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Jhanwar A, Sharma D, Das U. Unraveling the structural and functional dimensions of SARS-CoV2 proteins in the context of COVID-19 pathogenesis and therapeutics. Int J Biol Macromol 2024; 278:134850. [PMID: 39168210 DOI: 10.1016/j.ijbiomac.2024.134850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) has emerged as the causative agent behind the global pandemic of Coronavirus Disease 2019 (COVID-19). As the scientific community strives to comprehend the intricate workings of this virus, a fundamental aspect lies in deciphering the myriad proteins it expresses. This knowledge is pivotal in unraveling the complexities of the viral machinery and devising targeted therapeutic interventions. The proteomic landscape of SARS-CoV2 encompasses structural, non-structural, and open-reading frame proteins, each playing crucial roles in viral replication, host interactions, and the pathogenesis of COVID-19. This comprehensive review aims to provide an updated and detailed examination of the structural and functional attributes of SARS-CoV2 proteins. By exploring the intricate molecular architecture, we have highlighted the significance of these proteins in viral biology. Insights into their roles and interplay contribute to a deeper understanding of the virus's mechanisms, thereby paving the way for the development of effective therapeutic strategies. As the global scientific community strives to combat the ongoing pandemic, this synthesis of knowledge on SARS-CoV2 proteins serves as a valuable resource, fostering informed approaches toward mitigating the impact of COVID-19 and advancing the frontier of antiviral research.
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Affiliation(s)
- Aniruddh Jhanwar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Dipika Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
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2
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Hutchings CJ, Sato AK. Phage display technology and its impact in the discovery of novel protein-based drugs. Expert Opin Drug Discov 2024; 19:887-915. [PMID: 39074492 DOI: 10.1080/17460441.2024.2367023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/07/2024] [Indexed: 07/31/2024]
Abstract
INTRODUCTION Phage display technology is a well-established versatile in vitro display technology that has been used for over 35 years to identify peptides and antibodies for use as reagents and therapeutics, as well as exploring the diversity of alternative scaffolds as another option to conventional therapeutic antibody discovery. Such successes have been responsible for spawning a range of biotechnology companies, as well as many complementary technologies devised to expedite the drug discovery process and resolve bottlenecks in the discovery workflow. AREAS COVERED In this perspective, the authors summarize the application of phage display for drug discovery and provide examples of protein-based drugs that have either been approved or are being developed in the clinic. The amenability of phage display to generate functional protein molecules to challenging targets and recent developments of strategies and techniques designed to harness the power of sampling diverse repertoires are highlighted. EXPERT OPINION Phage display is now routinely combined with cutting-edge technologies to deep-mine antibody-based repertoires, peptide, or alternative scaffold libraries generating a wealth of data that can be leveraged, e.g. via artificial intelligence, to enable the potential for clinical success in the discovery and development of protein-based therapeutics.
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3
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Zhang QE, Lindenberger J, Parsons RJ, Thakur B, Parks R, Park CS, Huang X, Sammour S, Janowska K, Spence TN, Edwards RJ, Martin M, Williams WB, Gobeil S, Montefiori DC, Korber B, Saunders KO, Haynes BF, Henderson R, Acharya P. SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition. Mol Cell 2024; 84:2747-2764.e7. [PMID: 39059371 DOI: 10.1016/j.molcel.2024.06.028] [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: 02/14/2024] [Revised: 05/20/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]
Abstract
A recombinant lineage of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryoelectron microscopy (cryo-EM) structures of XBB.1.5, XBB.1.16, EG.5, and EG.5.1 spike (S) ectodomains to reveal reinforced 3-receptor binding domain (RBD)-down receptor-inaccessible closed states mediated by interprotomer RBD interactions previously observed in BA.1 and BA.2. Improved XBB.1.5 and XBB.1.16 RBD stability compensated for stability loss caused by early Omicron mutations, while the F456L substitution reduced EG.5 RBD stability. S1 subunit mutations had long-range impacts on conformation and epitope presentation in the S2 subunit. Our results reveal continued S protein evolution via simultaneous optimization of multiple parameters, including stability, receptor binding, and immune evasion, and the dramatic effects of relatively few residue substitutions in altering the S protein conformational landscape.
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Affiliation(s)
- Qianyi E Zhang
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA
| | | | - Ruth J Parsons
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA
| | - Bhishem Thakur
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Rob Parks
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Chan Soo Park
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Xiao Huang
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Salam Sammour
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | - Taylor N Spence
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Robert J Edwards
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Medicine, Durham, NC 27710, USA
| | - Mitchell Martin
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Wilton B Williams
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA; Duke University, Department of Integrative Immunology, Durham, NC 27710, USA
| | - Sophie Gobeil
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Université Laval, Institut de Biologie Intégrative et des Systèmes (IBIS), Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Centre de Recherche en Infectiologie de l'Université Laval, PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Québec, QC, Canada
| | - David C Montefiori
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; The New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Kevin O Saunders
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA; Duke University, Department of Integrative Immunology, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F Haynes
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Medicine, Durham, NC 27710, USA; Duke University, Department of Integrative Immunology, Durham, NC 27710, USA
| | - Rory Henderson
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Medicine, Durham, NC 27710, USA
| | - Priyamvada Acharya
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA.
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4
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Metzdorf K, Jacobsen H, Kim Y, Teixeira Alves LG, Kulkarni U, Brdovčak MC, Materljan J, Eschke K, Chaudhry MZ, Hoffmann M, Bertoglio F, Ruschig M, Hust M, Šustić M, Krmpotić A, Jonjić S, Widera M, Ciesek S, Pöhlmann S, Landthaler M, Čičin-Šain L. A single-dose MCMV-based vaccine elicits long-lasting immune protection in mice against distinct SARS-CoV-2 variants. Front Immunol 2024; 15:1383086. [PMID: 39119342 PMCID: PMC11306140 DOI: 10.3389/fimmu.2024.1383086] [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: 02/06/2024] [Accepted: 06/11/2024] [Indexed: 08/10/2024] Open
Abstract
Current vaccines against COVID-19 elicit immune responses that are overall strong but wane rapidly. As a consequence, the necessary booster shots have contributed to vaccine fatigue. Hence, vaccines that would provide lasting protection against COVID-19 are needed, but are still unavailable. Cytomegaloviruses (CMVs) elicit lasting and uniquely strong immune responses. Used as vaccine vectors, they may be attractive tools that obviate the need for boosters. Therefore, we tested the murine CMV (MCMV) as a vaccine vector against COVID-19 in relevant preclinical models of immunization and challenge. We have previously developed a recombinant MCMV vaccine vector expressing the spike protein of the ancestral SARS-CoV-2 (MCMVS). In this study, we show that the MCMVS elicits a robust and lasting protection in young and aged mice. Notably, spike-specific humoral and cellular immunity was not only maintained but also even increased over a period of at least 6 months. During that time, antibody avidity continuously increased and expanded in breadth, resulting in neutralization of genetically distant variants, like Omicron BA.1. A single dose of MCMVS conferred rapid virus clearance upon challenge. Moreover, MCMVS vaccination controlled two variants of concern (VOCs), the Beta (B.1.135) and the Omicron (BA.1) variants. Thus, CMV vectors provide unique advantages over other vaccine technologies, eliciting broadly reactive and long-lasting immune responses against COVID-19.
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MESH Headings
- Animals
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- Mice
- COVID-19 Vaccines/immunology
- COVID-19/prevention & control
- COVID-19/immunology
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Muromegalovirus/immunology
- Muromegalovirus/genetics
- Female
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- Mice, Inbred BALB C
- Humans
- Genetic Vectors
- Immunity, Cellular
- Immunity, Humoral
- Disease Models, Animal
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Affiliation(s)
- Kristin Metzdorf
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine, a Joint Venture of the Helmholtz Centre for Infection Medicine and the Hannover Medical School, Hannover, Germany
| | - Henning Jacobsen
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine, a Joint Venture of the Helmholtz Centre for Infection Medicine and the Hannover Medical School, Hannover, Germany
| | - Yeonsu Kim
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine, a Joint Venture of the Helmholtz Centre for Infection Medicine and the Hannover Medical School, Hannover, Germany
| | - Luiz Gustavo Teixeira Alves
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Upasana Kulkarni
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine, a Joint Venture of the Helmholtz Centre for Infection Medicine and the Hannover Medical School, Hannover, Germany
| | | | - Jelena Materljan
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
- Department of Histology and Embryology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Kathrin Eschke
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - M. Zeeshan Chaudhry
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Federico Bertoglio
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maximilian Ruschig
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Marko Šustić
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Astrid Krmpotić
- Department of Histology and Embryology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Stipan Jonjić
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany
- German Centre for Infection Research (DZIF), External Partner Site Frankfurt, Frankfurt, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine, a Joint Venture of the Helmholtz Centre for Infection Medicine and the Hannover Medical School, Hannover, Germany
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5
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Stern D, Dettmann P, Dorner BG, Mages HW. Protein G affinity chromatography is an underrated but very potent purification method for a broad range of species-independent and tag-less Fab-fragments. J Immunol Methods 2024; 529:113669. [PMID: 38582259 DOI: 10.1016/j.jim.2024.113669] [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: 01/31/2024] [Revised: 03/15/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Because of their superior properties for certain biological applications small antibody derivatives like fragment of antigen binding (Fab) have found widespread use in basic research and as therapeutics. However, generation of Fab-fragments is still a rather complex matter, reflected by the fact that a variety of methods and purification techniques are necessary for the production of all the different classes of Fab-fragments (kappa/lambda light chains, type of species). Here we demonstrate that Fab-fragments derived from six different antibodies of human or murine origin produced by transient expression in HEK cells can be purified in a single step to a high degree of purity by standard protein G affinity chromatography. This is most likely due to alternative contact sites for protein G located in the CH1 domain of the Fab heavy chain. Our data demonstrate that protein G affinity chromatography as for whole antibodies is a robust method for the purification of tag-less Fab-fragments independent of species, significantly simplifying the process of Fab-fragment purification.
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Affiliation(s)
- Daniel Stern
- Biological Toxins (ZBS 3), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany
| | - Paulin Dettmann
- Biological Toxins (ZBS 3), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany
| | - Brigitte G Dorner
- Biological Toxins (ZBS 3), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany
| | - Hans Werner Mages
- Biological Toxins (ZBS 3), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany.
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6
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Zhang QE, Lindenberger J, Parsons R, Thakur B, Parks R, Park CS, Huang X, Sammour S, Janowska K, Spence TN, Edwards RJ, Martin M, Williams WB, Gobeil S, Montefiori DC, Korber B, Saunders KO, Haynes BF, Haynes BF, Henderson R, Acharya P. SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.580004. [PMID: 38405707 PMCID: PMC10888797 DOI: 10.1101/2024.02.12.580004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
A recombinant lineage of the SARS-CoV-2 Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryo-EM structures of XBB.1.5, XBB.1.16, EG.5 and EG.5.1 spike (S) ectodomains to reveal reinforced 3-RBD-down receptor inaccessible closed states mediated by interprotomer receptor binding domain (RBD) interactions previously observed in BA.1 and BA.2. Improved XBB.1.5 and XBB.1.16 RBD stability compensated for stability loss caused by early Omicron mutations, while the F456L substitution reduced EG.5 RBD stability. S1 subunit mutations had long-range impacts on conformation and epitope presentation in the S2 subunit. Our results reveal continued S protein evolution via simultaneous optimization of multiple parameters including stability, receptor binding and immune evasion, and the dramatic effects of relatively few residue substitutions in altering the S protein conformational landscape.
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7
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Khalid K, Lim HX, Anwar A, Tan SH, Hwang JS, Ong SK, Poh CL. Preclinical Development of a Novel Epitope-based DNA Vaccine Candidate against SARS-CoV-2 and Evaluation of Immunogenicity in BALB/c Mice. AAPS PharmSciTech 2024; 25:60. [PMID: 38472523 DOI: 10.1208/s12249-024-02778-x] [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: 01/10/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
The protective efficacies of current licensed vaccines against COVID-19 have significantly reduced as a result of SARS-CoV-2 variants of concern (VOCs) which carried multiple mutations in the Spike (S) protein. Considering that these vaccines were developed based on the S protein of the original SARS-CoV-2 Wuhan strain, we designed a recombinant plasmid DNA vaccine based on highly conserved and immunogenic B and T cell epitopes against SARS-CoV-2 Wuhan strain and the Omicron VOC. Literature mining and bioinformatics were used to identify 6 immunogenic peptides from conserved regions of the SARS-CoV-2 S and membrane (M) proteins. Nucleotide sequences encoding these peptides representing highly conserved B and T cell epitopes were cloned into a pVAX1 vector to form the pVAX1/S2-6EHGFP recombinant DNA plasmid vaccine. The DNA vaccine was intranasally or intramuscularly administered to BALB/c mice and evaluations of humoral and cellular immune responses were performed. The intramuscular administration of pVAX1/S2-6EHGFP was associated with a significantly higher percentage of CD8+ T cells expressing IFN-γ when compared with the empty vector and PBS controls. Intramuscular or intranasal administrations of pVAX1/S2-6EHGFP resulted in robust IgG antibody responses. Sera from mice intramuscularly immunized with pVAX1/S2-6EHGFP were found to elicit neutralizing antibodies capable of SARS-CoV-2 Omicron variant with the ACE2 cell surface receptor. This study demonstrated that the DNA vaccine construct encoding highly conserved immunogenic B and T cell epitopes was capable of eliciting potent humoral and cellular immune responses in mice.
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Affiliation(s)
- Kanwal Khalid
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Hui Xuan Lim
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
- Sunway Microbiome Centre, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Ayaz Anwar
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Soon Hao Tan
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Jung Shan Hwang
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Seng-Kai Ong
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia.
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8
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Hu C, Hu W, Tang B, Bao Q, Jiang X, Tang L, Wang H, He L, Lv M, Xiao Y, Liu C, Li X, Liu Y, Li J, Huang G, Dong Z, Li Z, Guo T, Yang S. Plasma and urine proteomics and gut microbiota analysis reveal potential factors affecting COVID-19 vaccination response. iScience 2024; 27:108851. [PMID: 38318387 PMCID: PMC10838952 DOI: 10.1016/j.isci.2024.108851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/15/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024] Open
Abstract
The efficacy of COVID-19 vaccination relies on the induction of neutralizing antibodies, which can vary among vaccine recipients. In this study, we investigated the potential factors affecting the neutralizing antibody response by combining plasma and urine proteomics and gut microbiota analysis. We found that activation of the LXR/FXR pathway in plasma was associated with the production of ACE2-RBD-inhibiting antibodies, while urine proteins related to complement system, acute phase response signaling, LXR/FXR, and STAT3 pathways were correlated with neutralizing antibody production. Moreover, we observed a correlation between the gut microbiota and plasma and urine proteins, as well as the vaccination response. Based on the above data, we built a predictive model for vaccination response (AUC = 0.85). Our study provides insights into characteristic plasma and urine proteins and gut microbiota associated with the ACE2-RBD-inhibiting antibodies, which could benefit our understanding of the host response to COVID-19 vaccination.
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Affiliation(s)
- Changjiang Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
- iMarkerlab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang, China
- Center for Infectious Disease Research, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Weichao Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
- iMarkerlab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang, China
- Center for Infectious Disease Research, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Qiyu Bao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Xingyu Jiang
- Laboratory Medicine Center, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Li Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - He Wang
- iMarkerlab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang, China
- Center for Infectious Disease Research, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Lijiao He
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Moyang Lv
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Yufeng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Cheng Liu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Xinzhe Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Yunyi Liu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Jie Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Guiping Huang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Zhen Dong
- iMarkerlab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang, China
- Center for Infectious Disease Research, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Zhongjun Li
- Laboratory Medicine Center, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Tiannan Guo
- iMarkerlab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang, China
- Center for Infectious Disease Research, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Shiming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
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9
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Metzdorf K, Jacobsen H, Kim Y, Teixeira Alves LG, Kulkarni U, Eschke K, Chaudhry MZ, Hoffmann M, Bertoglio F, Ruschig M, Hust M, Cokarić Brdovčak M, Materljan J, Šustić M, Krmpotić A, Jonjić S, Widera M, Ciesek S, Pöhlmann S, Landthaler M, Čičin-Šain L. A single-dose MCMV-based vaccine elicits long-lasting immune protection in mice against distinct SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2022.11.25.517953. [PMID: 36482969 PMCID: PMC9727759 DOI: 10.1101/2022.11.25.517953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Current vaccines against COVID-19 elicit immune responses that are overall strong but wane rapidly. As a consequence, the necessary booster shots have led to vaccine fatigue. Hence, vaccines that would provide lasting protection against COVID-19 are needed, but are still unavailable. Cytomegaloviruses (CMV) elicit lasting and uniquely strong immune responses. Used as vaccine vectors, they may be attractive tools that obviate the need for boosters. Therefore, we tested the murine CMV (MCMV) as a vaccine vector against COVID-19 in relevant preclinical models of immunization and challenge. We have previously developed a recombinant murine CMV (MCMV) vaccine vector expressing the spike protein of the ancestral SARS-CoV-2 (MCMVS). In this study, we show that the MCMVS elicits a robust and lasting protection in young and aged mice. Notably, S-specific humoral and cellular immunity was not only maintained but even increased over a period of at least 6 months. During that time, antibody avidity continuously increased and expanded in breadth, resulting in neutralization of genetically distant variants, like Omicron BA.1. A single dose of MCMVS conferred rapid virus clearance upon challenge. Moreover, MCMVS vaccination controlled two immune-evading variants of concern (VoCs), the Beta (B.1.135) and the Omicron (BA.1) variants. Thus, CMV vectors provide unique advantages over other vaccine technologies, eliciting broadly reactive and long-lasting immune responses against COVID-19.
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Affiliation(s)
- Kristin Metzdorf
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Henning Jacobsen
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yeonsu Kim
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Luiz Gustavo Teixeira Alves
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Upasana Kulkarni
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kathrin Eschke
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - M. Zeeshan Chaudhry
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Federico Bertoglio
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maximilian Ruschig
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Department of Medical Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Jelena Materljan
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
- Department of Histology and Embryology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Marko Šustić
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Astrid Krmpotić
- Department of Histology and Embryology, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Stipan Jonjić
- Center for Proteomics, University of Rijeka, Faculty of Medicine, Rijeka, Croatia
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany
- German Centre for Infection Research (DZIF), External partner site Frankfurt, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine (CiiM), a joint venture of HZI and MHH, Hannover, Germany
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10
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Zadeh SMM, Bayat AA, Shahsavarani H, Karimi-Busheri F, Kiani J, Ghods R, Madjd Z. Novel neutralizing SARS-CoV-2-specific mAbs offer detection of RBD linear epitopes. Virol J 2024; 21:37. [PMID: 38317249 PMCID: PMC10845636 DOI: 10.1186/s12985-024-02304-2] [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: 08/17/2023] [Accepted: 01/26/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND To stop the spread of the COVID-19 disease, it is crucial to create molecular tools to investigate and diagnose COVID-19. Current efforts focus on developing specific neutralizing monoclonal antibodies (NmAbs) elicited against the receptor-binding domain (RBD). METHODS In the present study, recombinant RBD (rRBD) protein was produced in E. coli, followed by immunizing mice with purified rRBD. ELISA was applied to screen the hybridomas for positive reactivity with rRBD protein. The linear and conformational epitopes of the mAbs were subsequently identified using western blot. Finally, the reactivity, affinity, and neutralization activity of the purified mAbs were evaluated using ELISA. RESULTS All mAbs exhibited similar reactivity trends towards both eukaryotic RBD and prokaryotic rRBD in ELISA. Among them, 2E7-D2 and 2B4-G8 mAbs demonstrated higher reactivity than other mAbs. Additionally, in western blot assays, these two mAbs could detect reducing and non-reducing rRBD, indicating recognition of linear epitopes. Notably, five mAbs effectively blocked rRBD- angiotensin-converting enzyme 2 (ACE2) interaction, while two high-affinity mAbs exhibited potent neutralizing activity against eukaryotic RBD. CONCLUSION In the current study, we generated and characterized new RBD-specific mAbs using the hybridoma technique that recognized linear and conformational epitopes in RBD with neutralization potency. Our mAbs are novel candidates for diagnosing and treating SARS-CoV-2.
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Affiliation(s)
- Seyed Mostafa Mostafavi Zadeh
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Ahmad Bayat
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Hosein Shahsavarani
- Laboratory of Regenerative Medicine and Biomedical Innovations, Pasteur Institute of Iran, National Cell Bank, Tehran, Iran
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Feridoun Karimi-Busheri
- Department of Oncology, Faculty of Medicine, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Jafar Kiani
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Roya Ghods
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Zahra Madjd
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
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11
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Acar DD, Witkowski W, Wejda M, Wei R, Desmet T, Schepens B, De Cae S, Sedeyn K, Eeckhaut H, Fijalkowska D, Roose K, Vanmarcke S, Poupon A, Jochmans D, Zhang X, Abdelnabi R, Foo CS, Weynand B, Reiter D, Callewaert N, Remaut H, Neyts J, Saelens X, Gerlo S, Vandekerckhove L. Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted. EBioMedicine 2024; 100:104960. [PMID: 38232633 PMCID: PMC10803917 DOI: 10.1016/j.ebiom.2023.104960] [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: 05/01/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND SARS-CoV-2-neutralizing antibodies (nABs) showed great promise in the early phases of the COVID-19 pandemic. The emergence of resistant strains, however, quickly rendered the majority of clinically approved nABs ineffective. This underscored the imperative to develop nAB cocktails targeting non-overlapping epitopes. METHODS Undertaking a nAB discovery program, we employed a classical workflow, while integrating artificial intelligence (AI)-based prediction to select non-competing nABs very early in the pipeline. We identified and in vivo validated (in female Syrian hamsters) two highly potent nABs. FINDINGS Despite the promising results, in depth cryo-EM structural analysis demonstrated that the AI-based prediction employed with the intention to ensure non-overlapping epitopes was inaccurate. The two nABs in fact bound to the same receptor-binding epitope in a remarkably similar manner. INTERPRETATION Our findings indicate that, even in the Alphafold era, AI-based predictions of paratope-epitope interactions are rough and experimental validation of epitopes remains an essential cornerstone of a successful nAB lead selection. FUNDING Full list of funders is provided at the end of the manuscript.
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Affiliation(s)
- Delphine Diana Acar
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Wojciech Witkowski
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Magdalena Wejda
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Ruifang Wei
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Tim Desmet
- Department of Basic and Applied Medical Sciences, Ghent University, Ghent 9000, Belgium
| | - Bert Schepens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sieglinde De Cae
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Hannah Eeckhaut
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Daria Fijalkowska
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Kenny Roose
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sandrine Vanmarcke
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | | | - Dirk Jochmans
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Xin Zhang
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Rana Abdelnabi
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Caroline S Foo
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven 3000, Belgium
| | - Dirk Reiter
- Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Nico Callewaert
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Han Remaut
- Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels 1050, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels 1050, Belgium
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sarah Gerlo
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent 9000, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium.
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12
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Kim SE, Park SH, Park WJ, Kim G, Kim SY, Won H, Hwang YH, Lim H, Kim HG, Kim YJ, Kim D, Lee JA. Evaluation of immunogenicity-induced DNA vaccines against different SARS-CoV-2 variants. PLoS One 2023; 18:e0295594. [PMID: 38060612 PMCID: PMC10703263 DOI: 10.1371/journal.pone.0295594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 and caused the coronavirus disease 2019 (COVID-19) pandemic worldwide. As of September 2023, the number of confirmed coronavirus cases has reached over 770 million and caused nearly 7 million deaths. The World Health Organization assigned and informed the characterization of variants of concern (VOCs) to help control the COVID-19 pandemic through global monitoring of circulating viruses. Although many vaccines have been proposed, developing an effective vaccine against variants is still essential to reach the endemic stage of COVID-19. We designed five DNA vaccine candidates composed of the first isolated genotype and major SARS-CoV-2 strains from isolated Korean patients classified as VOCs, such as Alpha, Beta, Gamma, and Delta. To evaluate the immunogenicity of each genotype via homologous and heterologous vaccination, mice were immunized twice within a 3-week interval, and the blood and spleen were collected 1 week after the final vaccination to analyze the immune responses. The group vaccinated with DNA vaccine candidates based on the S genotype and the Alpha and Beta variants elicited both humoral and cellular immune responses, with higher total IgG levels and neutralizing antibody responses than the other groups. In particular, the vaccine candidate based on the Alpha variant induced a highly diverse cytokine response. Additionally, we found that the group subjected to homologous vaccination with the S genotype and heterologous vaccination with S/Alpha induced high total IgG levels and a neutralization antibody response. Homologous vaccination with the S genotype and heterologous vaccination with S/Alpha and S/Beta significantly induced IFN-γ immune responses. The immunogenicity after homologous vaccination with S and Alpha and heterologous vaccination with the S/Alpha candidate was better than that of the other groups, indicating the potential for developing novel DNA vaccines against different SARS-CoV-2 variants.
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Affiliation(s)
- Se Eun Kim
- National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - So Hee Park
- National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Woo-Jung Park
- National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Gayeong Kim
- National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Seo Yeon Kim
- National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Hyeran Won
- National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Yun-Ho Hwang
- National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Heeji Lim
- National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Hyeon Guk Kim
- National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - You-Jin Kim
- National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Dokeun Kim
- National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Jung-Ah Lee
- National Institute of Infectious Disease, National Institute of Health, Korea Disease Control and Prevention Agency, CheongJu, Chungcheongbuk-do, Republic of Korea
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13
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Abassi L, Bertoglio F, Mačak Šafranko Ž, Schirrmann T, Greweling-Pils M, Seifert O, Khan F, Katzmarzyk M, Jacobsen H, Gödecke N, Heine PA, Frenzel A, Nowack H, Dübel S, Kurolt IC, Kontermann RE, Markotić A, Schubert M, Hust M, Čičin-Šain L. Evaluation of the Neutralizing Antibody STE90-C11 against SARS-CoV-2 Delta Infection and Its Recognition of Other Variants of Concerns. Viruses 2023; 15:2153. [PMID: 38005829 PMCID: PMC10675157 DOI: 10.3390/v15112153] [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: 09/23/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 11/26/2023] Open
Abstract
As of now, the COVID-19 pandemic has spread to over 770 million confirmed cases and caused approximately 7 million deaths. While several vaccines and monoclonal antibodies (mAb) have been developed and deployed, natural selection against immune recognition of viral antigens by antibodies has fueled the evolution of new emerging variants and limited the immune protection by vaccines and mAb. To optimize the efficiency of mAb, it is imperative to understand how they neutralize the variants of concern (VoCs) and to investigate the mutations responsible for immune escape. In this study, we show the in vitro neutralizing effects of a previously described monoclonal antibody (STE90-C11) against the SARS-CoV-2 Delta variant (B.1.617.2) and its in vivo effects in therapeutic and prophylactic settings. We also show that the Omicron variant avoids recognition by this mAb. To define which mutations are responsible for the escape in the Omicron variant, we used a library of pseudovirus mutants carrying each of the mutations present in the Omicron VoC individually. We show that either 501Y or 417K point mutations were sufficient for the escape of Omicron recognition by STE90-C11. To test how escape mutations act against a combination of antibodies, we tested the same library against bispecific antibodies, recognizing two discrete regions of the spike antigen. While Omicron escaped the control by the bispecific antibodies, the same antibodies controlled all mutants with individual mutations.
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Affiliation(s)
- Leila Abassi
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (L.A.); (F.K.); (M.K.); (H.J.); (N.G.)
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany; (F.B.); (P.A.H.); (S.D.); (M.S.); (M.H.)
| | - Željka Mačak Šafranko
- Research Department, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, 10000 Zagreb, Croatia; (Ž.M.Š.); (I.-C.K.); (A.M.)
| | - Thomas Schirrmann
- YUMAB GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany; (T.S.); (A.F.)
| | - Marina Greweling-Pils
- Core Facility of Comparative Medicine, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Oliver Seifert
- Institute of Cell Biology and Immunology, University of Stuttgart, 70174 Stuttgart, Germany; (O.S.); (H.N.); (R.E.K.)
| | - Fawad Khan
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (L.A.); (F.K.); (M.K.); (H.J.); (N.G.)
| | - Maeva Katzmarzyk
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (L.A.); (F.K.); (M.K.); (H.J.); (N.G.)
| | - Henning Jacobsen
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (L.A.); (F.K.); (M.K.); (H.J.); (N.G.)
| | - Natascha Gödecke
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (L.A.); (F.K.); (M.K.); (H.J.); (N.G.)
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany; (F.B.); (P.A.H.); (S.D.); (M.S.); (M.H.)
| | - André Frenzel
- YUMAB GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany; (T.S.); (A.F.)
| | - Helena Nowack
- Institute of Cell Biology and Immunology, University of Stuttgart, 70174 Stuttgart, Germany; (O.S.); (H.N.); (R.E.K.)
| | - Stefan Dübel
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany; (F.B.); (P.A.H.); (S.D.); (M.S.); (M.H.)
| | - Ivan-Christian Kurolt
- Research Department, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, 10000 Zagreb, Croatia; (Ž.M.Š.); (I.-C.K.); (A.M.)
| | - Roland E. Kontermann
- Institute of Cell Biology and Immunology, University of Stuttgart, 70174 Stuttgart, Germany; (O.S.); (H.N.); (R.E.K.)
| | - Alemka Markotić
- Research Department, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, 10000 Zagreb, Croatia; (Ž.M.Š.); (I.-C.K.); (A.M.)
- School of Medicine, Catholic University of Croatia, 10000 Zagreb, Croatia
- Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany; (F.B.); (P.A.H.); (S.D.); (M.S.); (M.H.)
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany; (F.B.); (P.A.H.); (S.D.); (M.S.); (M.H.)
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (L.A.); (F.K.); (M.K.); (H.J.); (N.G.)
- Centre for Individualized Infection Medicine, a Joint Venture of HZI and MHH, 31625 Hannover, Germany
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14
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Liang Z, Lu X, Jiao X, He Y, Meng B, Xie J, Qu Z, Zhu M, Gong X, Zhao Y, Peng T, Fang X, Dai X. Traceable value of immunoglobulin G against receptor-binding domain of SARS-CoV-2 confirmation and application to point-of-care testing system development. Mikrochim Acta 2023; 190:417. [PMID: 37768390 DOI: 10.1007/s00604-023-06004-6] [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: 04/22/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
A highly purified and bioactive immunoglobulin G monoclonal antibody against receptor-binding domain of SARS-CoV-2 (RBD-IgG-MAb) has been accurately quantified by amino acid determination using isotope dilution liquid chromatography-mass spectrometry. Absolute quantification of RBD-IgG-MAb was achieved by averaging 4 amino acid certified reference materials, which allows the quantitative value (66.1 ± 5.8 μg/L) to be traced to SI unit (mol). Afterwards, the RBD-IgG-MAb was employed as control and calibration compound for the development of a point-of-care testing (POCT) system based on colloidal gold lateral flow immunoassay, which aimed to rapidly and accurately detect the level of protective RBD-IgG after vaccination. Under the detection parameters, a sigmoidal curve has been plotted between signal intensity and the logarithmic concentration for quantitative detection with the limit of detection of about 0.39 μg/mL. The relative standard deviations of intra-assay and inter-assay were lower than 2.3% and 14%, and the recoveries ranged from 87 to 100%, respectively. Fingertip blood samples from 37 volunteers after vaccination were analyzed by the POCT system; results showed that levels of RBD-IgG in 33 out of 37 samples ranged from 0.45 to 2.46 μg/mL with the average level of 0.91 μg/mL. The developed POCT system has been successfully established with the quantity-traceability RBD-IgG-MAb as control and calibration compound, and the scientific contribution of this work can be promoted to other areas.
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Affiliation(s)
- Zhanwei Liang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, People's Republic of China
| | - Xin Lu
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, People's Republic of China
| | - Xueshima Jiao
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, People's Republic of China
| | - Yi He
- Novoprotein Scientific Incorporation, Suzhou, 215200, People's Republic of China
| | - Bo Meng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, People's Republic of China
| | - Jie Xie
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, People's Republic of China
| | - Ziyu Qu
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, People's Republic of China
| | - Manman Zhu
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, People's Republic of China
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, People's Republic of China
| | - Yang Zhao
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, People's Republic of China
| | - Tao Peng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, People's Republic of China.
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, People's Republic of China.
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, People's Republic of China.
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15
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Williams AH, Zhan CG. Staying Ahead of the Game: How SARS-CoV-2 has Accelerated the Application of Machine Learning in Pandemic Management. BioDrugs 2023; 37:649-674. [PMID: 37464099 DOI: 10.1007/s40259-023-00611-8] [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: 05/28/2023] [Indexed: 07/20/2023]
Abstract
In recent years, machine learning (ML) techniques have garnered considerable interest for their potential use in accelerating the rate of drug discovery. With the emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the utilization of ML has become even more crucial in the search for effective antiviral medications. The pandemic has presented the scientific community with a unique challenge, and the rapid identification of potential treatments has become an urgent priority. Researchers have been able to accelerate the process of identifying drug candidates, repurposing existing drugs, and designing new compounds with desirable properties using machine learning in drug discovery. To train predictive models, ML techniques in drug discovery rely on the analysis of large datasets, including both experimental and clinical data. These models can be used to predict the biological activities, potential side effects, and interactions with specific target proteins of drug candidates. This strategy has proven to be an effective method for identifying potential coronavirus disease 2019 (COVID-19) and other disease treatments. This paper offers a thorough analysis of the various ML techniques implemented to combat COVID-19, including supervised and unsupervised learning, deep learning, and natural language processing. The paper discusses the impact of these techniques on pandemic drug development, including the identification of potential treatments, the understanding of the disease mechanism, and the creation of effective and safe therapeutics. The lessons learned can be applied to future outbreaks and drug discovery initiatives.
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Affiliation(s)
- Alexander H Williams
- Molecular Modeling and Biopharmaceutical Center, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536, USA
- GSK Upper Providence, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Chang-Guo Zhan
- Molecular Modeling and Biopharmaceutical Center, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536, USA.
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536, USA.
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16
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Chia WN, Tan CW, Tan AWK, Young B, Starr TN, Lopez E, Fibriansah G, Barr J, Cheng S, Yeoh AYY, Yap WC, Lim BL, Ng TS, Sia WR, Zhu F, Chen S, Zhang J, Kwek MSS, Greaney AJ, Chen M, Au GG, Paradkar PN, Peiris M, Chung AW, Bloom JD, Lye D, Lok S, Wang LF. Potent pan huACE2-dependent sarbecovirus neutralizing monoclonal antibodies isolated from a BNT162b2-vaccinated SARS survivor. SCIENCE ADVANCES 2023; 9:eade3470. [PMID: 37494438 PMCID: PMC10371021 DOI: 10.1126/sciadv.ade3470] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern such as Omicron hampered efforts in controlling the ongoing coronavirus disease 2019 pandemic due to their ability to escape neutralizing antibodies induced by vaccination or prior infection, highlighting the need to develop broad-spectrum vaccines and therapeutics. Most human monoclonal antibodies (mAbs) reported to date have not demonstrated true pan-sarbecovirus neutralizing breadth especially against animal sarbecoviruses. Here, we report the isolation and characterization of highly potent mAbs targeting the receptor binding domain (RBD) of huACE2-dependent sarbecovirus from a SARS-CoV survivor vaccinated with BNT162b2. Among the six mAbs identified, one (E7) showed better huACE2-dependent sarbecovirus neutralizing potency and breadth than any other mAbs reported to date. Mutagenesis and cryo-electron microscopy studies indicate that these mAbs have a unique RBD contact footprint and that E7 binds to a quaternary structure-dependent epitope.
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Affiliation(s)
- Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Aaron Wai Kit Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Barnaby Young
- National Center of Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Ester Lopez
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Guntur Fibriansah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Jennifer Barr
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Samuel Cheng
- School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Aileen Ying-Yan Yeoh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Wee Chee Yap
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Beng Lee Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Thiam-Seng Ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Wan Rong Sia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Shiwei Chen
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Jinyan Zhang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Madeline Sheng Si Kwek
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA, USA
| | - Mark Chen
- National Center of Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Gough G. Au
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Prasad N. Paradkar
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong, China
- Centre for Immunology & Infection, New Territories, Hong Kong, China
- HKU-Pasteur Research Pole, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Amy W. Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA, USA
| | - David Lye
- National Center of Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sheemei Lok
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore, Singapore
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17
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Giron CC, Laaksonen A, Barroso da Silva FL. Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies. J Biomol Struct Dyn 2023; 41:5707-5727. [PMID: 35815535 DOI: 10.1080/07391102.2022.2095305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/23/2022] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 remains a health threat with the continuous emergence of new variants. This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs). By using constant-pH Monte Carlo simulations, the free energy of interactions between the RBD from different variants and several partners (Angiotensin-Converting Enzyme-2 (ACE2) polymorphisms and various mAbs) were predicted. Computed RBD-ACE2-binding affinities were higher for two ACE2 polymorphisms (rs142984500 and rs4646116) typically found in Europeans which indicates a genetic susceptibility. This is amplified for Omicron (BA.1) and its sublineages BA.2 and BA.3. The antibody landscape was computationally investigated with the largest set of mAbs so far in the literature. From the 32 studied binders, groups of mAbs were identified from weak to strong binding affinities (e.g. S2K146). These mAbs with strong binding capacity and especially their combination are amenable to experimentation and clinical trials because of their high predicted binding affinities and possible neutralization potential for current known virus mutations and a universal coronavirus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Universidade Federal do Triângulo Mineiro, Hospital de Clínicas, Uberaba, MG, Brazil
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, PR China
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania
- Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, Luleå, Sweden
- Department of Chemical and Geological Sciences, University of Cagliari, Monserrato, Italy
| | - Fernando Luís Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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18
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Chung HY, Wickel J, Hahn N, Mein N, Schwarzbrunn M, Koch P, Ceanga M, Haselmann H, Baade-Büttner C, von Stackelberg N, Hempel N, Schmidl L, Groth M, Andreas N, Götze J, Coldewey SM, Bauer M, Mawrin C, Dargvainiene J, Leypoldt F, Steinke S, Wang ZQ, Hust M, Geis C. Microglia mediate neurocognitive deficits by eliminating C1q-tagged synapses in sepsis-associated encephalopathy. SCIENCE ADVANCES 2023; 9:eabq7806. [PMID: 37235660 DOI: 10.1126/sciadv.abq7806] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
Sepsis-associated encephalopathy (SAE) is a severe and frequent complication of sepsis causing delirium, coma, and long-term cognitive dysfunction. We identified microglia and C1q complement activation in hippocampal autopsy tissue of patients with sepsis and increased C1q-mediated synaptic pruning in a murine polymicrobial sepsis model. Unbiased transcriptomics of hippocampal tissue and isolated microglia derived from septic mice revealed an involvement of the innate immune system, complement activation, and up-regulation of lysosomal pathways during SAE in parallel to neuronal and synaptic damage. Microglial engulfment of C1q-tagged synapses could be prevented by stereotactic intrahippocampal injection of a specific C1q-blocking antibody. Pharmacologically targeting microglia by PLX5622, a CSF1-R inhibitor, reduced C1q levels and the number of C1q-tagged synapses, protected from neuronal damage and synapse loss, and improved neurocognitive outcome. Thus, we identified complement-dependent synaptic pruning by microglia as a crucial pathomechanism for the development of neuronal defects during SAE.
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Affiliation(s)
- Ha-Yeun Chung
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena 07747, Germany
| | - Jonathan Wickel
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena 07747, Germany
| | - Nina Hahn
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena 07747, Germany
| | - Nils Mein
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Meike Schwarzbrunn
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Philipp Koch
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena 07745, Germany
| | - Mihai Ceanga
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Holger Haselmann
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Carolin Baade-Büttner
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Nikolai von Stackelberg
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Nina Hempel
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Lars Schmidl
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
| | - Marco Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena 07745, Germany
| | - Nico Andreas
- Institute of Immunology, Jena University Hospital, Jena 07743, Germany
| | - Juliane Götze
- Department of Anaesthesiology and Intensive Care Medicine, Jena University Hospital, Jena 07747, Germany
- Septomics Research Center, Jena University Hospital, Jena 07745, Germany
| | - Sina M Coldewey
- Center for Sepsis Control and Care, Jena University Hospital, Jena 07747, Germany
- Department of Anaesthesiology and Intensive Care Medicine, Jena University Hospital, Jena 07747, Germany
- Septomics Research Center, Jena University Hospital, Jena 07745, Germany
| | - Michael Bauer
- Center for Sepsis Control and Care, Jena University Hospital, Jena 07747, Germany
- Department of Anaesthesiology and Intensive Care Medicine, Jena University Hospital, Jena 07747, Germany
| | - Christian Mawrin
- Department of Neuropathology, University of Magdeburg, Magdeburg, Germany
- Section of Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07749, Germany
| | | | - Frank Leypoldt
- Neuroimmunology, Institute of Clinical Chemistry, UKSH, Kiel/Lübeck, Germany
- Department of Neurology, Christian-Albrechts University, Kiel 24105, Germany
| | - Stephan Steinke
- Department Medical Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena 07745, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, Jena 07745, Germany
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Michael Hust
- Department Medical Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Christian Geis
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena 07747, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena 07747, Germany
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19
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Artificial intelligence-based HDX (AI-HDX) prediction reveals fundamental characteristics to protein dynamics: Mechanisms on SARS-CoV-2 immune escape. iScience 2023; 26:106282. [PMID: 36910327 PMCID: PMC9968663 DOI: 10.1016/j.isci.2023.106282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/10/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Three-dimensional structure and dynamics are essential for protein function. Advancements in hydrogen-deuterium exchange (HDX) techniques enable probing protein dynamic information in physiologically relevant conditions. HDX-coupled mass spectrometry (HDX-MS) has been broadly applied in pharmaceutical industries. However, it is challenging to obtain dynamics information at the single amino acid resolution and time consuming to perform the experiments and process the data. Here, we demonstrate the first deep learning model, artificial intelligence-based HDX (AI-HDX), that predicts intrinsic protein dynamics based on the protein sequence. It uncovers the protein structural dynamics by combining deep learning, experimental HDX, sequence alignment, and protein structure prediction. AI-HDX can be broadly applied to drug discovery, protein engineering, and biomedical studies. As a demonstration, we elucidated receptor-binding domain structural dynamics as a potential mechanism of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody efficacy and immune escape. AI-HDX fundamentally differs from the current AI tools for protein analysis and may transform protein design for various applications.
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20
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Development of an inhibiting antibody against equine interleukin 5 to treat insect bite hypersensitivity of horses. Sci Rep 2023; 13:4029. [PMID: 36899044 PMCID: PMC10000358 DOI: 10.1038/s41598-023-31173-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Insect bite hypersensitivity (IBH) is the most common allergic skin disease of horses. It is caused by insect bites of the Culicoides spp. which mediate a type I/IVb allergy with strong involvement of eosinophil cells. No specific treatment option is available so far. One concept could be the use of a therapeutic antibody targeting equine interleukin 5, the main activator and regulator of eosinophils. Therefore, antibodies were selected by phage display using the naïve human antibody gene libraries HAL9/10, tested in a cellular in vitro inhibition assay and subjected to an in vitro affinity maturation. In total, 28 antibodies were selected by phage display out of which eleven have been found to be inhibiting in the final format as chimeric immunoglobulin G with equine constant domains. The two most promising candidates were further improved by in vitro affinity maturation up to factor 2.5 regarding their binding activity and up to factor 2.0 regarding their inhibition effect. The final antibody named NOL226-2-D10 showed a strong inhibition of the interleukin 5 binding to its receptor (IC50 = 4 nM). Furthermore, a nanomolar binding activity (EC50 = 8.8 nM), stable behavior and satisfactory producibility were demonstrated. This antibody is an excellent candidate for in vivo studies for the treatment of equine IBH.
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21
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Langreder N, Schäckermann D, Unkauf T, Schubert M, Frenzel A, Bertoglio F, Hust M. Antibody Affinity and Stability Maturation by Error-Prone PCR. Methods Mol Biol 2023; 2702:395-410. [PMID: 37679631 DOI: 10.1007/978-1-0716-3381-6_20] [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: 09/09/2023]
Abstract
Human antibodies are the most important class of biologicals, and antibodies - human and nonhuman - are indispensable as research agents and for diagnostic assays. When generating antibodies, they sometimes show the desired specificity profile but lack sufficient affinity for the desired application. In this article, a phage display-based method and protocol to increase the affinity of recombinant antibody fragments is given.The given protocol starts with the construction of a mutated antibody gene library by error-prone PCR. Subsequently, the selection of high-affinity variants is performed by panning on immobilized antigen with washing conditions optimized for off-rate-dependent selection. A screening ELISA protocol to identify antibodies with improved affinity and an additional protocol to select antibodies with improved thermal stability is described.
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Affiliation(s)
- Nora Langreder
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dorina Schäckermann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Wirtschaftsgenossenschaft deutscher Tierärzte eG (WDT), Garbsen, Germany
| | - Tobias Unkauf
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Bayer Consumer Care AG, Basel, Switzerland
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - André Frenzel
- YUMAB GmbH, Science Campus Braunschweig-Süd, Braunschweig, Germany
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Choose Life Biotech SA, Bellinzona, Switzerland
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany.
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22
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Zekri L, Ruetalo N, Christie M, Walker C, Manz T, Rammensee HG, Salih HR, Schindler M, Jung G. Novel ACE2 fusion protein with adapting activity against SARS-CoV-2 variants in vitro. Front Immunol 2023; 14:1112505. [PMID: 36969164 PMCID: PMC10030959 DOI: 10.3389/fimmu.2023.1112505] [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: 11/30/2022] [Accepted: 02/22/2023] [Indexed: 03/29/2023] Open
Abstract
Despite the successful development of vaccines and neutralizing antibodies to limit the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerging variants prolong the pandemic and emphasize the persistent need to develop effective antiviral treatment regimens. Recombinant antibodies directed to the original SARS-CoV-2 have been successfully used to treat established viral disease. However, emerging viral variants escape the recognition by those antibodies. Here we report the engineering of an optimized ACE2 fusion protein, designated ACE2-M, which comprises a human IgG1 Fc domain with abrogated Fc-receptor binding linked to a catalytically-inactive ACE2 extracellular domain that displays increased apparent affinity to the B.1 spike protein. The affinity and neutralization capacity of ACE2-M is unaffected or even enhanced by mutations present in the spike protein of viral variants. In contrast, a recombinant neutralizing reference antibody, as well as antibodies present in the sera of vaccinated individuals, lose activity against such variants. With its potential to resist viral immune escape ACE2-M appears to be particularly valuable in the context of pandemic preparedness towards newly emerging coronaviruses.
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Affiliation(s)
- Latifa Zekri
- Department of Immunology, Institute for Cell Biology, Eberhard Karls Universität Tübingen, Tübingen, Germany
- German Cancer Research Center (DKFZ) Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- *Correspondence: Latifa Zekri,
| | - Natalia Ruetalo
- Institute for Medical Virology and Epidemiology, University Hospital Tübingen, Tübingen, Germany
| | - Mary Christie
- School of Life and Environmental Sciences and School of Life of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Carolin Walker
- Department of Immunology, Institute for Cell Biology, Eberhard Karls Universität Tübingen, Tübingen, Germany
- German Cancer Research Center (DKFZ) Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Timo Manz
- Department of Immunology, Institute for Cell Biology, Eberhard Karls Universität Tübingen, Tübingen, Germany
- German Cancer Research Center (DKFZ) Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, Eberhard Karls Universität Tübingen, Tübingen, Germany
- German Cancer Research Center (DKFZ) Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Helmut R. Salih
- German Cancer Research Center (DKFZ) Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology, University Hospital Tübingen, Tübingen, Germany
| | - Gundram Jung
- Department of Immunology, Institute for Cell Biology, Eberhard Karls Universität Tübingen, Tübingen, Germany
- German Cancer Research Center (DKFZ) Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
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23
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Steinke S, Roth KDR, Englick R, Langreder N, Ballmann R, Fühner V, Zilkens KJK, Moreira GMSG, Koch A, Azzali F, Russo G, Schubert M, Bertoglio F, Heine PA, Hust M. Mapping Epitopes by Phage Display. Methods Mol Biol 2023; 2702:563-585. [PMID: 37679639 DOI: 10.1007/978-1-0716-3381-6_28] [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: 09/09/2023]
Abstract
Monoclonal antibodies (mAbs) are valuable biological molecules, serving for many applications. Therefore, it is advantageous to know the interaction pattern between antibodies and their antigens. Regions on the antigen which are recognized by the antibodies are called epitopes, and the respective molecular counterpart of the epitope on the mAbs is called paratope. These epitopes can have many different compositions and/or structures. Knowing the epitope is a valuable information for the development or improvement of biological products, e.g., diagnostic assays, therapeutic mAbs, and vaccines, as well as for the elucidation of immune responses. Most of the techniques for epitope mapping rely on the presentation of the target, or parts of it, in a way that it can interact with a certain mAb. Among the techniques used for epitope mapping, phage display is a versatile technology that allows the display of a library of oligopeptides or fragments from a single gene product on the phage surface, which then can interact with several antibodies to define epitopes. In this chapter, a protocol for the construction of a single-target oligopeptide phage library, as well as for the panning procedure for epitope mapping using phage display is given.
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Affiliation(s)
- Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kristian Daniel Ralph Roth
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ruben Englick
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nora Langreder
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rico Ballmann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Viola Fühner
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Gustavo Marçal Schmidt Garcia Moreira
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Sector for Antibody and Protein Biochemistry, Tacalyx GmbH, Berlin, Germany
| | - Allan Koch
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Innovationszentrum Niedersachsen GmbH, startup.niedersachsen, Hannover, Germany
| | - Filippo Azzali
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Giulio Russo
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Choose Life Biotech SA, Bellinzona, Switzerland
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany.
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24
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Antunes A, Alvarez-Vallina L, Bertoglio F, Bouquin N, Cornen S, Duffieux F, Ferré P, Gillet R, Jorgensen C, Leick MB, Maillère B, Negre H, Pelegrin M, Poirier N, Reusch D, Robert B, Serre G, Vicari A, Villalba M, Volpers C, Vuddamalay G, Watier H, Wurch T, Zabeau L, Zielonka S, Zhang B, Beck A, Martineau P. 10th antibody industrial symposium: new developments in antibody and adoptive cell therapies. MAbs 2023; 15:2211692. [PMID: 37184206 DOI: 10.1080/19420862.2023.2211692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
The annual "Antibody Industrial Symposium", co-organized by LabEx MAbImprove and MabDesign, held its 10th anniversary edition in Montpellier, France, on June 28-29, 2022. The meeting focused on new results and concepts in antibody engineering (naked, mono- or multi-specific, conjugated to drugs or radioelements) and also on new cell-based therapies, such as chimeric antigenic receptor (CAR)-T cells. The symposium, which brought together scientists from academia and industry, also addressed issues concerning the production of these molecules and cells, and the necessary steps to ensure a strong intellectual property protection of these new molecules and approaches. These two days of exchanges allowed a rich discussion among the various actors in the field of therapeutic antibodies.
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Affiliation(s)
| | - Luis Alvarez-Vallina
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- H120-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Federico Bertoglio
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Braunschweig, Germany, Current address
| | | | | | | | | | | | - Christian Jorgensen
- IRMB, université de Montpellier, Inserm U1183, Montpellier, France
- Unité d'immunologie clinique et de thérapeutique des maladies ostéoarticulaires, département de rhumatologie, hôpital Lapeyronie, Montpellier, France
| | - Mark B Leick
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Bernard Maillère
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Hélène Negre
- Institut de Recherches Internationales Servier, Suresnes, France
| | | | | | - Dietmar Reusch
- Pharma Technical Development Analytics Biologics, Roche Diagnostics GmbH, Penzberg, Germany
| | - Bruno Robert
- IRCM, INSERM, U1194 Univ Montpellier, ICM, 208, rue des Apothicaires, Montpellier, France
| | - Guy Serre
- Institut Toulousain des maladies infectieuses et inflammatoires - INFINITY- Inserm, CNRS, Université Toulouse III, Toulouse, France
| | - Alain Vicari
- Calypso Biotech SA, Plan-les-Ouates, Switzerland
| | | | | | | | - Hervé Watier
- CEPR, INSERM U1100 Université de Tours, et CHU de Tours, Tours cedex, France
| | | | | | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Baolin Zhang
- Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Alain Beck
- Biologics CMC & Developability, Institut de Recherche Pierre Fabre, St Julien-en-Genevois Cedex, France
| | - Pierre Martineau
- IRCM, INSERM, U1194 Univ Montpellier, ICM, 208, rue des Apothicaires, Montpellier, France
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25
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Ballmann R, Schneider KT, Roth KDR, Dübel S. Antibody Batch Cloning. Methods Mol Biol 2023; 2702:411-417. [PMID: 37679632 DOI: 10.1007/978-1-0716-3381-6_21] [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: 09/09/2023]
Abstract
The antigen-binding ability of each antibody clone selected by phage display is usually initially ranked by a screening ELISA using monovalent scFv antibody fragments. Further characterization often requires bivalent antibody molecules such as IgG or scFv-Fc fusions. To produce these, the V region encoding genes of selected hits have to be cloned into a mammalian expression vector and analyzed as a bivalent molecule, requiring a laborious cloning procedure. We established a high-throughput procedure allowing rapid screening of candidates in bivalent formats. This protocol allows for the parallelized cloning of all selected antibody fragments into a mammalian expression vector in the 96-well plate format. The bivalent antibody molecules can then be produced and purified in 96-well plates for further analysis in microtiter plate assays.
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Affiliation(s)
- Rico Ballmann
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Braunschweig, Germany
| | - Kai-Thomas Schneider
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Braunschweig, Germany
| | - Kristian Daniel Ralph Roth
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Braunschweig, Germany
| | - Stefan Dübel
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Braunschweig, Germany.
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26
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Steinke S, Roth KDR, Ruschig M, Langreder N, Polten S, Schneider KT, Ballmann R, Russo G, Zilkens KJK, Schubert M, Bertoglio F, Hust M. Antibody Selection via Phage Display in Microtiter Plates. Methods Mol Biol 2023; 2702:247-260. [PMID: 37679623 DOI: 10.1007/978-1-0716-3381-6_12] [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: 09/09/2023]
Abstract
The most common and robust in vitro technology to generate monoclonal human antibodies is phage display. This technology is a widely used and powerful key technology for recombinant antibody selection. Phage display-derived antibodies are used as research tools, in diagnostic assays, and by 2022, 14 phage display-derived therapeutic antibodies were approved. In this review, we describe a fast high-throughput antibody (scFv) selection procedure in 96-well microtiter plates. The given detailed protocol allows the antibody selection ("panning"), screening, and identification of monoclonal antibodies in less than 2 weeks. Furthermore, we describe an on-rate panning approach for the selection of monoclonal antibodies with fast on-rates.
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Affiliation(s)
- Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kristian Daniel Ralph Roth
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maximilian Ruschig
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nora Langreder
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Saskia Polten
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kai-Thomas Schneider
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rico Ballmann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Giulio Russo
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Choose Life Biotech SA, Bellinzona, Switzerland
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany.
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27
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Ruschig M, Heine PA, Fühner V, Zilkens KJK, Steinke S, Schubert M, Bertoglio F, Hust M. Construction of Human Immune and Naive scFv Phage Display Libraries. Methods Mol Biol 2023; 2702:15-37. [PMID: 37679613 DOI: 10.1007/978-1-0716-3381-6_2] [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: 09/09/2023]
Abstract
Antibody phage display is a widely used in vitro selection technology for the generation of human recombinant antibodies and has yielded thousands of useful antibodies for research, diagnostics, and therapy. In order to successfully generate antibodies using phage display, the basis is the construction of high-quality antibody gene libraries. Here, we describe detailed methods for the construction of such high-quality immune and naive scFv gene libraries of human origin. These protocols were used to develop human naive (e.g., HAL9/10) and immune libraries, which resulted in thousands of specific antibodies for all kinds of applications.
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Affiliation(s)
- Maximilian Ruschig
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Viola Fühner
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Choose Life Biotech SA, Bellinzona, Switzerland
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany.
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28
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Conformational Dynamics of the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Biomedicines 2022; 10:biomedicines10123233. [PMID: 36551988 PMCID: PMC9775641 DOI: 10.3390/biomedicines10123233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/22/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Variants of SARS-CoV-2 keep emerging and causing new waves of COVID-19 around the world. Effective new approaches in drug development are based on the binding of agents, such as neutralizing monoclonal antibodies to a receptor-binding domain (RBD) of SARS-CoV-2 spike protein. However, mutations in RBD may lower the affinity of previously developed antibodies. Therefore, rapid analysis of new variants and selection of a binding partner with high affinity is of great therapeutic importance. Here, we explore a computational approach based on molecular dynamics simulations and conformational clusterization techniques for the wild-type and omicron variants of RBD. Biochemical experiments support the hypothesis of the presence of several conformational states within the RBD assembly. The development of such an approach will facilitate the selection of neutralization drugs with higher affinity based on the primary structure of the target antigen.
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29
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Liu Y, Arase H. Neutralizing and enhancing antibodies against SARS-CoV-2. Inflamm Regen 2022; 42:58. [PMID: 36471381 PMCID: PMC9720987 DOI: 10.1186/s41232-022-00233-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/30/2022] [Indexed: 12/12/2022] Open
Abstract
The high transmissibility and rapid global spread of SARS-CoV-2 since 2019 has led to a huge burden on healthcare worldwide. Anti-SARS-CoV-2 neutralizing antibodies play an important role in not only protecting against infection but also in clearing the virus and are essential to providing long-term immunity. On the other hand, antibodies against the virus are not always protective. With the emergence of SARS-CoV-2 immune escape variants, vaccine design strategies as well as antibody-mediated therapeutic approaches have become more important. We review some of the findings on SARS-CoV-2 antibodies, focusing on both basic research and clinical applications.
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Affiliation(s)
- Yafei Liu
- grid.136593.b0000 0004 0373 3971Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka, 565-0871 Japan
| | - Hisashi Arase
- grid.136593.b0000 0004 0373 3971Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka, 565-0871 Japan
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30
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Parray HA, Narayanan N, Garg S, Rizvi ZA, Shrivastava T, Kushwaha S, Singh J, Murugavelu P, Anantharaj A, Mehdi F, Raj N, Singh S, Dandotiya J, Lukose A, Jamwal D, Kumar S, Chiranjivi AK, Dhyani S, Mishra N, Kumar S, Jakhar K, Sonar S, Panchal AK, Tripathy MR, Chowdhury SR, Ahmed S, Samal S, Mani S, Bhattacharyya S, Das S, Sinha S, Luthra K, Batra G, Sehgal D, Medigeshi GR, Sharma C, Awasthi A, Garg PK, Nair DT, Kumar R. A broadly neutralizing monoclonal antibody overcomes the mutational landscape of emerging SARS-CoV-2 variants of concern. PLoS Pathog 2022; 18:e1010994. [PMID: 36508467 PMCID: PMC9779650 DOI: 10.1371/journal.ppat.1010994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/22/2022] [Accepted: 11/08/2022] [Indexed: 12/14/2022] Open
Abstract
The emergence of new variants of SARS-CoV-2 necessitates unremitting efforts to discover novel therapeutic monoclonal antibodies (mAbs). Here, we report an extremely potent mAb named P4A2 that can neutralize all the circulating variants of concern (VOCs) with high efficiency, including the highly transmissible Omicron. The crystal structure of the P4A2 Fab:RBD complex revealed that the residues of the RBD that interact with P4A2 are a part of the ACE2-receptor-binding motif and are not mutated in any of the VOCs. The pan coronavirus pseudotyped neutralization assay confirmed that the P4A2 mAb is specific for SARS-CoV-2 and its VOCs. Passive administration of P4A2 to K18-hACE2 transgenic mice conferred protection, both prophylactically and therapeutically, against challenge with VOCs. Overall, our data shows that, the P4A2 mAb has immense therapeutic potential to neutralize the current circulating VOCs. Due to the overlap between the P4A2 epitope and ACE2 binding site on spike-RBD, P4A2 may also be highly effective against a number of future variants.
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Affiliation(s)
- Hilal Ahmad Parray
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Naveen Narayanan
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sonal Garg
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Zaigham Abbas Rizvi
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Tripti Shrivastava
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sachin Kushwaha
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Janmejay Singh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Praveenkumar Murugavelu
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Anbalagan Anantharaj
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Farha Mehdi
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Nisha Raj
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Shivam Singh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Jyotsna Dandotiya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Asha Lukose
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Deepti Jamwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sandeep Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Adarsh K. Chiranjivi
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Samridhi Dhyani
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Nitesh Mishra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjeev Kumar
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Kamini Jakhar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sudipta Sonar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Anil Kumar Panchal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Manas Ranjan Tripathy
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Shirlie Roy Chowdhury
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Shubbir Ahmed
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sweety Samal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Shailendra Mani
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Supratik Das
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Subrata Sinha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Gaurav Batra
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Devinder Sehgal
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Guruprasad R. Medigeshi
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Chandresh Sharma
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Pramod Kumar Garg
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Deepak T. Nair
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Rajesh Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
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31
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Zhang X, Hong B, Wei P, Pei P, Xu H, Chen L, Tong Y, Chen J, Luo SZ, Fan H, He C. Pathogen-host adhesion between SARS-CoV-2 spike proteins from different variants and human ACE2 studied at single-molecule and single-cell levels. Emerg Microbes Infect 2022; 11:2658-2669. [PMID: 36153659 PMCID: PMC9639500 DOI: 10.1080/22221751.2022.2128887] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/21/2022] [Indexed: 11/03/2022]
Abstract
The binding of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein onto human angiotensin-converting enzyme 2 (ACE2) is considered as the first step for the virus to adhere onto the host cells during the infection. Here, we investigated the adhesion of spike proteins from different variants and ACE2 using single-molecule and single-cell force spectroscopy. We found that the unbinding force and binding probability of the spike protein from Delta variant to the ACE2 were the highest among the variants tested in our study at both single-molecule and single-cell levels. As the most popular variants, the Omicron variants have slightly higher unbinding force to the ACE2 than wild type. Molecular dynamics simulation showed that ACE2-RBD (Omicron BA.1) complex is destabilized by the E484A and Y505H mutations and stabilized by S477N and N501Y mutations, when compared with Delta variant. In addition, a neutralizing antibody, produced by immunization with wild type spike protein, could effectively inhibit the binding of spike proteins from wild type, Delta and Omicron variants (BA.1 and BA.5) onto ACE2. Our results provide new insight for the molecular mechanism of the adhesive interactions between spike protein and ACE2 and suggest that effective monoclonal antibody can be prepared using wild type spike protein against different variants.
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Affiliation(s)
- Xiaoxu Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Bixia Hong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Peng Wei
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Pengfei Pei
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Haifeng Xu
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Long Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Jialin Chen
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, People’s Republic of China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, People’s Republic of China
| | - Shi-Zhong Luo
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Huahao Fan
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Chengzhi He
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
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Focosi D, McConnell S, Casadevall A, Cappello E, Valdiserra G, Tuccori M. Monoclonal antibody therapies against SARS-CoV-2. THE LANCET. INFECTIOUS DISEASES 2022; 22:e311-e326. [PMID: 35803289 PMCID: PMC9255948 DOI: 10.1016/s1473-3099(22)00311-5] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 12/13/2022]
Abstract
Monoclonal antibodies (mAbs) targeting the spike protein of SARS-CoV-2 have been widely used in the ongoing COVID-19 pandemic. In this paper, we review the properties of mAbs and their effect as therapeutics in the pandemic, including structural classification, outcomes in clinical trials that led to the authorisation of mAbs, and baseline and treatment-emergent immune escape. We show how the omicron (B.1.1.529) variant of concern has reset treatment strategies so far, discuss future developments that could lead to improved outcomes, and report the intrinsic limitations of using mAbs as therapeutic agents.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Scott McConnell
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
| | - Arturo Casadevall
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
| | - Emiliano Cappello
- Unit of Adverse Drug Reactions Monitoring, Pisa University Hospital, Pisa, Italy; Unit of Pharmacology and Pharmacovigilance, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Giulia Valdiserra
- Unit of Adverse Drug Reactions Monitoring, Pisa University Hospital, Pisa, Italy; Unit of Pharmacology and Pharmacovigilance, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Marco Tuccori
- Unit of Pharmacology and Pharmacovigilance, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.
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Antoine D, Mohammadi M, McDermott CE, Walsh E, Johnson PA, Wawrousek KE, Wall JG. Isolation of SARS-CoV-2-blocking recombinant antibody fragments and characterisation of their binding to variant spike proteins. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2022.1028186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
COVID-19 is a severe acute respiratory disease caused by SARS-CoV-2. From its initial appearance in Wuhan, China in 2019, it developed rapidly into a global pandemic. In addition to vaccines, therapeutic antibodies play an important role in immediately treating susceptible individuals to lessen severity of the disease. In this study, phage display technology was utilised to isolate human scFv antibody fragments that bind the receptor-binding domain (RBD) of SARS-CoV-2 Wuhan-Hu-1 spike protein. Of eight RBD-binding scFvs isolated, two inhibited interaction of RBD with ACE2 protein on VeroE6 cells. Both scFvs also exhibited binding to SARS-CoV-2 Delta variant spike protein but not to Omicron variant spike protein in a Raman spectroscopy immunotest. The study demonstrates the potential of recombinant antibody approaches to rapidly isolate antibody moieties with virus neutralisation potential.
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Jaron M, Lehky M, Zarà M, Zaydowicz CN, Lak A, Ballmann R, Heine PA, Wenzel EV, Schneider KT, Bertoglio F, Kempter S, Köster RW, Barbieri SS, van den Heuvel J, Hust M, Dübel S, Schubert M. Baculovirus-Free SARS-CoV-2 Virus-like Particle Production in Insect Cells for Rapid Neutralization Assessment. Viruses 2022. [PMID: 36298643 DOI: 10.3390/v14102087/s1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Virus-like particles (VLPs) resemble authentic virus while not containing any genomic information. Here, we present a fast and powerful method for the production of SARS-CoV-2 VLP in insect cells and the application of these VLPs to evaluate the inhibition capacity of monoclonal antibodies and sera of vaccinated donors. Our method avoids the baculovirus-based approaches commonly used in insect cells by employing direct plasmid transfection to co-express SARS-CoV-2 envelope, membrane, and spike protein that self-assemble into VLPs. After optimization of the expression plasmids and vector ratios, VLPs with an ~145 nm diameter and the typical "Corona" aura were obtained, as confirmed by nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM). Fusion of the membrane protein to GFP allowed direct quantification of binding inhibition to angiotensin II-converting enzyme 2 (ACE2) on cells by therapeutic antibody candidates or sera from vaccinated individuals. Neither VLP purification nor fluorescent labeling by secondary antibodies are required to perform these flow cytometric assays.
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Affiliation(s)
- Marcel Jaron
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Michael Lehky
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Marta Zarà
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Chris Nicole Zaydowicz
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Aidin Lak
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering, Technische Universität Braunschweig, Hans-Sommer-Straße 66, 38106 Braunschweig, Germany
| | - Rico Ballmann
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Philip Alexander Heine
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | | | - Kai-Thomas Schneider
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Federico Bertoglio
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Susanne Kempter
- Department of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Reinhard Wolfgang Köster
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Silvia Stella Barbieri
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Joop van den Heuvel
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Stefan Dübel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Maren Schubert
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
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Jaron M, Lehky M, Zarà M, Zaydowicz CN, Lak A, Ballmann R, Heine PA, Wenzel EV, Schneider KT, Bertoglio F, Kempter S, Köster RW, Barbieri SS, van den Heuvel J, Hust M, Dübel S, Schubert M. Baculovirus-Free SARS-CoV-2 Virus-like Particle Production in Insect Cells for Rapid Neutralization Assessment. Viruses 2022; 14:v14102087. [PMID: 36298643 PMCID: PMC9606917 DOI: 10.3390/v14102087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/16/2022] Open
Abstract
Virus-like particles (VLPs) resemble authentic virus while not containing any genomic information. Here, we present a fast and powerful method for the production of SARS-CoV-2 VLP in insect cells and the application of these VLPs to evaluate the inhibition capacity of monoclonal antibodies and sera of vaccinated donors. Our method avoids the baculovirus-based approaches commonly used in insect cells by employing direct plasmid transfection to co-express SARS-CoV-2 envelope, membrane, and spike protein that self-assemble into VLPs. After optimization of the expression plasmids and vector ratios, VLPs with an ~145 nm diameter and the typical “Corona” aura were obtained, as confirmed by nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM). Fusion of the membrane protein to GFP allowed direct quantification of binding inhibition to angiotensin II-converting enzyme 2 (ACE2) on cells by therapeutic antibody candidates or sera from vaccinated individuals. Neither VLP purification nor fluorescent labeling by secondary antibodies are required to perform these flow cytometric assays.
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Affiliation(s)
- Marcel Jaron
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Michael Lehky
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Marta Zarà
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Chris Nicole Zaydowicz
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Aidin Lak
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering, Technische Universität Braunschweig, Hans-Sommer-Straße 66, 38106 Braunschweig, Germany
| | - Rico Ballmann
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Philip Alexander Heine
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | | | - Kai-Thomas Schneider
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Federico Bertoglio
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Susanne Kempter
- Department of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Reinhard Wolfgang Köster
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Silvia Stella Barbieri
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Joop van den Heuvel
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Stefan Dübel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Maren Schubert
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
- Correspondence:
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Shah M, Woo HG. The paradigm of immune escape by SARS-CoV-2 variants and strategies for repositioning subverted mAbs against escaped VOCs. Mol Ther 2022; 30:3101-3105. [PMID: 36087577 PMCID: PMC9462941 DOI: 10.1016/j.ymthe.2022.08.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
The perpetual emergence of SARS-CoV-2 variants is a serious issue that makes it difficult for the therapeutic antibodies and vaccines to end the COVID-19 pandemic. This article discusses the trend of increasing host fitness and immune escape by the virus and how to devise computational strategies for antibodies design and their affinity maturation against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Masaud Shah
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Hyun Goo Woo
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; Department of Biomedical Science, Graduate School, Ajou University, Suwon 16499, Republic of Korea.
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SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun 2022; 13:4696. [PMID: 35982054 PMCID: PMC9388680 DOI: 10.1038/s41467-022-32262-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 07/21/2022] [Indexed: 11/18/2022] Open
Abstract
Mutations in the spike glycoproteins of SARS-CoV-2 variants of concern have independently been shown to enhance aspects of spike protein fitness. Here, we describe an antibody fragment (VH ab6) that neutralizes all major variants including the recently emerged BA.1 and BA.2 Omicron subvariants, with a unique mode of binding revealed by cryo-EM studies. Further, we provide a comparative analysis of the mutational effects within previously emerged variant spikes and identify the structural role of mutations within the NTD and RBD in evading antibody neutralization. Our analysis shows that the highly mutated Gamma N-terminal domain exhibits considerable structural rearrangements, partially explaining its decreased neutralization by convalescent sera. Our results provide mechanistic insights into the structural, functional, and antigenic consequences of SARS-CoV-2 spike mutations and highlight a spike protein vulnerability that may be exploited to achieve broad protection against circulating variants. SARS-CoV-2 variants have accumulated multiple defining mutations within their spike glycoproteins. Here, the authors report a structural basis for broad neutralization of several variants by a heavy chain antibody fragment and provide a mutational analysis focusing on antibody evasion, receptor engagement, and spike protein structure.
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38
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Biavasco R, De Giovanni M. The Relative Positioning of B and T Cell Epitopes Drives Immunodominance. Vaccines (Basel) 2022; 10:vaccines10081227. [PMID: 36016115 PMCID: PMC9413633 DOI: 10.3390/vaccines10081227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 12/05/2022] Open
Abstract
Humoral immunity is crucial for protection against invading pathogens. Broadly neutralizing antibodies (bnAbs) provide sterilizing immunity by targeting conserved regions of viral variants and represent the goal of most vaccination approaches. While antibodies can be selected to bind virtually any region of a given antigen, the consistent induction of bnAbs in the context of influenza and HIV has represented a major roadblock. Many possible explanations have been considered; however, none of the arguments proposed to date seem to fully recapitulate the observed counter-selection for broadly protective antibodies. Antibodies can influence antigen presentation by enhancing the processing of CD4 epitopes adjacent to the binding region while suppressing the overlapping ones. We analyze the relative positioning of dominant B and T cell epitopes in published antigens that elicit strong and poor humoral responses. In strong immunogenic antigens, regions bound by immunodominant antibodies are frequently adjacent to CD4 epitopes, potentially boosting their presentation. Conversely, poorly immunogenic regions targeted by bnAbs in HIV and influenza overlap with clusters of dominant CD4 epitopes, potentially conferring an intrinsic disadvantage for bnAb-bearing B cells in germinal centers. Here, we propose the theory of immunodominance relativity, according to which the relative positioning of immunodominant B and CD4 epitopes within a given antigen drives immunodominance. Thus, we suggest that the relative positioning of B-T epitopes may be one additional mechanism that cooperates with other previously described processes to influence immunodominance. If demonstrated, this theory can improve the current understanding of immunodominance, provide a novel explanation for HIV and influenza escape from humoral responses, and pave the way for a new rational design of universal vaccines.
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Affiliation(s)
- Riccardo Biavasco
- Department of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Marco De Giovanni
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Correspondence:
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Li Y, Zheng P, Liu T, Shi C, Wang B, Xu Y, Jin T. Structural Requirements and Plasticity of Receptor-Binding Domain in Human Coronavirus Spike. Front Mol Biosci 2022; 9:930931. [PMID: 35903152 PMCID: PMC9315343 DOI: 10.3389/fmolb.2022.930931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/22/2022] Open
Abstract
The most recent human coronaviruses including severe acute respiratory syndrome coronavirus-2 causing severe respiratory tract infection and high pathogenicity bring significant global public health concerns. Infections are initiated by recognizing host cell receptors by coronavirus spike protein S1 subunit, and then S2 mediates membrane fusion. However, human coronavirus spikes undergo frequent mutation, which may result in diverse pathogenesis and infectivity. In this review, we summarize some of these recent structural and mutational characteristics of RBD of human coronavirus spike protein and their interaction with specific human cell receptors and analyze the structural requirements and plasticity of RBD. Stability of spike protein, affinity toward receptor, virus fitness, and infectivity are the factors controlling the viral tropisms. Thus, understanding the molecular details of RBDs and their mutations is critical in deciphering virus evolution. Structural information of spike and receptors of human coronaviruses not only reveals the molecular mechanism of host–microbe interaction and pathogenesis but also helps develop effective drug to control these infectious pathogens and cope with the future emerging coronavirus outbreaks.
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Affiliation(s)
- Yajuan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Peiyi Zheng
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tingting Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Cuixiao Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Bo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tengchuan Jin
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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Azali MA, Mohamed S, Harun A, Hussain FA, Shamsuddin S, Johan MF. Application of Baculovirus Expression Vector system (BEV) for COVID-19 diagnostics and therapeutics: a review. J Genet Eng Biotechnol 2022; 20:98. [PMID: 35792966 PMCID: PMC9259773 DOI: 10.1186/s43141-022-00368-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/20/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND The baculovirus expression vector system has been developed for expressing a wide range of proteins, including enzymes, glycoproteins, recombinant viruses, and vaccines. The availability of the SARS-CoV-2 genome sequence has enabled the synthesis of SARS-CoV2 proteins in a baculovirus-insect cell platform for various applications. The most cloned SARS-CoV-2 protein is the spike protein, which plays a critical role in SARS-CoV-2 infection. It is available in its whole length or as subunits like S1 or the receptor-binding domain (RBD). Non-structural proteins (Nsps), another recombinant SARS-CoV-2 protein generated by the baculovirus expression vector system (BEV), are used in the identification of new medications or the repurposing of existing therapies for the treatment of COVID-19. Non-SARS-CoV-2 proteins generated by BEV for SARS-CoV-2 diagnosis or treatment include moloney murine leukemia virus reverse transcriptase (MMLVRT), angiotensin converting enzyme 2 (ACE2), therapeutic proteins, and recombinant antibodies. The recombinant proteins were modified to boost the yield or to stabilize the protein. CONCLUSION This review covers the wide application of the recombinant protein produced using the baculovirus expression technology for COVID-19 research. A lot of improvements have been made to produce functional proteins with high yields. However, there is still room for improvement and there are parts of this field of research that have not been investigated yet.
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Affiliation(s)
- Muhammad Azharuddin Azali
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.,School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, 22200, Besut, Terengganu, Malaysia
| | - Salmah Mohamed
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, 22200, Besut, Terengganu, Malaysia
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Faezahtul Arbaeyah Hussain
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Shaharum Shamsuddin
- School of Health Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Muhammad Farid Johan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
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Lin Q, Lu C, Hong Y, Li R, Chen J, Chen W, Chen J. Animal models for studying coronavirus infections and developing antiviral agents and vaccines. Antiviral Res 2022; 203:105345. [PMID: 35605699 PMCID: PMC9122840 DOI: 10.1016/j.antiviral.2022.105345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/30/2022] [Accepted: 05/17/2022] [Indexed: 01/17/2023]
Abstract
In addition to severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 has become the third deadly coronavirus that infects humans and causes the new coronavirus disease (COVID-19). COVID-19 has already caused more than six million deaths worldwide and it is likely the biggest pandemic of this century faced by mankind. Although many studies on SARS-CoV-2 have been conducted, a detailed understanding of SARS-CoV-2 and COVID-19 is still lacking. Animal models are indispensable for studying its pathogenesis and developing vaccines and antivirals. In this review, we analyze animal models of coronavirus infections and explore their applications on antivirals and vaccines.
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Affiliation(s)
- Qisheng Lin
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Chunni Lu
- Centre for Inflammatory Diseases, Monash University Department of Medicine, Monash Medical Centre, Monash University, Clayton, Victoria 3168, Australia
| | - Yuqi Hong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Runfeng Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Jinding Chen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia.
| | - Jianxin Chen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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Koley T, Goswami A, Kumar M, Upadhyay N, Hariprasad G. Comparative Structural Analysis of Human ACE2 Receptor with Spike Protein of SARS-CoV-2 Variants: Implications to Understand Infectivity of the Virus. Adv Appl Bioinform Chem 2022; 15:21-27. [PMID: 35734581 PMCID: PMC9208465 DOI: 10.2147/aabc.s360787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/01/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Spike protein on SARS-CoV-2 virus plays an integral part during infection as cell entry depends on binding of this protein to human ACE2 receptor. Understanding of infectivity by these variants necessitates a comparative structural analysis of complexes of spike protein-receptor binding domain (RBD) of these variants to receptor. Methodology Wild type SARS-CoV-2 spike protein sequence was retrieved from the UniProt database, and mutations of five variants at receptor binding domain were manually incorporated and aligned using Clustal Omega. Crystal structure complexes of human ACE2 receptor with spike protein RBD domain of SARS-CoV-2 variants of wild type, α, β, and δ were extracted from the RCSB database. Wild type SARS-CoV-2 complex with receptor was used as template to generate model complexes of receptor with spike protein RBD of γ and omicron variants through WinCoot program. These were energy minimized and validated and molecular dynamic simulation was performed using Desmond simulation program. Results Mutations are distributed across the entire length of RBD, but the maximum number of mutations are seen at 11 positions within binding interface motifs of six variant sequences. Interface of spike protein RBDs with human ACE2-receptor shows different mix of hydrogen bonded and ionic interactions. Alpha and β variants have few interactions, while γ and δ variants have higher number of interactions compared to wild type variant. Omicron variant, with 10 polar interactions including two ionic bonds, has the highest binding energy. Conclusion Different mutations on RBD of spike protein results in varying quantity and quality of interactions, thereby affecting potency of each variant. Variations in binding are due to interactions of mutant residues and induced conformational changes on loops of RBDs. Variants α and β have a low potency, while, γ, δ, and omicron have a higher potency. These results correlate with viral infectivity and place clinical observations in the right perspective.
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Affiliation(s)
- Tirthankar Koley
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Arunima Goswami
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Neelam Upadhyay
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Gururao Hariprasad
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
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Ballmann R, Hotop SK, Bertoglio F, Steinke S, Heine PA, Chaudhry MZ, Jahn D, Pucker B, Baldanti F, Piralla A, Schubert M, Čičin-Šain L, Brönstrup M, Hust M, Dübel S. ORFeome Phage Display Reveals a Major Immunogenic Epitope on the S2 Subdomain of SARS-CoV-2 Spike Protein. Viruses 2022; 14:1326. [PMID: 35746797 PMCID: PMC9229677 DOI: 10.3390/v14061326] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
The development of antibody therapies against SARS-CoV-2 remains a challenging task during the ongoing COVID-19 pandemic. All approved therapeutic antibodies are directed against the receptor binding domain (RBD) of the spike, and therefore lose neutralization efficacy against emerging SARS-CoV-2 variants, which frequently mutate in the RBD region. Previously, phage display has been used to identify epitopes of antibody responses against several diseases. Such epitopes have been applied to design vaccines or neutralize antibodies. Here, we constructed an ORFeome phage display library for the SARS-CoV-2 genome. Open reading frames (ORFs) representing the SARS-CoV-2 genome were displayed on the surface of phage particles in order to identify enriched immunogenic epitopes from COVID-19 patients. Library quality was assessed by both NGS and epitope mapping of a monoclonal antibody with a known binding site. The most prominent epitope captured represented parts of the fusion peptide (FP) of the spike. It is associated with the cell entry mechanism of SARS-CoV-2 into the host cell; the serine protease TMPRSS2 cleaves the spike within this sequence. Blocking this mechanism could be a potential target for non-RBD binding therapeutic anti-SARS-CoV-2 antibodies. As mutations within the FP amino acid sequence have been rather rare among SARS-CoV-2 variants so far, this may provide an advantage in the fight against future virus variants.
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Affiliation(s)
- Rico Ballmann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Sven-Kevin Hotop
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - M. Zeeshan Chaudhry
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Dieter Jahn
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany;
| | - Boas Pucker
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstr 1, 38106 Braunschweig, Germany;
| | - Fausto Baldanti
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy;
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Fondazione Policlinico, 27100 Pavia, Italy;
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Fondazione Policlinico, 27100 Pavia, Italy;
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Luka Čičin-Šain
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Mark Brönstrup
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Stefan Dübel
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
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Sarker H, Panigrahi R, Hardy E, Glover JNM, Elahi S, Fernandez-Patron C. Glucocorticoids Bind to SARS-CoV-2 S1 at Multiple Sites Causing Cooperative Inhibition of SARS-CoV-2 S1 Interaction With ACE2. Front Immunol 2022; 13:906687. [PMID: 35784352 PMCID: PMC9242398 DOI: 10.3389/fimmu.2022.906687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/12/2022] [Indexed: 12/15/2022] Open
Abstract
Dexamethasone may reduce mortality in COVID-19 patients. Whether dexamethasone or endogenous glucocorticoids, such as cortisol, biochemically interact with SARS-CoV-2 spike 1 protein (S1), or its cellular receptor ACE2, is unknown. Using molecular dynamics (MD) simulations and binding energy calculations, we identified 162 druggable pockets in various conformational states of S1 and all possible binding pockets for cortisol and dexamethasone. Through biochemical binding studies, we confirmed that cortisol and dexamethasone bind to S1. Limited proteolysis and mass spectrometry analyses validated several MD identified binding pockets for cortisol and dexamethasone on S1. Interaction assays indicated that cortisol and dexamethasone separately and cooperatively disrupt S1 interaction with ACE2, through direct binding to S1, without affecting ACE2 catalytic activity. Cortisol disrupted the binding of the mutant S1 Beta variant (E484K, K417N, N501Y) to ACE2. Delta and Omicron variants are mutated in or near identified cortisol-binding pockets in S1, which may affect cortisol binding to them. In the presence of cortisol, we find increased inhibition of S1 binding to ACE2 by an anti-SARS-CoV-2 S1 human chimeric monoclonal antibody against the receptor binding domain. Whether glucocorticoid/S1 direct interaction is an innate defence mechanism that may have contributed to mild or asymptomatic SARS-CoV-2 infection deserves further investigation.
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Affiliation(s)
- Hassan Sarker
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Rashmi Panigrahi
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | | | - J. N. Mark Glover
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Shokrollah Elahi
- Department of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Carlos Fernandez-Patron
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Carlos Fernandez-Patron,
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45
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Miersch S, Sharma N, Saberianfar R, Chen C, Caccuri F, Zani A, Caruso A, Case JB, Diamond MS, Amarasinghe GK, Novelli G, Sidhu SS. Ultrapotent and broad neutralization of SARS-CoV-2 variants by modular, tetravalent, bi-paratopic antibodies. Cell Rep 2022; 39:110905. [PMID: 35617963 PMCID: PMC9108025 DOI: 10.1016/j.celrep.2022.110905] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/09/2022] [Accepted: 05/10/2022] [Indexed: 01/18/2023] Open
Abstract
Neutralizing antibodies (nAbs) that target the SARS-CoV-2 spike protein have received emergency use approval for treatment of COVID-19. However, with the emergence of variants of concern, there is a need for new treatment options. We report a format that enables modular assembly of bi-paratopic tetravalent nAbs with antigen-binding sites from two distinct nAbs. The tetravalent nAb purifies in high yield and exhibits biophysical characteristics that are comparable to those of clinically used therapeutic antibodies. The tetravalent nAb binds to the spike protein trimer at least 100-fold more tightly than bivalent IgGs (apparent KD < 1 pM) and neutralizes a broad array of SARS-CoV-2 pseudoviruses, chimeric viruses, and authentic viral variants with high potency. Together, these results establish the tetravalent diabody-Fc-Fab as a robust, modular platform for rapid production of drug-grade nAbs with potencies and breadth of coverage that greatly exceed those of conventional bivalent IgGs.
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Affiliation(s)
- Shane Miersch
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada.
| | - Nitin Sharma
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Chao Chen
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Francesca Caccuri
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia Medical School, 25123 Brescia, Italy
| | - Alberto Zani
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia Medical School, 25123 Brescia, Italy
| | - Arnaldo Caruso
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia Medical School, 25123 Brescia, Italy
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy; Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, USA
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada.
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Villacrés B, Paz E, Burbano MJ, Villacrés-Granda I, Armijos D, Aguirre M. Neutralizing activity to SARS-CoV-2 in 1.2 to 10.0 month convalescent plasma samples of COVID-19: a transversal surrogate in vitro study performed in Quito-Ecuador. J Med Virol 2022; 94:4246-4252. [PMID: 35585654 PMCID: PMC9347805 DOI: 10.1002/jmv.27866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/26/2022] [Accepted: 05/17/2022] [Indexed: 12/03/2022]
Abstract
Coronavirus disease 2019 (COVID‐19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection, was first reported in Wuhan, China, in December 2019. Diagnostic methods for the detection of the virus and seroconversion of neutralizing antibodies (NAbs) in plasma have been developed specifically, but some of them require a BSL3 facility. In this study, we used the SARS‐CoV‐2 Surrogate Virus Neutralization Test Kit to determine the presence or absence of NAbs anti‐receptor binding domain of the viral spike (S) glycoprotein in a BSL2 facility. The sample population was chosen in Quito, Ecuador, with a total of 88 COVID‐19 positive convalescent patients. We determined that 97.7% of the analyzed convalescent sera maintained the presence of NAbs with neutralizing activity, and this activity remained until 10 months after the infection in some cases. In addition, the relationship between the presence of NAbs and immunoglobulin G was significant compared to immunoglobulin M, which tended to be absent over time.
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Affiliation(s)
| | - Elius Paz
- Centro de Investigación Genética y Genómica - UTE, Quito, Ecuador
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47
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Zuo F, Abolhassani H, Du L, Piralla A, Bertoglio F, de Campos-Mata L, Wan H, Schubert M, Cassaniti I, Wang Y, Sammartino JC, Sun R, Vlachiotis S, Bergami F, Kumagai-Braesch M, Andréll J, Zhang Z, Xue Y, Wenzel EV, Calzolai L, Varani L, Rezaei N, Chavoshzadeh Z, Baldanti F, Hust M, Hammarström L, Marcotte H, Pan-Hammarström Q. Heterologous immunization with inactivated vaccine followed by mRNA-booster elicits strong immunity against SARS-CoV-2 Omicron variant. Nat Commun 2022; 13:2670. [PMID: 35562366 PMCID: PMC9106736 DOI: 10.1038/s41467-022-30340-5] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/27/2022] [Indexed: 12/19/2022] Open
Abstract
The recent emergence of the Omicron variant has raised concerns on vaccine efficacy and the urgent need to study more efficient vaccination strategies. Here we observed that an mRNA vaccine booster in individuals vaccinated with two doses of inactivated vaccine significantly increased the plasma level of specific antibodies that bind to the receptor-binding domain (RBD) or the spike (S) ectodomain (S1 + S2) of both the G614 and the Omicron variants, compared to two doses of homologous inactivated vaccine. The level of RBD- and S-specific IgG antibodies and virus neutralization titers against variants of concern in the heterologous vaccination group were similar to that in individuals receiving three doses of homologous mRNA-vaccine or a boost of mRNA vaccine after infection, but markedly higher than that in individuals receiving three doses of a homologous inactivated vaccine. This heterologous vaccination regime furthermore significantly enhanced the RBD-specific memory B cell response and S1-specific T cell response, compared to two or three doses of homologous inactivated vaccine. Our study demonstrates that mRNA vaccine booster in individuals vaccinated with inactivated vaccines can be highly beneficial, as it markedly increases the humoral and cellular immune responses against the virus, including the Omicron variant.
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Affiliation(s)
- Fanglei Zuo
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Likun Du
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Federico Bertoglio
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Leire de Campos-Mata
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Hui Wan
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Maren Schubert
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Irene Cassaniti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Yating Wang
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Josè Camilla Sammartino
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Rui Sun
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Stelios Vlachiotis
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Federica Bergami
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Makiko Kumagai-Braesch
- Division of Transplantation Surgery, CLINTEC, Karolinska Institutet at Karolinska University Hospital, Stockholm, Sweden
| | - Juni Andréll
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Zhaoxia Zhang
- Department of Aging Neurology orthopedics, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Yintong Xue
- Department of Immunology, Peking University Health Science Center, Beijing, China
| | - Esther Veronika Wenzel
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
- Abcalis GmbH, Science Campus Braunschweig-Süd, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Luigi Calzolai
- European Commission, Joint Research Centre, Ispra, Italy
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Chavoshzadeh
- Pediatric Infections Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Michael Hust
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Harold Marcotte
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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48
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Engelhart E, Lopez R, Emerson R, Lin C, Shikany C, Guion D, Kelley M, Younger D. Massively Multiplexed Affinity Characterization of Therapeutic Antibodies Against SARS-CoV-2 Variants. Antib Ther 2022; 5:130-137. [PMID: 35769631 PMCID: PMC9129155 DOI: 10.1093/abt/tbac011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Antibody therapies represent a valuable tool to reduce COVID-19 deaths and hospitalizations. Multiple antibody candidates have been granted emergency use authorization by the FDA and many more are in clinical trials. Most antibody therapies for COVID-19 are engineered to bind to the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein and disrupt its interaction with ACE2. Notably, several SARS-CoV-2 strains have accrued mutations throughout the RBD that improve ACE2 binding affinity, enhance viral transmission, and escape some existing antibody therapies. Here, we measure the binding affinity of 33 therapeutic antibodies against a large panel of SARS-CoV-2 variants and related strains of clinical significance using AlphaSeq, a high-throughput yeast mating based assay to determine epitopic residues, determine which mutations result in loss of binding, and predict how future RBD variants may impact antibody efficacy. We find that some antibodies are more susceptible to mutations in the RBD than others, for example Imdevimab and Sotrovimab display no loss in binding to B.1.1.7, B.1.351 and P.1 variants whereas we observe a 10-fold loss in binding of Etesevimab and Regdanvimab to these variants.
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49
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Gruell H, Vanshylla K, Weber T, Barnes CO, Kreer C, Klein F. Antibody-Mediated Neutralization of SARS-CoV-2. Immunity 2022; 55:925-944. [PMID: 35623355 PMCID: PMC9118976 DOI: 10.1016/j.immuni.2022.05.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022]
Abstract
Neutralizing antibodies can block infection, clear pathogens, and are essential to provide long-term immunity. Since the onset of the pandemic, SARS-CoV-2 neutralizing antibodies have been comprehensively investigated and critical information on their development, function, and potential use to prevent and treat COVID-19 have been revealed. With the emergence of SARS-CoV-2 immune escape variants, humoral immunity is being challenged, and a detailed understanding of neutralizing antibodies is essential to guide vaccine design strategies as well as antibody-mediated therapies. In this review, we summarize some of the key findings on SARS-CoV-2 neutralizing antibodies, with a focus on their clinical application.
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Affiliation(s)
- Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Timm Weber
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Christopher O Barnes
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
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50
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Strohl WR, Ku Z, An Z, Carroll SF, Keyt BA, Strohl LM. Passive Immunotherapy Against SARS-CoV-2: From Plasma-Based Therapy to Single Potent Antibodies in the Race to Stay Ahead of the Variants. BioDrugs 2022; 36:231-323. [PMID: 35476216 PMCID: PMC9043892 DOI: 10.1007/s40259-022-00529-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic is now approaching 2 years old, with more than 440 million people infected and nearly six million dead worldwide, making it the most significant pandemic since the 1918 influenza pandemic. The severity and significance of SARS-CoV-2 was recognized immediately upon discovery, leading to innumerable companies and institutes designing and generating vaccines and therapeutic antibodies literally as soon as recombinant SARS-CoV-2 spike protein sequence was available. Within months of the pandemic start, several antibodies had been generated, tested, and moved into clinical trials, including Eli Lilly's bamlanivimab and etesevimab, Regeneron's mixture of imdevimab and casirivimab, Vir's sotrovimab, Celltrion's regdanvimab, and Lilly's bebtelovimab. These antibodies all have now received at least Emergency Use Authorizations (EUAs) and some have received full approval in select countries. To date, more than three dozen antibodies or antibody combinations have been forwarded into clinical trials. These antibodies to SARS-CoV-2 all target the receptor-binding domain (RBD), with some blocking the ability of the RBD to bind human ACE2, while others bind core regions of the RBD to modulate spike stability or ability to fuse to host cell membranes. While these antibodies were being discovered and developed, new variants of SARS-CoV-2 have cropped up in real time, altering the antibody landscape on a moving basis. Over the past year, the search has widened to find antibodies capable of neutralizing the wide array of variants that have arisen, including Alpha, Beta, Gamma, Delta, and Omicron. The recent rise and dominance of the Omicron family of variants, including the rather disparate BA.1 and BA.2 variants, demonstrate the need to continue to find new approaches to neutralize the rapidly evolving SARS-CoV-2 virus. This review highlights both convalescent plasma- and polyclonal antibody-based approaches as well as the top approximately 50 antibodies to SARS-CoV-2, their epitopes, their ability to bind to SARS-CoV-2 variants, and how they are delivered. New approaches to antibody constructs, including single domain antibodies, bispecific antibodies, IgA- and IgM-based antibodies, and modified ACE2-Fc fusion proteins, are also described. Finally, antibodies being developed for palliative care of COVID-19 disease, including the ramifications of cytokine release syndrome (CRS) and acute respiratory distress syndrome (ARDS), are described.
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Affiliation(s)
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
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