, concerns during applications, such as rapid immune clearance, altering immune activation modes, insufficient gene transduction efficiency, and so forth, highlight the crucial issues of excessive therapeutic doses and the associated biosafety risks. To address these concerns, synthetic nanomaterials featuring unique physical/chemical properties are frequently exploited as efficient drug delivery vehicles or treatments in biomedical domains. By constant endeavor, researchers nowadays can create adaptable living virus-based nanohybrids (LVN) that not only overcome the limitations of virotherapy, but also combine the benefits of natural substances and nanotechnology to produce novel and promising therapeutic and diagnostic agents. In this review, we discuss the fundamental physiochemical properties of the viruses, and briefly outline the basic construction methodologies of LVN. We then emphasize their distinct diagnostic and therapeutic performances for various diseases. Furthermore, we survey the foreseeable challenges and future perspectives in this interdisciplinary area to offer insights. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Lulu Jin
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Zhengwei Mao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
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83
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Tan S, Zhao J, Hu X, Li Y, Wu Z, Lu G, Yu Z, Du B, Liu Y, Li L, Chen Y, Li Y, Yao Y, Zhang X, Rao J, Gao G, Peng Y, Liu H, Yuan Z, Liu J, Wang Q, Hu H, Gao X, Zhou H, Yu H, Xu Y, Yu W, Feng L, Wang M, Shan C, Lu J, Lin J. Preclinical evaluation of RQ3013, a broad-spectrum mRNA vaccine against SARS-CoV-2 variants. Sci Bull (Beijing) 2023; 68:3192-3206. [PMID: 37993332 DOI: 10.1016/j.scib.2023.11.024] [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: 09/17/2023] [Revised: 10/19/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023]
Abstract
The global emergence of SARS-CoV-2 variants has led to increasing breakthrough infections in vaccinated populations, calling for an urgent need to develop more effective and broad-spectrum vaccines to combat COVID-19. Here we report the preclinical development of RQ3013, an mRNA vaccine candidate intended to bring broad protection against SARS-CoV-2 variants of concern (VOCs). RQ3013, which contains pseudouridine-modified mRNAs formulated in lipid nanoparticles, encodes the spike (S) protein harboring a combination of mutations responsible for immune evasion of VOCs. Here we characterized the expressed S immunogen and evaluated the immunogenicity, efficacy, and safety of RQ3013 in various animal models. RQ3013 elicited robust immune responses in mice, hamsters, and nonhuman primates (NHP). It can induce high titers of antibodies with broad cross-neutralizing ability against the wild-type, B.1.1.7, B.1.351, B.1.617.2, and the newly emerging Omicron variants. In mice and NHP, two doses of RQ3013 protected the upper and lower respiratory tract against infection by SARS-CoV-2 and its variants. Furthermore, our safety assessment of RQ3013 in NHP showed no observable adverse effects. These results provide strong support for the evaluation of RQ3013 in clinical trials and suggest that it may be a promising candidate for broad protection against COVID-19 and its variants.
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Affiliation(s)
- Shudan Tan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Jinghua Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Xue Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yufeng Li
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zihan Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Guoliang Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Zhaoli Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Binhe Du
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Yan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Li Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Yuchen Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Ye Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Yanfeng Yao
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xiaoyu Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Juhong Rao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ge Gao
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yun Peng
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hang Liu
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhiming Yuan
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jia Liu
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qianran Wang
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hengrui Hu
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xiaobo Gao
- Shanghai RNACure Biopharma Co., Ltd., Shanghai 200438, China
| | - Hui Zhou
- Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China; Shanghai RNACure Biopharma Co., Ltd., Shanghai 200438, China
| | - Hang Yu
- Shanghai RNACure Biopharma Co., Ltd., Shanghai 200438, China
| | - Yingjie Xu
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wei Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China.
| | - Lin Feng
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou 510060, China.
| | - Manli Wang
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Chao Shan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Jing Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China; Shanghai RNACure Biopharma Co., Ltd., Shanghai 200438, China.
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China.
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Malewana RD, Stalls V, May A, Lu X, Martinez DR, Schäfer A, Li D, Barr M, Sutherland LL, Lee E, Parks R, Beck WE, Newman A, Bock KW, Minai M, Nagata BM, DeMarco CT, Denny TN, Oguin TH, Rountree W, Wang Y, Mansouri K, Edwards RJ, Sempowski GD, Eaton A, Muramatsu H, Henderson R, Tam Y, Barbosa C, Tang J, Cain DW, Santra S, Moore IN, Andersen H, Lewis MG, Golding H, Seder R, Khurana S, Montefiori DC, Pardi N, Weissman D, Baric RS, Acharya P, Haynes BF, Saunders KO. Broadly neutralizing antibody induction by non-stabilized SARS-CoV-2 Spike mRNA vaccination in nonhuman primates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572191. [PMID: 38187726 PMCID: PMC10769253 DOI: 10.1101/2023.12.18.572191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Immunization with mRNA or viral vectors encoding spike with diproline substitutions (S-2P) has provided protective immunity against severe COVID-19 disease. How immunization with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spike elicits neutralizing antibodies (nAbs) against difficult-to-neutralize variants of concern (VOCs) remains an area of great interest. Here, we compare immunization of macaques with mRNA vaccines expressing ancestral spike either including or lacking diproline substitutions, and show the diproline substitutions were not required for protection against SARS-CoV-2 challenge or induction of broadly neutralizing B cell lineages. One group of nAbs elicited by the ancestral spike lacking diproline substitutions targeted the outer face of the receptor binding domain (RBD), neutralized all tested SARS-CoV-2 VOCs including Omicron XBB.1.5, but lacked cross-Sarbecovirus neutralization. Structural analysis showed that the macaque broad SARS-CoV-2 VOC nAbs bound to the same epitope as a human broad SARS-CoV-2 VOC nAb, DH1193. Vaccine-induced antibodies that targeted the RBD inner face neutralized multiple Sarbecoviruses, protected mice from bat CoV RsSHC014 challenge, but lacked Omicron variant neutralization. Thus, ancestral SARS-CoV-2 spike lacking proline substitutions encoded by nucleoside-modified mRNA can induce B cell lineages binding to distinct RBD sites that either broadly neutralize animal and human Sarbecoviruses or recent Omicron VOCs.
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Affiliation(s)
- R. Dilshan Malewana
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Victoria Stalls
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Aaron May
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David R. Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Immunobiology, Yale Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dapeng Li
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laura L. Sutherland
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Esther Lee
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Whitney Edwards Beck
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin W. Bock
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Mahnaz Minai
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Bianca M. Nagata
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - C. Todd DeMarco
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas N. Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas H. Oguin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wes Rountree
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gregory D. Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hiromi Muramatsu
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ying Tam
- Acuitas Therapeutics, LLC, Vancouver, BC, V6T 1Z3, Canada
| | | | - Juanjie Tang
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD 20871, USA
| | - Derek W. Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Ian N. Moore
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | | | | | - Hana Golding
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD 20871, USA
| | - Robert Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD 20871, USA
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Norbert Pardi
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
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85
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Baboo S, Diedrich JK, Torres JL, Copps J, Singh B, Garrett PT, Ward AB, Paulson JC, Yates JR. Evolving spike-protein N-glycosylation in SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539897. [PMID: 37214937 PMCID: PMC10197516 DOI: 10.1101/2023.05.08.539897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavily N-glycosylated spike-protein of SARS-CoV-2 plays a pivotal role in initiating infection and is the target for host immune-response, both of which are impacted by host-installed N-glycans. Using highly-sensitive DeGlyPHER approach, we compared the N-glycan landscape on spikes of the SARS-CoV-2 Wuhan-Hu-1 strain to seven WHO-defined variants of concern/interest, using recombinantly expressed, soluble spike-protein trimers, sharing same stabilizing-mutations. We found that N-glycan processing is conserved at most sites. However, in multiple variants, processing of N-glycans from high mannose- to complex-type is reduced at sites N165, N343 and N616, implicated in spike-protein function.
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Affiliation(s)
- Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jolene K. Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Bhavya Singh
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Patrick T. Garrett
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - James C. Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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86
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Fauquet J, Carette J, Duez P, Zhang J, Nachtergael A. Microfluidic Diffusion Sizing Applied to the Study of Natural Products and Extracts That Modulate the SARS-CoV-2 Spike RBD/ACE2 Interaction. Molecules 2023; 28:8072. [PMID: 38138562 PMCID: PMC10745392 DOI: 10.3390/molecules28248072] [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: 10/30/2023] [Revised: 11/29/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The interaction between SARS-CoV-2 spike RBD and ACE2 proteins is a crucial step for host cell infection by the virus. Without it, the entire virion entrance mechanism is compromised. The aim of this study was to evaluate the capacity of various natural product classes, including flavonoids, anthraquinones, saponins, ivermectin, chloroquine, and erythromycin, to modulate this interaction. To accomplish this, we applied a recently developed a microfluidic diffusional sizing (MDS) technique that allows us to probe protein-protein interactions via measurements of the hydrodynamic radius (Rh) and dissociation constant (KD); the evolution of Rh is monitored in the presence of increasing concentrations of the partner protein (ACE2); and the KD is determined through a binding curve experimental design. In a second time, with the protein partners present in equimolar amounts, the Rh of the protein complex was measured in the presence of different natural products. Five of the nine natural products/extracts tested were found to modulate the formation of the protein complex. A methanol extract of Chenopodium quinoa Willd bitter seed husks (50 µg/mL; bisdesmoside saponins) and the flavonoid naringenin (1 µM) were particularly effective. This rapid selection of effective modulators will allow us to better understand agents that may prevent SARS-CoV-2 infection.
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Affiliation(s)
- Jason Fauquet
- Unit of Therapeutic Chemistry and Pharmacognosy, University of Mons (UMONS), 7000 Mons, Belgium; (J.F.); (P.D.); (A.N.)
| | - Julie Carette
- Unit of Therapeutic Chemistry and Pharmacognosy, University of Mons (UMONS), 7000 Mons, Belgium; (J.F.); (P.D.); (A.N.)
| | - Pierre Duez
- Unit of Therapeutic Chemistry and Pharmacognosy, University of Mons (UMONS), 7000 Mons, Belgium; (J.F.); (P.D.); (A.N.)
| | - Jiuliang Zhang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Amandine Nachtergael
- Unit of Therapeutic Chemistry and Pharmacognosy, University of Mons (UMONS), 7000 Mons, Belgium; (J.F.); (P.D.); (A.N.)
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87
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. AlphaFold2-Enabled Atomistic Modeling of Epistatic Binding Mechanisms for the SARS-CoV-2 Spike Omicron XBB.1.5, EG.5 and FLip Variants: Convergent Evolution Hotspots Cooperate to Control Stability and Conformational Adaptability in Balancing ACE2 Binding and Antibody Resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571185. [PMID: 38168257 PMCID: PMC10760024 DOI: 10.1101/2023.12.11.571185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In this study, we combined AI-based atomistic structural modeling and microsecond molecular simulations of the SARS-CoV-2 Spike complexes with the host receptor ACE2 for XBB.1.5+L455F, XBB.1.5+F456L(EG.5) and XBB.1.5+L455F/F456L (FLip) lineages to examine the mechanisms underlying the role of convergent evolution hotspots in balancing ACE2 binding and antibody evasion. Using the ensemble-based mutational scanning of the spike protein residues and physics-based rigorous computations of binding affinities, we identified binding energy hotspots and characterized molecular basis underlying epistatic couplings between convergent mutational hotspots. Consistent with the experiments, the results revealed the mediating role of Q493 hotspot in synchronization of epistatic couplings between L455F and F456L mutations providing a quantitative insight into the mechanism underlying differences between XBB lineages. Mutational profiling is combined with network-based model of epistatic couplings showing that the Q493, L455 and F456 sites mediate stable communities at the binding interface with ACE2 and can serve as stable mediators of non-additive couplings. Structure-based mutational analysis of Spike protein binding with the class 1 antibodies quantified the critical role of F456L and F486P mutations in eliciting strong immune evasion response. The results of this analysis support a mechanism in which the emergence of EG.5 and FLip variants may have been dictated by leveraging strong epistatic effects between several convergent revolutionary hotspots that provide synergy between the improved ACE2 binding and broad neutralization resistance. This interpretation is consistent with the notion that functionally balanced substitutions which simultaneously optimize immune evasion and high ACE2 affinity may continue to emerge through lineages with beneficial pair or triplet combinations of RBD mutations involving mediators of epistatic couplings and sites in highly adaptable RBD regions.
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88
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Zhang H, Wang Z, Nguyen HTT, Watson AJ, Lao Q, Li A, Zhu J. Integrin α 5β 1 contributes to cell fusion and inflammation mediated by SARS-CoV-2 spike via RGD-independent interaction. Proc Natl Acad Sci U S A 2023; 120:e2311913120. [PMID: 38060559 PMCID: PMC10723138 DOI: 10.1073/pnas.2311913120] [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: 07/17/2023] [Accepted: 11/03/2023] [Indexed: 12/17/2023] Open
Abstract
The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infects host cells by engaging its spike (S) protein with human ACE2 receptor. Recent studies suggest the involvement of integrins in SARS-CoV-2 infection through interaction with the S protein, but the underlying mechanism is not well understood. This study investigated the role of integrin α5β1, which recognizes the Arg-Gly-Asp (RGD) motif in its physiological ligands, in S-mediated virus entry and cell-cell fusion. Our results showed that α5β1 does not directly contribute to S-mediated cell entry, but it enhances S-mediated cell-cell fusion in collaboration with ACE2. This effect cannot be inhibited by the putative α5β1 inhibitor ATN-161 or the high-affinity RGD-mimetic inhibitor MK-0429 but requires the participation of α5 cytoplasmic tail (CT). We detected a direct interaction between α5β1 and the S protein, but this interaction does not rely on the RGD-containing receptor binding domain of the S1 subunit of the S protein. Instead, it involves the S2 subunit of the S protein and α5β1 homo-oligomerization. Furthermore, we found that the S protein induces inflammatory responses in human endothelial cells, characterized by NF-κB activation, gasdermin D cleavage, and increased secretion of proinflammatory cytokines IL-6 and IL-1β. These effects can be attenuated by the loss of α5 expression or inhibition of the α5 CT binding protein phosphodiesterase-4D (PDE4D), suggesting the involvement of α5 CT and PDE4D pathway. These findings provide molecular insights into the pathogenesis of SARS-CoV-2 mediated by a nonclassical RGD-independent ligand-binding and signaling function of integrin α5β1 and suggest potential targets for antiviral treatment.
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Affiliation(s)
- Heng Zhang
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - Zhengli Wang
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - Huong T. T. Nguyen
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - Abigail J. Watson
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - Qifang Lao
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - An Li
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - Jieqing Zhu
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI53226
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Lipskij A, Arbeitman C, Rojas P, Ojeda-May P, Garcia ME. Dramatic Differences between the Structural Susceptibility of the S1 Pre- and S2 Postfusion States of the SARS-CoV-2 Spike Protein to External Electric Fields Revealed by Molecular Dynamics Simulations. Viruses 2023; 15:2405. [PMID: 38140646 PMCID: PMC10748067 DOI: 10.3390/v15122405] [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: 10/31/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
In its prefusion state, the SARS-CoV-2 spike protein (similarly to other class I viral fusion proteins) is metastable, which is considered to be an important feature for optimizing or regulating its functions. After the binding process of its S1 subunit (S1) with ACE2, the spike protein (S) undergoes a dramatic conformational change where S1 splits from the S2 subunit, which then penetrates the membrane of the host cell, promoting the fusion of the viral and cell membranes. This results in the infection of the host cell. In a previous work, we showed-using large-scale molecular dynamics simulations-that the application of external electric fields (EFs) induces drastic changes and damage in the receptor-binding domain (RBD) of the wild-type spike protein, as well of the Alpha, Beta, and Gamma variants, leaving a structure which cannot be recognized anymore by ACE2. In this work, we first extend the study to the Delta and Omicron variants and confirm the high sensitivity and extreme vulnerability of the RBD of the prefusion state of S to moderate EF (as weak as 104 V/m), but, more importantly, we also show that, in contrast, the S2 subunit of the postfusion state of the spike protein does not suffer structural damage even if electric field intensities four orders of magnitude higher are applied. These results provide a solid scientific basis to confirm the connection between the prefusion-state metastability of the SARS-CoV-2 spike protein and its susceptibility to be damaged by EF. After the virus docks to the ACE2 receptor, the stable and robust postfusion conformation develops, which exhibits a similar resistance to EF (damage threshold higher than 108 V/m) like most globular proteins.
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Affiliation(s)
- Alexander Lipskij
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
| | - Claudia Arbeitman
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
- CONICET Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, Buenos Aires C1425FQB, Argentina
- GIBIO-Universidad Tecnológica Nacional-Facultad Regional Buenos Aires, Medrano 951, Buenos Aires C1179AAQ, Argentina
| | - Pablo Rojas
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
| | - Pedro Ojeda-May
- High Performance Computing Center North (HPC2N), Umeå University, S-90187 Umeå, Sweden;
| | - Martin E. Garcia
- Theoretical Physics and Center of Interdisciplinary Nanostructure Science and Technology, FB10, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany; (A.L.); (C.A.); (P.R.)
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90
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Gartner MJ, Lee LYY, Mordant FL, Suryadinata R, Chen J, Robinson P, Polo JM, Subbarao K. Ancestral, Delta, and Omicron (BA.1) SARS-CoV-2 strains are dependent on serine proteases for entry throughout the human respiratory tract. MED 2023; 4:944-955.e7. [PMID: 37769654 DOI: 10.1016/j.medj.2023.08.006] [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: 02/10/2023] [Revised: 07/30/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and became the globally dominant variant by January 2022. Authentic virus and pseudovirus systems have shown Omicron spike has an increased dependence on the endosomal pathway for entry. METHODS We investigated the entry mechanisms of Omicron, Delta, and ancestral viruses in cell models that represent different parts of the human respiratory tract, including nasal epithelial cells (hNECs), large-airway epithelial cells (LAECs), small-airway epithelial cells, and embryonic stem cell-derived type II alveolar cells. FINDINGS Omicron had an early replication advantage in LAECs, while Delta grew to higher titers in all cells. Omicron maintained dependence on serine proteases for entry in all culture systems. While serine protease inhibition with camostat was less robust for Omicron in hNECs, endosomal entry was not enhanced. CONCLUSIONS Our findings demonstrate that entry of Omicron BA.1 SARS-CoV-2 is dependent on serine proteases for entry throughout the respiratory tract. FUNDING This work was supported by The Medical Research Future Fund (MRF9200007; K.S., J.M.P.) and the DHHS Victorian State Government grant (Victorian State Government; DJPR/COVID-19; K.S, J.M.P.). K.S. is supported by a National Health and Medical Research Council of Australia Investigator grant (APP1177174).
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Affiliation(s)
- Matthew J Gartner
- Department of Microbiology and Immunology, the University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Leo Yi Yang Lee
- Department of Microbiology and Immunology, the University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Francesca L Mordant
- Department of Microbiology and Immunology, the University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Randy Suryadinata
- Department of Respiratory Medicine, Royal Children's Hospital, Parkville, VIC 3052, Australia; Infection and Immunity, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia
| | - Philip Robinson
- Department of Respiratory Medicine, Royal Children's Hospital, Parkville, VIC 3052, Australia; Infection and Immunity, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia; Department of Paediatrics, the University of Melbourne at the Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Adelaide Centre for Epigenetics, University of Adelaide, Adelaide, SA 5005, Australia; South Australian Immunogenomics Cancer Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, the University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; WHO Collaborating Centre for Reference and Research on Influenza, the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
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91
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Kibria MG, Lavine CL, Tang W, Wang S, Gao H, Shi W, Zhu H, Voyer J, Rits‐Volloch S, Keerti, Bi C, Peng H, Wesemann DR, Lu J, Xie H, Seaman MS, Chen B. Antibody-mediated SARS-CoV-2 entry in cultured cells. EMBO Rep 2023; 24:e57724. [PMID: 38277394 PMCID: PMC10702815 DOI: 10.15252/embr.202357724] [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: 06/27/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 01/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters host cells by first engaging its cellular receptor angiotensin converting enzyme 2 (ACE2) to induce conformational changes in the virus-encoded spike protein and fusion between the viral and target cell membranes. Here, we report that certain monoclonal neutralizing antibodies against distinct epitopic regions of the receptor-binding domain of the spike can replace ACE2 to serve as a receptor and efficiently support membrane fusion and viral infectivity in vitro. These receptor-like antibodies can function in the form of a complex of their soluble immunoglobulin G with Fc-gamma receptor I, a chimera of their antigen-binding fragment with the transmembrane domain of ACE2 or a membrane-bound B cell receptor, indicating that ACE2 and its specific interaction with the spike protein are dispensable for SARS-CoV-2 entry. These results suggest that antibody responses against SARS-CoV-2 may help expand the viral tropism to otherwise nonpermissive cell types with potential implications for viral transmission and pathogenesis.
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Affiliation(s)
- Md Golam Kibria
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
- Department of PediatricsHarvard Medical SchoolBostonMAUSA
| | - Christy L Lavine
- Center for Virology and Vaccine ResearchBeth Israel Deaconess Medical CenterBostonMAUSA
| | - Weichun Tang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMDUSA
| | | | - Hailong Gao
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
- Department of PediatricsHarvard Medical SchoolBostonMAUSA
| | - Wei Shi
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
- Department of PediatricsHarvard Medical SchoolBostonMAUSA
| | - Haisun Zhu
- Institute for Protein Innovation, Harvard Institutes of MedicineBostonMAUSA
| | - Jewel Voyer
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
| | | | - Keerti
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's HospitalRagon Institute of MGH, MIT and HarvardBostonMAUSA
| | - Caihong Bi
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's HospitalRagon Institute of MGH, MIT and HarvardBostonMAUSA
| | - Hanqin Peng
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
| | - Duane R Wesemann
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's HospitalRagon Institute of MGH, MIT and HarvardBostonMAUSA
| | - Jianming Lu
- Codex BioSolutions, Inc.RockvilleMDUSA
- Department of Biochemistry and Molecular and Cellular BiologyGeorgetown UniversityWashingtonDCUSA
| | - Hang Xie
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMDUSA
| | - Michael S Seaman
- Center for Virology and Vaccine ResearchBeth Israel Deaconess Medical CenterBostonMAUSA
| | - Bing Chen
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
- Department of PediatricsHarvard Medical SchoolBostonMAUSA
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92
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Ávila-Nieto C, Vergara-Alert J, Amengual-Rigo P, Ainsua-Enrich E, Brustolin M, Rodríguez de la Concepción ML, Pedreño-Lopez N, Rodon J, Urrea V, Pradenas E, Marfil S, Ballana E, Riveira-Muñoz E, Pérez M, Roca N, Tarrés-Freixas F, Carabelli J, Cantero G, Pons-Grífols A, Rovirosa C, Aguilar-Gurrieri C, Ortiz R, Barajas A, Trinité B, Lepore R, Muñoz-Basagoiti J, Perez-Zsolt D, Izquierdo-Useros N, Valencia A, Blanco J, Clotet B, Guallar V, Segalés J, Carrillo J. Novel Spike-stabilized trimers with improved production protect K18-hACE2 mice and golden Syrian hamsters from the highly pathogenic SARS-CoV-2 Beta variant. Front Immunol 2023; 14:1291972. [PMID: 38124756 PMCID: PMC10731958 DOI: 10.3389/fimmu.2023.1291972] [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: 09/10/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Most COVID-19 vaccines are based on the SARS-CoV-2 Spike glycoprotein (S) or their subunits. However, S shows some structural instability that limits its immunogenicity and production, hampering the development of recombinant S-based vaccines. The introduction of the K986P and V987P (S-2P) mutations increases the production and immunogenicity of the recombinant S trimer, suggesting that these two parameters are related. Nevertheless, S-2P still shows some molecular instability and it is produced with low yield. Here we described a novel set of mutations identified by molecular modeling and located in the S2 region of the S-2P that increase its production up to five-fold. Besides their immunogenicity, the efficacy of two representative S-2P-based mutants, S-29 and S-21, protecting from a heterologous SARS-CoV-2 Beta variant challenge was assayed in K18-hACE2 mice (an animal model of severe SARS-CoV-2 disease) and golden Syrian hamsters (GSH) (a moderate disease model). S-21 induced higher level of WH1 and Delta variants neutralizing antibodies than S-2P in K18-hACE2 mice three days after challenge. Viral load in nasal turbinate and oropharyngeal samples were reduced in S-21 and S-29 vaccinated mice. Despite that, only the S-29 protein protected 100% of K18-hACE2 mice from severe disease. When GSH were analyzed, all immunized animals were protected from disease development irrespectively of the immunogen they received. Therefore, the higher yield of S-29, as well as its improved immunogenicity and efficacy protecting from the highly pathogenic SARS-CoV-2 Beta variant, pinpoint the S-29 mutant as an alternative to the S-2P protein for future SARS-CoV-2 vaccine development.
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Affiliation(s)
| | - Júlia Vergara-Alert
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Pep Amengual-Rigo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Marco Brustolin
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | | | | | - Jordi Rodon
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Victor Urrea
- IrsiCaixa AIDS Research Institute, Badalona, Spain
| | | | | | - Ester Ballana
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | | | - Mònica Pérez
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Núria Roca
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | | | | | - Guillermo Cantero
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | | | | | | | - Raquel Ortiz
- IrsiCaixa AIDS Research Institute, Badalona, Spain
| | - Ana Barajas
- IrsiCaixa AIDS Research Institute, Badalona, Spain
| | | | - Rosalba Lepore
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | | | - Nuria Izquierdo-Useros
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Alfonso Valencia
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic – Central University of Catalonia (UVic – UCC), Vic, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic – Central University of Catalonia (UVic – UCC), Vic, Spain
- Fundació Lluita contra les Infeccions, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Victor Guallar
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Joaquim Segalés
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, Cerdanyola del Vallès, Spain
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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93
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Wang X, Sun L, Liu Z, Xing L, Zhu Y, Xu W, Xia S, Lu L, Jiang S. An engineered recombinant protein containing three structural domains in SARS-CoV-2 S2 protein has potential to act as a pan-human coronavirus entry inhibitor or vaccine antigen. Emerg Microbes Infect 2023; 12:2244084. [PMID: 37534910 PMCID: PMC10424610 DOI: 10.1080/22221751.2023.2244084] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/16/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023]
Abstract
The threat to global health caused by three highly pathogenic human coronaviruses (HCoV), SARS-CoV-2, MERS-CoV and SARS-CoV, calls for the development of pan-HCoV therapeutics and vaccines. This study reports the design and engineering of a recombinant protein designated HR1LS. It contains three linked molecules, each consisting of three structural domains, including a heptad repeat 1 (HR1), a central helix (CH), and a stem helix (SH) region, in the S2 subunit of SARS-CoV-2 spike (S) protein. It was found that HR1LS protein automatically formed a trimer able to bind with heptad repeat 2 (HR2) region in the SARS-CoV-2 S2 subunit, thus potently inhibiting HCoV fusion and entry into host cells. Furthermore, immunization of mice with HR1LS, when combined with CF501 adjuvant, resulted in the production of neutralizing antibodies against infection of SARS-CoV-2 and its variants, as well as SARS-CoV, MERS-CoV, HCoV-229E, HCoV-NL63 and MjHKU4r-CoV-1. These results suggest that HR1LS is a promising candidate for further development as a novel HR1-trimer-based pan-HCoV entry inhibitor or vaccine for the treatment and prevention of infection by SARS-CoV-2 and its variants, but also other HCoVs with the potential to cause future emerging and re-emerging infectious coronavirus diseases.
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Affiliation(s)
- Xinling Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Lujia Sun
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Zezhong Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
- Department of Pharmacology & Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, Shanghai, People’s Republic of China
| | - Lixiao Xing
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Reproduction Regulation of National Population and Family Planning Commission, The Shanghai Institute of Planned Parenthood Research, Institute of Reproduction and Development, Fudan University, Shanghai, People’s Republic of China
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94
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Hu X, Liao M, Ding K, Wang J, Xu H, Tao K, Zhou F, Lu JR. Neutron reflection and scattering in characterising peptide assemblies. Adv Colloid Interface Sci 2023; 322:103033. [PMID: 37931380 DOI: 10.1016/j.cis.2023.103033] [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: 08/04/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023]
Abstract
Self-assemblies of de novo designed short peptides at interface and in bulk solution provide potential platforms for developing applications in many medical and technological areas. However, characterising how bioinspired supramolecular nanostructures evolve with dynamic self-assembling processes and respond to different stimuli remains challenging. Neutron scattering technologies including small angle neutron scattering (SANS) and neutron reflection (NR) can be advantageous and complementary to other state-of-the-art techniques in tracing structural changes under different conditions. With more neutron sources now available, SANS and NR are becoming increasingly popular in studying self-assembling processes of diverse peptide and protein systems, but the difficulty in experimental manipulation and data analysis can deter beginners. This review will introduce the basic theory, general experimental setup and data analysis of SANS and NR, followed by provision of their applications in characterising interfacial and solution self-assemblies of representative peptides and proteins. SANS and NR are remarkably effective in determining the morphological features self-assembled short peptides, especially size and shape transitions as a result of either sequence changes or in response to environmental stimuli, demonstrating the unique capability of NR and SANS in unravelling the interactive processes. These examples highlight the potential of NR and SANS in supporting the development of novel short peptides and proteins as biopharmaceutical candidates in the fight against many diseases and infections that share common features of membrane interactive processes.
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Affiliation(s)
- Xuzhi Hu
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, UK.; Lanzhou Institute of Chemical Physics, Tianshui Middle Road, Lanzhou 730000, Gansu, China
| | - Mingrui Liao
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Ke Ding
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Jiqian Wang
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Hai Xu
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Kai Tao
- State Key Laboratory of Fluid Power and Mechatronic Systems, Key Laboratory of Advanced Manufacturing Technology of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, Hangzhou 310058, China; Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Zhejiang University, Hangzhou 311215, China
| | - Feng Zhou
- Lanzhou Institute of Chemical Physics, Tianshui Middle Road, Lanzhou 730000, Gansu, China
| | - Jian R Lu
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, UK..
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95
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Lei R, Qing E, Odle A, Yuan M, Tan TJ, So N, Ouyang WO, Wilson IA, Gallagher T, Perlman S, Wu NC, Wong LYR. Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569051. [PMID: 38076875 PMCID: PMC10705381 DOI: 10.1101/2023.11.28.569051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we performed a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identified mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we showed that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Abby Odle
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Natalie So
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wenhao O. Ouyang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Center for Virus-Host-Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
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96
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Geng Q, Wan Y, Hsueh FC, Shang J, Ye G, Bu F, Herbst M, Wilkens R, Liu B, Li F. Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein. eLife 2023; 12:e74060. [PMID: 37991488 PMCID: PMC10695562 DOI: 10.7554/elife.74060] [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: 09/20/2021] [Accepted: 11/21/2023] [Indexed: 11/23/2023] Open
Abstract
SARS-CoV-2 spike protein plays a key role in mediating viral entry and inducing host immune responses. It can adopt either an open or closed conformation based on the position of its receptor-binding domain (RBD). It is yet unclear what causes these conformational changes or how they influence the spike's functions. Here, we show that Lys417 in the RBD plays dual roles in the spike's structure: it stabilizes the closed conformation of the trimeric spike by mediating inter-spike-subunit interactions; it also directly interacts with ACE2 receptor. Hence, a K417V mutation has opposing effects on the spike's function: it opens up the spike for better ACE2 binding while weakening the RBD's direct binding to ACE2. The net outcomes of this mutation are to allow the spike to bind ACE2 with higher probability and mediate viral entry more efficiently, but become more exposed to neutralizing antibodies. Given that residue 417 has been a viral mutational hotspot, SARS-CoV-2 may have been evolving to strike a balance between infection potency and immune evasion, contributing to its pandemic spread.
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Affiliation(s)
- Qibin Geng
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Yushun Wan
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Fu-Chun Hsueh
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Jian Shang
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Gang Ye
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Fan Bu
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Morgan Herbst
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Rowan Wilkens
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Bin Liu
- Hormel Institute, University of MinnesotaAustinUnited States
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
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97
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Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Accurate Characterization of Conformational Ensembles and Binding Mechanisms of the SARS-CoV-2 Omicron BA.2 and BA.2.86 Spike Protein with the Host Receptor and Distinct Classes of Antibodies Using AlphaFold2-Augmented Integrative Computational Modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.18.567697. [PMID: 38045395 PMCID: PMC10690158 DOI: 10.1101/2023.11.18.567697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The latest wave SARS-CoV-2 Omicron variants displayed a growth advantage and the increased viral fitness through convergent evolution of functional hotspots that work synchronously to balance fitness requirements for productive receptor binding and efficient immune evasion. In this study, we combined AlphaFold2-based structural modeling approaches with all-atom MD simulations and mutational profiling of binding energetics and stability for prediction and comprehensive analysis of the structure, dynamics, and binding of the SARS-CoV-2 Omicron BA.2.86 spike variant with ACE2 host receptor and distinct classes of antibodies. We adapted several AlphaFold2 approaches to predict both structure and conformational ensembles of the Omicron BA.2.86 spike protein in the complex with the host receptor. The results showed that AlphaFold2-predicted conformational ensemble of the BA.2.86 spike protein complex can accurately capture the main dynamics signatures obtained from microscond molecular dynamics simulations. The ensemble-based dynamic mutational scanning of the receptor binding domain residues in the BA.2 and BA.2.86 spike complexes with ACE2 dissected the role of the BA.2 and BA.2.86 backgrounds in modulating binding free energy changes revealing a group of conserved hydrophobic hotspots and critical variant-specific contributions of the BA.2.86 mutational sites R403K, F486P and R493Q. To examine immune evasion properties of BA.2.86 in atomistic detail, we performed large scale structure-based mutational profiling of the S protein binding interfaces with distinct classes of antibodies that displayed significantly reduced neutralization against BA.2.86 variant. The results quantified specific function of the BA.2.86 mutations to ensure broad resistance against different classes of RBD antibodies. This study revealed the molecular basis of compensatory functional effects of the binding hotspots, showing that BA.2.86 lineage may have primarily evolved to improve immune escape while modulating binding affinity with ACE2 through cooperative effect of R403K, F486P and R493Q mutations. The study supports a hypothesis that the impact of the increased ACE2 binding affinity on viral fitness is more universal and is mediated through cross-talk between convergent mutational hotspots, while the effect of immune evasion could be more variant-dependent.
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Aliper ET, Efremov RG. Inconspicuous Yet Indispensable: The Coronavirus Spike Transmembrane Domain. Int J Mol Sci 2023; 24:16421. [PMID: 38003610 PMCID: PMC10671605 DOI: 10.3390/ijms242216421] [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: 08/31/2023] [Revised: 11/07/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Membrane-spanning portions of proteins' polypeptide chains are commonly known as their transmembrane domains (TMDs). The structural organisation and dynamic behaviour of TMDs from proteins of various families, be that receptors, ion channels, enzymes etc., have been under scrutiny on the part of the scientific community for the last few decades. The reason for such attention is that, apart from their obvious role as an "anchor" in ensuring the correct orientation of the protein's extra-membrane domains (in most cases functionally important), TMDs often actively and directly contribute to the operation of "the protein machine". They are capable of transmitting signals across the membrane, interacting with adjacent TMDs and membrane-proximal domains, as well as with various ligands, etc. Structural data on TMD arrangement are still fragmentary at best due to their complex molecular organisation as, most commonly, dynamic oligomers, as well as due to the challenges related to experimental studies thereof. Inter alia, this is especially true for viral fusion proteins, which have been the focus of numerous studies for quite some time, but have provoked unprecedented interest in view of the SARS-CoV-2 pandemic. However, despite numerous structure-centred studies of the spike (S) protein effectuating target cell entry in coronaviruses, structural data on the TMD as part of the entire spike protein are still incomplete, whereas this segment is known to be crucial to the spike's fusogenic activity. Therefore, in attempting to bring together currently available data on the structure and dynamics of spike proteins' TMDs, the present review aims to tackle a highly pertinent task and contribute to a better understanding of the molecular mechanisms underlying virus-mediated fusion, also offering a rationale for the design of novel efficacious methods for the treatment of infectious diseases caused by SARS-CoV-2 and related viruses.
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Affiliation(s)
- Elena T. Aliper
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Roman G. Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Department of Applied Mathematics, National Research University Higher School of Economics, Moscow 101000, Russia
- L.D. Landau School of Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny 141701, Russia
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Keitany GJ, Rubin BER, Garrett ME, Musa A, Tracy J, Liang Y, Ebert P, Moore AJ, Guan J, Eggers E, Lescano N, Brown R, Carbo A, Al-Asadi H, Ching T, Day A, Harris R, Linkem C, Popov D, Wilkins C, Li L, Wang J, Liu C, Chen L, Dines JN, Atyeo C, Alter G, Baldo L, Sherwood A, Howie B, Klinger M, Yusko E, Robins HS, Benzeno S, Gilbert AE. Multimodal, broadly neutralizing antibodies against SARS-CoV-2 identified by high-throughput native pairing of BCRs from bulk B cells. Cell Chem Biol 2023; 30:1377-1389.e8. [PMID: 37586370 PMCID: PMC10659930 DOI: 10.1016/j.chembiol.2023.07.011] [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: 09/20/2022] [Revised: 04/25/2023] [Accepted: 07/23/2023] [Indexed: 08/18/2023]
Abstract
TruAB Discovery is an approach that integrates cellular immunology, high-throughput immunosequencing, bioinformatics, and computational biology in order to discover naturally occurring human antibodies for prophylactic or therapeutic use. We adapted our previously described pairSEQ technology to pair B cell receptor heavy and light chains of SARS-CoV-2 spike protein-binding antibodies derived from enriched antigen-specific memory B cells and bulk antibody-secreting cells. We identified approximately 60,000 productive, in-frame, paired antibody sequences, from which 2,093 antibodies were selected for functional evaluation based on abundance, isotype and patterns of somatic hypermutation. The exceptionally diverse antibodies included RBD-binders with broad neutralizing activity against SARS-CoV-2 variants, and S2-binders with broad specificity against betacoronaviruses and the ability to block membrane fusion. A subset of these RBD- and S2-binding antibodies demonstrated robust protection against challenge in hamster and mouse models. This high-throughput approach can accelerate discovery of diverse, multifunctional antibodies against any target of interest.
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Affiliation(s)
| | | | | | - Andrea Musa
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Jeff Tracy
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Yu Liang
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Peter Ebert
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | - Erica Eggers
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | - Ryan Brown
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Adria Carbo
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | - Austin Day
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | | | | | - Lianqu Li
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Jiao Wang
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Chuanxin Liu
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Li Chen
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Lance Baldo
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | - Bryan Howie
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Mark Klinger
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Erik Yusko
- Adaptive Biotechnologies, Seattle, WA 98109, USA
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100
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Song A, Phandthong R, Talbot P. Endocytosis inhibitors block SARS-CoV-2 pseudoparticle infection of mink lung epithelium. Front Microbiol 2023; 14:1258975. [PMID: 38033586 PMCID: PMC10682793 DOI: 10.3389/fmicb.2023.1258975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Both spill over and spill back of SARS-CoV-2 virus have been reported on mink farms in Europe and the United States. Zoonosis is a public health concern as dangerous mutated forms of the virus could be introduced into the human population through spillback. Methods The purpose of our study was to determine the SARS-CoV-2 entry mechanism using the mink lung epithelial cell line (Mv1Lu) and to block entry with drug inhibitors. Results Mv1Lu cells were susceptible to SARS-CoV-2 viral pseudoparticle infection, validating them as a suitable disease model for COVID-19. Inhibitors of TMPRSS2 and of endocytosis, two pathways of viral entry, were tested to identify those that blocked infection. TMPRSS2 inhibitors had minimal impact, which can be explained by the apparent lack of activity of this enzyme in the mink and its localization within the cell, not on the cell surface. Discussion Dyngo4a, a small molecule endocytosis inhibitor, significantly reduced infection, supporting the conclusion that the entry of the SARS-CoV-2 virus into Mv1Lu cells occurs primarily through endocytosis. The small molecule inhibitors that were effective in this study could potentially be used therapeutically to prevent SARS-CoV-2 infection in mink populations. This study will facilitate the development of therapeutics to prevent zoonotic transmission of SARS-CoV-2 variants to other animals, including humans.
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Affiliation(s)
- Ann Song
- Cell, Molecular, and Developmental Biology Graduate Program, University of California, Riverside, Riverside, CA, United States
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Rattapol Phandthong
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Prue Talbot
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
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