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Lapuente D, Winkler TH, Tenbusch M. B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity. Cell Mol Immunol 2024; 21:144-158. [PMID: 37945737 PMCID: PMC10805925 DOI: 10.1038/s41423-023-01095-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 prompted scientific, medical, and biotech communities to investigate infection- and vaccine-induced immune responses in the context of this pathogen. B-cell and antibody responses are at the center of these investigations, as neutralizing antibodies (nAbs) are an important correlate of protection (COP) from infection and the primary target of SARS-CoV-2 vaccine modalities. In addition to absolute levels, nAb longevity, neutralization breadth, immunoglobulin isotype and subtype composition, and presence at mucosal sites have become important topics for scientists and health policy makers. The recent pandemic was and still is a unique setting in which to study de novo and memory B-cell (MBC) and antibody responses in the dynamic interplay of infection- and vaccine-induced immunity. It also provided an opportunity to explore new vaccine platforms, such as mRNA or adenoviral vector vaccines, in unprecedented cohort sizes. Combined with the technological advances of recent years, this situation has provided detailed mechanistic insights into the development of B-cell and antibody responses but also revealed some unexpected findings. In this review, we summarize the key findings of the last 2.5 years regarding infection- and vaccine-induced B-cell immunity, which we believe are of significant value not only in the context of SARS-CoV-2 but also for future vaccination approaches in endemic and pandemic settings.
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Affiliation(s)
- Dennis Lapuente
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
| | - Thomas H Winkler
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany.
| | - Matthias Tenbusch
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany
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102
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Dong M, Galvan Achi JM, Du R, Rong L, Cui Q. Development of SARS-CoV-2 entry antivirals. CELL INSIGHT 2024; 3:100144. [PMID: 38323318 PMCID: PMC10844678 DOI: 10.1016/j.cellin.2023.100144] [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] [Received: 11/11/2023] [Revised: 12/17/2023] [Accepted: 12/17/2023] [Indexed: 02/08/2024]
Abstract
The global outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) threatened human health and public safety. The development of anti-SARS-CoV-2 therapies have been essential to curb the spread of SARS-CoV-2. Particularly, antivirals targeting viral entry have become an attractive target for the development of anti-SARS-CoV-2 therapies. In this review, we elucidate the mechanism of SARS-CoV-2 viral entry and summarize the development of antiviral inhibitors targeting viral entry. Moreover, we speculate upon future directions toward more potent inhibitors of SARS-CoV-2 entry. This study is expected to provide novel insights for the efficient discovery of promising candidate drugs against the entry of SARS-CoV-2, and contribute to the development of broad-spectrum anti-coronavirus drugs.
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Affiliation(s)
- Meiyue Dong
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China
| | - Jazmin M. Galvan Achi
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL60612, USA
| | - Ruikun Du
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China
- Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, Shandong, 266122, China
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL60612, USA
| | - Qinghua Cui
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China
- Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, Shandong, 266122, China
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103
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Ose NJ, Campitelli P, Modi T, Can Kazan I, Kumar S, Banu Ozkan S. Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557827. [PMID: 37745560 PMCID: PMC10515954 DOI: 10.1101/2023.09.14.557827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 Spike (S) protein. With this approach, we first identified Candidate Adaptive Polymorphisms (CAPs) of the SARS-CoV-2 Spike protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.
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Affiliation(s)
- Nicholas J. Ose
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - I. Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - S. Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
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104
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Liu J, Lu Y, Zhu L. A kinetic model for solving a combination optimization problem in ab-initio Cryo-EM 3D reconstruction. Brief Bioinform 2024; 25:bbad473. [PMID: 38261343 PMCID: PMC10805181 DOI: 10.1093/bib/bbad473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/22/2023] [Accepted: 11/28/2023] [Indexed: 01/24/2024] Open
Abstract
Cryo-Electron Microscopy (cryo-EM) is a widely used and effective method for determining the three-dimensional (3D) structure of biological molecules. For ab-initio Cryo-EM 3D reconstruction using single particle analysis (SPA), estimating the projection direction of the projection image is a crucial step. However, the existing SPA methods based on common lines are sensitive to noise. The error in common line detection will lead to a poor estimation of the projection directions and thus may greatly affect the final reconstruction results. To improve the reconstruction results, multiple candidate common lines are estimated for each pair of projection images. The key problem then becomes a combination optimization problem of selecting consistent common lines from multiple candidates. To solve the problem efficiently, a physics-inspired method based on a kinetic model is proposed in this work. More specifically, hypothetical attractive forces between each pair of candidate common lines are used to calculate a hypothetical torque exerted on each projection image in the 3D reconstruction space, and the rotation under the hypothetical torque is used to optimize the projection direction estimation of the projection image. This way, the consistent common lines along with the projection directions can be found directly without enumeration of all the combinations of the multiple candidate common lines. Compared with the traditional methods, the proposed method is shown to be able to produce more accurate 3D reconstruction results from high noise projection images. Besides the practical value, the proposed method also serves as a good reference for solving similar combinatorial optimization problems.
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Affiliation(s)
- Jiaxuan Liu
- School of Information Science and Engineering, Lanzhou
| | - Yonggang Lu
- School of Information Science and Engineering, Lanzhou
| | - Li Zhu
- School of Life Sciences, Lanzhou University
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105
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Bedding MJ, Franck C, Johansen-Leete J, Aggarwal A, Maxwell JWC, Patel K, Hawkins PME, Low JKK, Siddiquee R, Sani HM, Ford DJ, Turville S, Mackay JP, Passioura T, Christie M, Payne RJ. Discovery of High Affinity Cyclic Peptide Ligands for Human ACE2 with SARS-CoV-2 Entry Inhibitory Activity. ACS Chem Biol 2024; 19:141-152. [PMID: 38085789 DOI: 10.1021/acschembio.3c00568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
The development of effective antiviral compounds is essential for mitigating the effects of the COVID-19 pandemic. Entry of SARS-CoV-2 virions into host cells is mediated by the interaction between the viral spike (S) protein and membrane-bound angiotensin-converting enzyme 2 (ACE2) on the surface of epithelial cells. Inhibition of this viral protein-host protein interaction is an attractive avenue for the development of antiviral molecules with numerous spike-binding molecules generated to date. Herein, we describe an alternative approach to inhibit the spike-ACE2 interaction by targeting the spike-binding interface of human ACE2 via mRNA display. Two consecutive display selections were performed to direct cyclic peptide ligand binding toward the spike binding interface of ACE2. Through this process, potent cyclic peptide binders of human ACE2 (with affinities in the picomolar to nanomolar range) were identified, two of which neutralized SARS-CoV-2 entry. This work demonstrates the potential of targeting ACE2 for the generation of anti-SARS-CoV-2 therapeutics as well as broad spectrum antivirals for the treatment of SARS-like betacoronavirus infection.
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Affiliation(s)
- Max J Bedding
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Charlotte Franck
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jason Johansen-Leete
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Joshua W C Maxwell
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Karishma Patel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Paige M E Hawkins
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Rezwan Siddiquee
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Hakimeh Moghaddas Sani
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Daniel J Ford
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Toby Passioura
- Sydney Analytical Core Research Facility, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mary Christie
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
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106
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Petersen BM, Kirby MB, Chrispens KM, Irvin OM, Strawn IK, Haas CM, Walker AM, Baumer ZT, Ulmer SA, Ayala E, Rhodes ER, Guthmiller JJ, Steiner PJ, Whitehead TA. An integrated technology for quantitative wide mutational scanning of human antibody Fab libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575852. [PMID: 38293170 PMCID: PMC10827193 DOI: 10.1101/2024.01.16.575852] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Antibodies are engineerable quantities in medicine. Learning antibody molecular recognition would enable the in silico design of high affinity binders against nearly any proteinaceous surface. Yet, publicly available experiment antibody sequence-binding datasets may not contain the mutagenic, antigenic, or antibody sequence diversity necessary for deep learning approaches to capture molecular recognition. In part, this is because limited experimental platforms exist for assessing quantitative and simultaneous sequence-function relationships for multiple antibodies. Here we present MAGMA-seq, an integrated technology that combines multiple antigens and multiple antibodies and determines quantitative biophysical parameters using deep sequencing. We demonstrate MAGMA-seq on two pooled libraries comprising mutants of ten different human antibodies spanning light chain gene usage, CDR H3 length, and antigenic targets. We demonstrate the comprehensive mapping of potential antibody development pathways, sequence-binding relationships for multiple antibodies simultaneously, and identification of paratope sequence determinants for binding recognition for broadly neutralizing antibodies (bnAbs). MAGMA-seq enables rapid and scalable antibody engineering of multiple lead candidates because it can measure binding for mutants of many given parental antibodies in a single experiment.
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Affiliation(s)
- Brian M. Petersen
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Monica B. Kirby
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Karson M. Chrispens
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Olivia M. Irvin
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Isabell K. Strawn
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Cyrus M. Haas
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Alexis M. Walker
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Zachary T. Baumer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Sophia A. Ulmer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Edgardo Ayala
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Emily R. Rhodes
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Jenna J. Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Paul J. Steiner
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Timothy A. Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
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107
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Lim S, Kwon HJ, Jeong DG, Nie H, Lee S, Ko SR, Lee KS, Ryu YB, Mason HS, Kim HS, Shin AY, Kwon SY. Enhanced binding and inhibition of SARS-CoV-2 by a plant-derived ACE2 protein containing a fused mu tailpiece. Biotechnol J 2024; 19:e2300319. [PMID: 37853601 DOI: 10.1002/biot.202300319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/27/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Infectious diseases such as Coronavirus disease 2019 (COVID-19) and Middle East respiratory syndrome (MERS) present an increasingly persistent crisis in many parts of the world. COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The angiotensin-converting enzyme 2 (ACE2) is a crucial cellular receptor for SARS-CoV-2 infection. Inhibition of the interaction between SARS-CoV-2 and ACE2 has been proposed as a target for the prevention and treatment of COVID-19. We produced four recombinant plant-derived ACE2 isoforms with or without the mu tailpiece (μ-tp) of immunoglobulin M (IgM) and the KDEL endoplasmic reticulum retention motif in a plant expression system. The plant-derived ACE2 isoforms bound whole SARS-CoV-2 virus and the isolated receptor binding domains of SARS-CoV-2 Alpha, Beta, Gamma, Delta, and Omicron variants. Fusion of μ-tp and KDEL to the ACE2 protein (ACE2 μK) had enhanced binding activity with SARS-CoV-2 in comparison with unmodified ACE2 protein derived from CHO cells. Furthermore, the plant-derived ACE2 μK protein exhibited no cytotoxic effects on Vero E6 cells and effectively inhibited SARS-CoV-2 infection. The efficient and rapid scalability of plant-derived ACE2 μK protein offers potential for the development of preventive and therapeutic agents in the early response to future viral outbreaks.
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Affiliation(s)
- Sohee Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hyung-Jun Kwon
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Dae Gwin Jeong
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Bio-Analytical Science Division, Korea Research Institute of Bioscience and Biotechnology School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Hualin Nie
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Sanghee Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea Research Institute of Bioscience and Biotechnology School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Seo-Rin Ko
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Kyu-Sun Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Bio-Analytical Science Division, Korea Research Institute of Bioscience and Biotechnology School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Young Bae Ryu
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Hugh S Mason
- Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute at ASU, Tempe, Arizona, USA
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea Research Institute of Bioscience and Biotechnology School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea Research Institute of Bioscience and Biotechnology School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
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108
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Johnson L, Bartlett ML, Ramirez F, Heger CD, Smith DR. Development of automated microfluidic immunoassays for the detection of SARS-CoV-2 antibodies and antigen. J Immunol Methods 2024; 524:113586. [PMID: 38040191 DOI: 10.1016/j.jim.2023.113586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19) global pandemic. Rapid and sensitive detection of the virus soon after infection is important for the treatment and prevention of transmission of COVID-19, and detection of antibodies is important for epidemiology, assessment of vaccine immunogenicity, and identification of the natural reservoir and intermediate host(s). Patient nasal or oropharyngeal swabs or saliva used in conjunction with polymerase chain reaction (PCR) detect SARS-CoV-2 RNA, whereas lateral flow immunoassays (LFI) detect SARS-CoV-2 proteins. Enzyme-linked immunosorbent assays (ELISA) detect anti-SARS-CoV-2 antibodies in blood. Although effective, these assays have poor sensitivity (e.g., LFI) or are labor intensive and time consuming (PCR and ELISA). Here we describe the development of rapid, automated ELISA-based immunoassays to detect SARS-CoV-2 antigens and antibodies against the virus. The Simple Plex™ platform uses rapid microfluidic reaction kinetics for sensitive analyte detection with small sample volumes. We developed three sensitive <90-min Simple Plex immunoassays that measure either the SARS-CoV-2 antigens or the immune response to SARS-CoV-2, including neutralizing antibodies, in serum from COVID-19 patients.
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Affiliation(s)
- Linwood Johnson
- Microbiology and Immunology Department, Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, USA
| | - Maggie L Bartlett
- Microbiology and Immunology Department, Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, USA
| | | | | | - Darci R Smith
- Microbiology and Immunology Department, Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, USA.
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109
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Zhang H, Liu Y, Liu Z. Nanomedicine approaches against SARS-CoV-2 and variants. J Control Release 2024; 365:101-111. [PMID: 37951476 DOI: 10.1016/j.jconrel.2023.11.004] [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: 07/26/2023] [Revised: 10/27/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
The world is grappling with the ongoing crisis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a global pandemic that continues to have a detrimental impact on public health and economies worldwide. The virus's relentless mutation has led to more transmissible, immune-evasive strains, thereby escalating the incidence of reinfection. This underscores the urgent need for highly effective and safe countermeasures against SARS-CoV-2 and its evolving variants. In the current context, nanomedicine presents an innovative and promising alternative to mitigate the impacts of this pandemic wave. It does so by harnessing the structural and functional properties at a nanoscale in a straightforward and adaptable manner. This review emphasizes the most recent progress in the development of nanovaccines, nanodecoys, and nanodisinfectants to tackle SARS-CoV-2 and its variants. Notably, the insights gained and strategies implemented in managing the ongoing pandemic may also offer invaluable guidance for the development of potent nanomedicines to combat future pandemics.
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Affiliation(s)
- Han Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China.
| | - Yanbin Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China
| | - Zhuang Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou 215123, China.
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110
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Zeng W, Jia X, Chi X, Zhang X, Li E, Wu Y, Liu Y, Han J, Ni K, Ye X, Hu X, Ma H, Yu C, Chiu S, Jin T. An engineered bispecific nanobody in tetrameric secretory IgA format confers broad neutralization against SARS-CoV-1&2 and most variants. Int J Biol Macromol 2023; 253:126817. [PMID: 37690653 DOI: 10.1016/j.ijbiomac.2023.126817] [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: 07/28/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
SARS-CoV-2, a type of respiratory virus, has exerted a great impact on global health and economy over the past three years. Antibody-based therapy was initially successful but later failed due to the accumulation of mutations in the spike protein of the virus. Strategies that enable antibodies to resist virus escape are therefore of great significance. Here, we engineer a bispecific SARS-CoV-2 neutralizing nanobody in secretory Immunoglobulin A (SIgA) format, named S2-3-IgA2m2, which shows broad and potent neutralization against SARS-CoV-1, SARS-CoV-2 and its variants of concern (VOCs) including XBB and BQ.1.1. S2-3-IgA2m2 is ∼1800-fold more potent than its parental IgG counterpart in neutralizing XBB. S2-3-IgA2m2 is stable in mouse lungs at least for three days when administrated by nasal delivery. In hamsters infected with BA.5, three intranasal doses of S2-3-IgA2m2 at 1 mg/kg significantly reduce viral RNA loads and completely eliminate infectious particles in the trachea and lungs. Notably, even at single dose of 1 mg/kg, S2-3-IgA2m2 prophylactically administered through the intranasal route drastically reduces airway viral RNA loads and infectious particles. This study provides an effective weapon combating SARS-CoV-2, proposes a new strategy overcoming the virus escape, and lays strategic reserves for rapid response to potential future outbreaks of "SARS-CoV-3".
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Affiliation(s)
- Weihong Zeng
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Xiaoying Jia
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430062, China
| | - Xiangyang Chi
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Xinghai Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430062, China
| | - Entao Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yan Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430062, China
| | - Yang Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430062, China
| | - Jin Han
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Kang Ni
- Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaodong Ye
- Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaowen Hu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Huan Ma
- Institute of Clinical Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China.
| | - Changming Yu
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing 100071, China.
| | - Sandra Chiu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Tengchuan Jin
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China; Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui, China.
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111
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Li K, Huntwork RHC, Horn GQ, Abraha M, Hastie KM, Li H, Rayaprolu V, Olmedillas E, Feeney E, Cronin K, Schendel SL, Heise M, Bedinger D, Mattocks MD, Baric RS, Alam SM, Ollmann Saphire E, Tomaras GD, Dennison SM. Cryptic-site-specific antibodies to the SARS-CoV-2 receptor binding domain can retain functional binding affinity to spike variants. J Virol 2023; 97:e0107023. [PMID: 38019013 PMCID: PMC10746274 DOI: 10.1128/jvi.01070-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/05/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Multiple SARS-CoV-2 variants of concern have emerged and caused a significant number of infections and deaths worldwide. These variants of concern contain mutations that might significantly affect antigen-targeting by antibodies. It is therefore important to further understand how antibody binding and neutralization are affected by the mutations in SARS-CoV-2 variants. We highlighted how antibody epitope specificity can influence antibody binding to SARS-CoV-2 spike protein variants and neutralization of SARS-CoV-2 variants. We showed that weakened spike binding and neutralization of Beta (B.1.351) and Omicron (BA.1) variants compared to wildtype are not universal among the panel of antibodies and identified antibodies of a specific binding footprint exhibiting consistent enhancement of spike binding and retained neutralization to Beta variant. These data and analysis can inform how antigen-targeting by antibodies might evolve during a pandemic and prepare for potential future sarbecovirus outbreaks.
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Affiliation(s)
- Kan Li
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Richard H. C. Huntwork
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Gillian Q. Horn
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Milite Abraha
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Kathryn M. Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Haoyang Li
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Vamseedhar Rayaprolu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Eduardo Olmedillas
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Elizabeth Feeney
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Kenneth Cronin
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Sharon L. Schendel
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Mark Heise
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Melissa D. Mattocks
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ralph S. Baric
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
- Department of Pathology, Duke University, Durham, North Carolina, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Georgia D. Tomaras
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - S. Moses Dennison
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
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112
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Adams LJ, VanBlargan LA, Liu Z, Gilchuk P, Zhao H, Chen RE, Raju S, Chong Z, Whitener BM, Shrihari S, Jethva PN, Gross ML, Crowe JE, Whelan SPJ, Diamond MS, Fremont DH. A broadly reactive antibody targeting the N-terminal domain of SARS-CoV-2 spike confers Fc-mediated protection. Cell Rep Med 2023; 4:101305. [PMID: 38039973 PMCID: PMC10772349 DOI: 10.1016/j.xcrm.2023.101305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 08/21/2023] [Accepted: 11/06/2023] [Indexed: 12/03/2023]
Abstract
Most neutralizing anti-SARS-CoV-2 monoclonal antibodies (mAbs) target the receptor binding domain (RBD) of the spike (S) protein. Here, we characterize a panel of mAbs targeting the N-terminal domain (NTD) or other non-RBD epitopes of S. A subset of NTD mAbs inhibits SARS-CoV-2 entry at a post-attachment step and avidly binds the surface of infected cells. One neutralizing NTD mAb, SARS2-57, protects K18-hACE2 mice against SARS-CoV-2 infection in an Fc-dependent manner. Structural analysis demonstrates that SARS2-57 engages an antigenic supersite that is remodeled by deletions common to emerging variants. In neutralization escape studies with SARS2-57, this NTD site accumulates mutations, including a similar deletion, but the addition of an anti-RBD mAb prevents such escape. Thus, our study highlights a common strategy of immune evasion by SARS-CoV-2 variants and how targeting spatially distinct epitopes, including those in the NTD, may limit such escape.
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Affiliation(s)
- Lucas J Adams
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Haiyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rita E Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Saravanan Raju
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zhenlu Chong
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bradley M Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Swathi Shrihari
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Prashant N Jethva
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, 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.
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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113
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Baboo S, Diedrich JK, Torres JL, Copps J, Singh B, Garrett PT, Ward AB, Paulson JC, Yates JR. Evolving spike-protein N-glycosylation in SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539897. [PMID: 37214937 PMCID: PMC10197516 DOI: 10.1101/2023.05.08.539897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavily N-glycosylated spike-protein of SARS-CoV-2 plays a pivotal role in initiating infection and is the target for host immune-response, both of which are impacted by host-installed N-glycans. Using highly-sensitive DeGlyPHER approach, we compared the N-glycan landscape on spikes of the SARS-CoV-2 Wuhan-Hu-1 strain to seven WHO-defined variants of concern/interest, using recombinantly expressed, soluble spike-protein trimers, sharing same stabilizing-mutations. We found that N-glycan processing is conserved at most sites. However, in multiple variants, processing of N-glycans from high mannose- to complex-type is reduced at sites N165, N343 and N616, implicated in spike-protein function.
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Affiliation(s)
- Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jolene K. Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Bhavya Singh
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Patrick T. Garrett
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - James C. Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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114
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Lusiany T, Terada T, Kishikawa JI, Hirose M, Chen DV, Sugihara F, Ismanto HS, van Eerden FJ, Li S, Kato T, Arase H, Yoshiharu M, Okada M, Standley DM. Enhancement of SARS-CoV-2 Infection via Crosslinking of Adjacent Spike Proteins by N-Terminal Domain-Targeting Antibodies. Viruses 2023; 15:2421. [PMID: 38140662 PMCID: PMC10747171 DOI: 10.3390/v15122421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The entry of SARS-CoV-2 into host cells is mediated by the interaction between the spike receptor-binding domain (RBD) and host angiotensin-converting enzyme 2 (ACE2). Certain human antibodies, which target the spike N-terminal domain (NTD) at a distant epitope from the host cell binding surface, have been found to augment ACE2 binding and enhance SARS-CoV-2 infection. Notably, these antibodies exert their effect independently of the antibody fragment crystallizable (Fc) region, distinguishing their mode of action from previously described antibody-dependent infection-enhancing (ADE) mechanisms. Building upon previous hypotheses and experimental evidence, we propose that these NTD-targeting infection-enhancing antibodies (NIEAs) achieve their effect through the crosslinking of neighboring spike proteins. In this study, we present refined structural models of NIEA fragment antigen-binding region (Fab)-NTD complexes, supported by molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry (HDX-MS). Furthermore, we provide direct evidence confirming the crosslinking of spike NTDs by NIEAs. Collectively, our findings advance our understanding of the molecular mechanisms underlying NIEAs and their impact on SARS-CoV-2 infection.
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Affiliation(s)
- Tina Lusiany
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Tokyo 113-8657, Japan;
| | - Jun-ichi Kishikawa
- Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (J.-i.K.); (M.H.); (T.K.)
| | - Mika Hirose
- Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (J.-i.K.); (M.H.); (T.K.)
| | - David Virya Chen
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan;
| | - Fuminori Sugihara
- Core Facility, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Osaka 565-0871, Japan;
| | - Hendra Saputra Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
| | - Floris J. van Eerden
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
| | - Songling Li
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
| | - Takayuki Kato
- Cryo-EM Structural Biology, Institute for Protein Research, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (J.-i.K.); (M.H.); (T.K.)
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan;
- Department of Immunochemistry, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Matsuura Yoshiharu
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan;
| | - Masato Okada
- Center for Advanced Modalities and DDS, Osaka University, 2-8 Yamadaoka, Suita 565-0871, Japan;
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan (H.S.I.); (S.L.)
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; (D.V.C.); (F.J.v.E.)
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115
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Mink S, Fraunberger P. Anti-SARS-CoV-2 Antibody Testing: Role and Indications. J Clin Med 2023; 12:7575. [PMID: 38137643 PMCID: PMC10744049 DOI: 10.3390/jcm12247575] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/20/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Since the onset of the COVID-19 pandemic in March 2020, over 769 million confirmed COVID-19 cases, including close to 7 million COVID-19-related deaths, have been reported. Although mortality rates have dropped notably compared to the first months of the pandemic, spikes in reported cases and mortality rates continue to be registered. Both recent spikes in case numbers and the continued emergence of new variants suggest that vulnerable patient groups, including older adults, immunocompromised patients, and patients with severe comorbidities, are going to continue to be affected by COVID-19. In order to curb the pandemic, relieve the pressure on primary care facilities, and reduce mortality rates, global vaccination programs have been established by the WHO, with over 13.5 billion vaccine doses having been administered globally. In most immunocompetent individuals, vaccination against COVID-19 results in the production of anti-SARS-CoV-2 spike antibodies. However, certain patient subsets have inadequate or reduced immune responses, and immune responses are known to decrease with age. General recommendations on the timing of booster vaccinations may therefore be insufficient to protect vulnerable patients. This review aims to evaluate the clinical role of anti-SARS-CoV-2 antibodies, focusing on measurement indications, prognostic value, and potential as a correlate of protection to guide future booster vaccination strategies.
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Affiliation(s)
- Sylvia Mink
- Central Medical Laboratories, 6800 Feldkirch, Austria
- Private University in the Principality of Liechtenstein, 9495 Triesen, Liechtenstein
| | - Peter Fraunberger
- Central Medical Laboratories, 6800 Feldkirch, Austria
- Private University in the Principality of Liechtenstein, 9495 Triesen, Liechtenstein
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116
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Schoefbaenker M, Neddermeyer R, Guenther T, Mueller MM, Romberg ML, Classen N, Hennies MT, Hrincius ER, Ludwig S, Kuehn JE, Lorentzen EU. Surrogate Virus Neutralisation Test Based on Nanoluciferase-Tagged Antigens to Quantify Inhibitory Antibodies against SARS-CoV-2 and Characterise Omicron-Specific Reactivity in a Vaccination Cohort. Vaccines (Basel) 2023; 11:1832. [PMID: 38140236 PMCID: PMC10748151 DOI: 10.3390/vaccines11121832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Virus-specific antibodies are crucial for protective immunity against SARS-CoV-2. Assessing functional antibodies through conventional or pseudotyped virus neutralisation tests (pVNT) requires high biosafety levels. Alternatively, the virus-free surrogate virus neutralisation test (sVNT) quantifies antibodies interfering with spike binding to angiotensin-converting enzyme 2. We evaluated secreted nanoluciferase-tagged spike protein fragments as diagnostic antigens in the sVNT in a vaccination cohort. Initially, spike fragments were tested in a capture enzyme immunoassay (EIA), identifying the receptor binding domain (RBD) as the optimal diagnostic antigen. The sensitivity of the in-house sVNT applying the nanoluciferase-labelled RBD equalled or surpassed that of a commercial sVNT (cPass, GenScript Diagnostics) and an in-house pVNT four weeks after the first vaccination (98% vs. 94% and 72%, respectively), reaching 100% in all assays four weeks after the second and third vaccinations. When testing serum reactivity with Omicron BA.1 spike, the sVNT and pVNT displayed superior discrimination between wild-type- and variant-specific serum reactivity compared to a capture EIA. This was most pronounced after the first and second vaccinations, with the third vaccination resulting in robust, cross-reactive BA.1 construct detection. In conclusion, utilising nanoluciferase-labelled antigens permits the quantification of SARS-CoV-2-specific inhibitory antibodies. Designed as flexible modular systems, the assays can be readily adjusted for monitoring vaccine efficacy.
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Affiliation(s)
- Michael Schoefbaenker
- Institute of Virology, Department of Molecular Virology, University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (M.S.); (E.R.H.); (S.L.)
| | - Rieke Neddermeyer
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Theresa Guenther
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Marlin M. Mueller
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Marie-Luise Romberg
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Nica Classen
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
- Institute of Pharmaceutical Biology and Phytochemistry, University of Muenster, Corrensstr. 48, D-48149 Muenster, Germany
| | - Marc T. Hennies
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Eike R. Hrincius
- Institute of Virology, Department of Molecular Virology, University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (M.S.); (E.R.H.); (S.L.)
| | - Stephan Ludwig
- Institute of Virology, Department of Molecular Virology, University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany; (M.S.); (E.R.H.); (S.L.)
| | - Joachim E. Kuehn
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
| | - Eva U. Lorentzen
- Institute of Virology, Department of Clinical Virology, University of Muenster, Von-Stauffenberg-Str. 36, D-48151 Muenster, Germany; (R.N.); (T.G.); (M.M.M.); (M.-L.R.); (N.C.); (M.T.H.); (J.E.K.)
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117
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Dang F, Bai L, Dong J, Hu X, Wang J, Paulo JA, Xiong Y, Liang X, Sun Y, Chen Y, Guo M, Wang X, Huang Z, Inuzuka H, Chen L, Chu C, Liu J, Zhang T, Rezaeian AH, Liu J, Kaniskan HÜ, Zhong B, Zhang J, Letko M, Jin J, Lan K, Wei W. USP2 inhibition prevents infection with ACE2-dependent coronaviruses in vitro and is protective against SARS-CoV-2 in mice. Sci Transl Med 2023; 15:eadh7668. [PMID: 38055802 PMCID: PMC10787358 DOI: 10.1126/scitranslmed.adh7668] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Targeting angiotensin-converting enzyme 2 (ACE2) represents a promising and effective approach to combat not only the COVID-19 pandemic but also potential future pandemics arising from coronaviruses that depend on ACE2 for infection. Here, we report ubiquitin specific peptidase 2 (USP2) as a host-directed antiviral target; we further describe the development of MS102, an orally available USP2 inhibitor with viable antiviral activity against ACE2-dependent coronaviruses. Mechanistically, USP2 serves as a physiological deubiquitinase of ACE2, and targeted inhibition with specific small-molecule inhibitor ML364 leads to a marked and reversible reduction in ACE2 protein abundance, thereby blocking various ACE2-dependent coronaviruses tested. Using human ACE2 transgenic mouse models, we further demonstrate that ML364 efficiently controls disease caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as evidenced by reduced viral loads and ameliorated lung inflammation. Furthermore, we improved the in vivo performance of ML364 in terms of both pharmacokinetics and antiviral activity. The resulting lead compound, MS102, holds promise as an oral therapeutic option for treating infections with coronaviruses that are reliant on ACE2.
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Affiliation(s)
- Fabin Dang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lei Bai
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiazhen Dong
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoping Hu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jingchao Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Joao A. Paulo
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xiaowei Liang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yishuang Sun
- Medical Research Institute, Wuhan University, Wuhan 430071, China
| | - Yuncai Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ming Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xin Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhixiang Huang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Li Chen
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Chen Chu
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Jianping Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Tao Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Abdol-Hossein Rezaeian
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Husnu Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bo Zhong
- Medical Research Institute, Wuhan University, Wuhan 430071, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Jinfang Zhang
- Medical Research Institute, Wuhan University, Wuhan 430071, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Michael Letko
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA 99163 USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Medical Research Institute, Wuhan University, Wuhan 430071, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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Kibria MG, Lavine CL, Tang W, Wang S, Gao H, Shi W, Zhu H, Voyer J, Rits‐Volloch S, Keerti, Bi C, Peng H, Wesemann DR, Lu J, Xie H, Seaman MS, Chen B. Antibody-mediated SARS-CoV-2 entry in cultured cells. EMBO Rep 2023; 24:e57724. [PMID: 38277394 PMCID: PMC10702815 DOI: 10.15252/embr.202357724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 01/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters host cells by first engaging its cellular receptor angiotensin converting enzyme 2 (ACE2) to induce conformational changes in the virus-encoded spike protein and fusion between the viral and target cell membranes. Here, we report that certain monoclonal neutralizing antibodies against distinct epitopic regions of the receptor-binding domain of the spike can replace ACE2 to serve as a receptor and efficiently support membrane fusion and viral infectivity in vitro. These receptor-like antibodies can function in the form of a complex of their soluble immunoglobulin G with Fc-gamma receptor I, a chimera of their antigen-binding fragment with the transmembrane domain of ACE2 or a membrane-bound B cell receptor, indicating that ACE2 and its specific interaction with the spike protein are dispensable for SARS-CoV-2 entry. These results suggest that antibody responses against SARS-CoV-2 may help expand the viral tropism to otherwise nonpermissive cell types with potential implications for viral transmission and pathogenesis.
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Affiliation(s)
- Md Golam Kibria
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
- Department of PediatricsHarvard Medical SchoolBostonMAUSA
| | - Christy L Lavine
- Center for Virology and Vaccine ResearchBeth Israel Deaconess Medical CenterBostonMAUSA
| | - Weichun Tang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMDUSA
| | | | - Hailong Gao
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
- Department of PediatricsHarvard Medical SchoolBostonMAUSA
| | - Wei Shi
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
- Department of PediatricsHarvard Medical SchoolBostonMAUSA
| | - Haisun Zhu
- Institute for Protein Innovation, Harvard Institutes of MedicineBostonMAUSA
| | - Jewel Voyer
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
| | | | - Keerti
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's HospitalRagon Institute of MGH, MIT and HarvardBostonMAUSA
| | - Caihong Bi
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's HospitalRagon Institute of MGH, MIT and HarvardBostonMAUSA
| | - Hanqin Peng
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
| | - Duane R Wesemann
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's HospitalRagon Institute of MGH, MIT and HarvardBostonMAUSA
| | - Jianming Lu
- Codex BioSolutions, Inc.RockvilleMDUSA
- Department of Biochemistry and Molecular and Cellular BiologyGeorgetown UniversityWashingtonDCUSA
| | - Hang Xie
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMDUSA
| | - Michael S Seaman
- Center for Virology and Vaccine ResearchBeth Israel Deaconess Medical CenterBostonMAUSA
| | - Bing Chen
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
- Department of PediatricsHarvard Medical SchoolBostonMAUSA
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119
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Jawad B, Adhikari P, Podgornik R, Ching WY. Impact of BA.1, BA.2, and BA.4/BA.5 Omicron mutations on therapeutic monoclonal antibodies. Comput Biol Med 2023; 167:107576. [PMID: 37871435 DOI: 10.1016/j.compbiomed.2023.107576] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 10/01/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
The emergence of Omicron SARS-CoV-2 subvariants (BA.1, BA.2, BA.4, and BA.5), with an unprecedented number of mutations in their receptor-binding domain (RBD) of the spike-protein, has fueled a resurgence of COVID-19 infections, posing a major challenge to the efficacy of existing vaccines and monoclonal antibody (mAb) therapeutics. We conducted a systematic molecular dynamics (MD) simulation to investigate how the RBD mutations of these subvariants affect the interactions with broad mAbs including AstraZeneca (COV2-2196 and COV2-2130), Brii Biosciences (BRII-196), Celltrion (CT-P59), Eli Lilly (LY-CoV555 and LY-CoV016), Regeneron (REGN10933 and REGN10987), Vir Biotechnology (S309), and S2X259. Our results show a complete loss of binding for COV2-2196, BRII-196, CT-P59, and LY-CoV555 with all Omicron RBDs. Additionally, REGN10987 totally loses its binding with BA.1, but retains a partial binding with BA.2 and BA.4/5. The binding reduction is significant for LY-CoV016 and REGN10933 but moderate for COV2-2130. S309 and S2X259 retain their binding with BA.1 but exhibit decreased binding with other subvariants. We introduce a mutational escape map for each mAb to identify the key RBD sites and the corresponding critical mutations. Overall, our findings suggest that the majority of therapeutic mAbs have diminished or missing activity against Omicron subvariants, indicating the urgent need for a new therapeutic mAb with a better design.
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Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, 64110, United States; Department of Applied Sciences, University of Technology, Baghdad, 10066, Iraq.
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, 64110, United States
| | - Rudolf Podgornik
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing, 100049, China; CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100090, China; Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, 64110, United States
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120
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Thakur S, Planeta Kepp K, Mehra R. Predicting virus Fitness: Towards a structure-based computational model. J Struct Biol 2023; 215:108042. [PMID: 37931730 DOI: 10.1016/j.jsb.2023.108042] [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: 07/25/2023] [Revised: 10/12/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Predicting the impact of new emerging virus mutations is of major interest in surveillance and for understanding the evolutionary forces of the pathogens. The SARS-CoV-2 surface spike-protein (S-protein) binds to human ACE2 receptors as a critical step in host cell infection. At the same time, S-protein binding to human antibodies neutralizes the virus and prevents interaction with ACE2. Here we combine these two binding properties in a simple virus fitness model, using structure-based computation of all possible mutation effects averaged over 10 ACE2 complexes and 10 antibody complexes of the S-protein (∼380,000 computed mutations), and validated the approach against diverse experimental binding/escape data of ACE2 and antibodies. The ACE2-antibody selectivity change caused by mutation (i.e., the differential change in binding to ACE2 vs. immunity-inducing antibodies) is proposed to be a key metric of fitness model, enabling systematic error cancelation when evaluated. In this model, new mutations become fixated if they increase the selective binding to ACE2 relative to circulating antibodies, assuming that both are present in the host in a competitive binding situation. We use this model to categorize viral mutations that may best reach ACE2 before being captured by antibodies. Our model may aid the understanding of variant-specific vaccines and molecular mechanisms of viral evolution in the context of a human host.
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Affiliation(s)
- Shivani Thakur
- Department of Chemistry, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India
| | - Kasper Planeta Kepp
- DTU Chemistry, Technical University of Denmark, Building 206, 2800 Kongens Lyngby, Denmark
| | - Rukmankesh Mehra
- Department of Chemistry, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India; Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India.
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121
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Kumar S, Delipan R, Chakraborty D, Kanjo K, Singh R, Singh N, Siddiqui S, Tyagi A, Jha V, Thakur KG, Pandey R, Varadarajan R, Ringe RP. Mutations in S2 subunit of SARS-CoV-2 Omicron spike strongly influence its conformation, fusogenicity, and neutralization sensitivity. J Virol 2023; 97:e0092223. [PMID: 37861334 PMCID: PMC10688319 DOI: 10.1128/jvi.00922-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE The Omicron subvariants have substantially evaded host-neutralizing antibodies and adopted an endosomal route of entry. The virus has acquired several mutations in the receptor binding domain and N-terminal domain of S1 subunit, but remarkably, also incorporated mutations in S2 which are fixed in Omicron sub-lineage. Here, we found that the mutations in the S2 subunit affect the structural and biological properties such as neutralization escape, entry route, fusogenicity, and protease requirement. In vivo, these mutations may have significant roles in tropism and replication. A detailed understanding of the effects of S2 mutations on Spike function, immune evasion, and viral entry would inform the vaccine design, as well as therapeutic interventions aiming to block the essential proteases for virus entry. Thus, our study has identified the crucial role of S2 mutations in stabilizing the Omicron spike and modulating neutralization resistance to antibodies targeting the S1 subunit.
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Affiliation(s)
- Sahil Kumar
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Rathina Delipan
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | | | - Kawkab Kanjo
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | | | - Nittu Singh
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Samreen Siddiqui
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Akansha Tyagi
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Vinitaa Jha
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Krishan G. Thakur
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | | | - Rajesh P. Ringe
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
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122
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Niedre-Otomere B, Kampenusa I, Trofimova J, Bodrenko J, Vangravs R, Skenders G, Nikisins S, Savicka O. Multiplexed RT-qPCR Coupled with Whole-Genome Sequencing to Monitor a SARS-CoV-2 Omicron Variant of Concern in a Hospital Laboratory Setting in Latvia. Diagnostics (Basel) 2023; 13:3467. [PMID: 37998603 PMCID: PMC10670528 DOI: 10.3390/diagnostics13223467] [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: 10/13/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023] Open
Abstract
At the end of 2021, the SARS-CoV-2 Omicron variant of concern (VOC) displaced the previously dominant Delta VOC and enhanced diagnostic and therapeutic challenges worldwide. Respiratory specimens submitted to the Riga East University Hospital Laboratory Service by the central and regional hospitals of Latvia from January to March 2022 that were positive for SARS-CoV-2 RNA were tested by commercial multiplexed RT-qPCR targeting three of the Omicron VOC signature mutations: ΔH69/V70, E484A, and N501Y. Of the specimens tested and analyzed in parallel by whole-genome sequencing (WGS), 964 passed the internal quality criteria (genome coverage ≥90%, read depth ≥400×) and the Nextstrain's quality threshold for "good". We validated the detection accuracy of RT-qPCR for each target individually by using WGS as a control. The results were concordant with both approaches for 938 specimens, with the correct classification rate exceeding 96% for each target (CI 95%); however, the presumptive WHO label was misassigned for 21 specimens. The RT-qPCR genotyping provided an acceptable means to pre-monitor the prevalence of the two presumptive Omicron VOC sublineages, BA.1 and BA.2.
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123
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Keitany GJ, Rubin BER, Garrett ME, Musa A, Tracy J, Liang Y, Ebert P, Moore AJ, Guan J, Eggers E, Lescano N, Brown R, Carbo A, Al-Asadi H, Ching T, Day A, Harris R, Linkem C, Popov D, Wilkins C, Li L, Wang J, Liu C, Chen L, Dines JN, Atyeo C, Alter G, Baldo L, Sherwood A, Howie B, Klinger M, Yusko E, Robins HS, Benzeno S, Gilbert AE. Multimodal, broadly neutralizing antibodies against SARS-CoV-2 identified by high-throughput native pairing of BCRs from bulk B cells. Cell Chem Biol 2023; 30:1377-1389.e8. [PMID: 37586370 PMCID: PMC10659930 DOI: 10.1016/j.chembiol.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/25/2023] [Accepted: 07/23/2023] [Indexed: 08/18/2023]
Abstract
TruAB Discovery is an approach that integrates cellular immunology, high-throughput immunosequencing, bioinformatics, and computational biology in order to discover naturally occurring human antibodies for prophylactic or therapeutic use. We adapted our previously described pairSEQ technology to pair B cell receptor heavy and light chains of SARS-CoV-2 spike protein-binding antibodies derived from enriched antigen-specific memory B cells and bulk antibody-secreting cells. We identified approximately 60,000 productive, in-frame, paired antibody sequences, from which 2,093 antibodies were selected for functional evaluation based on abundance, isotype and patterns of somatic hypermutation. The exceptionally diverse antibodies included RBD-binders with broad neutralizing activity against SARS-CoV-2 variants, and S2-binders with broad specificity against betacoronaviruses and the ability to block membrane fusion. A subset of these RBD- and S2-binding antibodies demonstrated robust protection against challenge in hamster and mouse models. This high-throughput approach can accelerate discovery of diverse, multifunctional antibodies against any target of interest.
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Affiliation(s)
| | | | | | - Andrea Musa
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Jeff Tracy
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Yu Liang
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Peter Ebert
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | - Erica Eggers
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | - Ryan Brown
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Adria Carbo
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | - Austin Day
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | | | | | - Lianqu Li
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Jiao Wang
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Chuanxin Liu
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Li Chen
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Lance Baldo
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | - Bryan Howie
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Mark Klinger
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Erik Yusko
- Adaptive Biotechnologies, Seattle, WA 98109, USA
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Gayvert K, McKay S, Lim WK, Baum A, Kyratsous C, Copin R, Atwal GS. Evolutionary trajectory of SARS-CoV-2 genome shifts during widespread vaccination and emergence of Omicron variant. NPJ VIRUSES 2023; 1:5. [PMID: 40295667 PMCID: PMC11721106 DOI: 10.1038/s44298-023-00007-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/25/2023] [Indexed: 04/30/2025]
Abstract
Understanding the adaptation of SARS-CoV-2 is critical for the development of effective treatments against this exceptionally successful human pathogen. To predict the emergence of new variants that may escape host immunity or increase virulence, it is important to characterize the biological forces driving its evolution. We conducted a comprehensive population genetic study of over thirteen million SARS-CoV-2 genome sequences, collected over a timeframe of ~3 years, to investigate these forces. Our analysis revealed that during the first year of the pandemic (2020 to 2021), the SARS-CoV-2 genome was subject to strong conservation, with only 3.6% of sites under diversifying pressure in the receptor binding domain (RBD) of the Spike protein. However, we observed a sharp increase in the diversification of the RBD during 2021 (8.1% of sites under diversifying pressure up to 2022), indicating selective pressures that promote the accumulation of mutations. This period coincided with broad viral infection and adoption of vaccination worldwide, and we observed the acquisition of mutations that later defined the Omicron lineages in independent SARS-CoV-2 strains, suggesting that diversifying selection at these sites could have led to their fixation in Omicron lineages by convergent evolution. Since the emergence of Omicron, we observed a further decrease in the conservation of structural genes, including M, N, and the spike proteins (13.1% of RBD sites under diversifying pressure up to 2023), and identified new sites defining future potential emerging strains. Our results exhibit that ongoing rapid antigenic evolution continues to produce new high-frequency functional variants. Sites under selection are critical for virus fitness, and currently known T cell epitope sequences are highly conserved. Altogether, our study provides a comprehensive dynamic map of sites under selection and conservation across the entirety of the SARS-CoV-2 genome.
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Affiliation(s)
| | - Sheldon McKay
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10091, USA
| | - Wei Keat Lim
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10091, USA
| | - Alina Baum
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10091, USA
| | | | - Richard Copin
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10091, USA.
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125
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Dasgupta A, Gangai S, Narayan R, Kapoor S. Mapping the Lipid Signatures in COVID-19 Infection: Diagnostic and Therapeutic Solutions. J Med Chem 2023; 66:14411-14433. [PMID: 37899546 DOI: 10.1021/acs.jmedchem.3c01238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
The COVID-19 pandemic ignited research centered around the identification of robust biomarkers and therapeutic targets. SARS-CoV-2, the virus responsible, hijacks the metabolic machinery of the host cells. It relies on lipids and lipoproteins of host cells for entry, trafficking, immune evasion, viral replication, and exocytosis. The infection causes host cell lipid metabolic remodelling. Targeting lipid-based processes is thus a promising strategy for countering COVID-19. Here, we review the role of lipids in the different steps of the SARS-CoV-2 pathogenesis and identify lipid-centric targetable avenues. We discuss lipidome changes in infected patients and their relevance as potential clinical diagnostic or prognostic biomarkers. We summarize the emerging direct and indirect therapeutic approaches for targeting COVID-19 using lipid-inspired approaches. Given that viral protein-targeted therapies may become less effective due to mutations in emerging SARS-CoV-2 variants, lipid-inspired interventions may provide additional and perhaps better means of combating this and future pandemics.
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Affiliation(s)
- Aishi Dasgupta
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- IIT-Bombay Monash Academy, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Shon Gangai
- School of Chemical and Materials Sciences (SCMS), Institute of Technology Goa, Farmagudi, Ponda, Goa 403401, India
| | - Rishikesh Narayan
- School of Chemical and Materials Sciences (SCMS), Institute of Technology Goa, Farmagudi, Ponda, Goa 403401, India
- School of Interdisciplinary Life Sciences (SILS), Institute of Technology Goa, Farmagudi, Ponda, Goa 403401, India
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- IIT-Bombay Monash Academy, Indian Institute of Technology Bombay, Mumbai 400076, India
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8528, Japan
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126
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Le K, Kannappan S, Kim T, Lee JH, Lee HR, Kim KK. Structural understanding of SARS-CoV-2 virus entry to host cells. Front Mol Biosci 2023; 10:1288686. [PMID: 38033388 PMCID: PMC10683510 DOI: 10.3389/fmolb.2023.1288686] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major global health concern associated with millions of fatalities worldwide. Mutant variants of the virus have further exacerbated COVID-19 mortality and infection rates, emphasizing the urgent need for effective preventive strategies. Understanding the viral infection mechanism is crucial for developing therapeutics and vaccines. The entry of SARS-CoV-2 into host cells is a key step in the infection pathway and has been targeted for drug development. Despite numerous reviews of COVID-19 and the virus, there is a lack of comprehensive reviews focusing on the structural aspects of viral entry. In this review, we analyze structural changes in Spike proteins during the entry process, dividing the entry process into prebinding, receptor binding, proteolytic cleavage, and membrane fusion steps. By understanding the atomic-scale details of viral entry, we can better target the entry step for intervention strategies. We also examine the impacts of mutations in Spike proteins, including the Omicron variant, on viral entry. Structural information provides insights into the effects of mutations and can guide the development of therapeutics and vaccines. Finally, we discuss available structure-based approaches for the development of therapeutics and vaccines. Overall, this review provides a detailed analysis of the structural aspects of SARS-CoV-2 viral entry, highlighting its significance in the development of therapeutics and vaccines against COVID-19. Therefore, our review emphasizes the importance of structural information in combating SARS-CoV-2 infection.
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Affiliation(s)
- Kim Le
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
| | - Shrute Kannappan
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
- Research Center for Advanced Materials Technology Core Research Institute, Suwon, Republic of Korea
| | - Truc Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jung Heon Lee
- Research Center for Advanced Materials Technology Core Research Institute, Suwon, Republic of Korea
- School of Advanced Materials and Science Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hye-Ra Lee
- Department of Biotechnology and Bioinformatics, College of Science and Technology, Korea University, Sejong, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Sungkyunkwan University, Suwon, Republic of Korea
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Bhattacharya M, Chatterjee S, Lee SS, Dhama K, Chakraborty C. Antibody evasion associated with the RBD significant mutations in several emerging SARS-CoV-2 variants and its subvariants. Drug Resist Updat 2023; 71:101008. [PMID: 37757651 DOI: 10.1016/j.drup.2023.101008] [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: 01/18/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
Since the origin of the wild strain of SARS-CoV-2, several variants have emerged, which were designated as VOC, VOI, and VUM from time to time. The Omicron variant is noted as the recent VOC. After the origin of the Omicron variant on November 2021, several subvariants of Omicron have originated subsequently, like BA.1/2, BA.2.75/2.75.2, BA.4/5, BF.7, BQ.1/1.1, XBB.1/1.5, etc. which are circulated throughout the globe. Scientists reported that antibody escape is a common phenomenon observed in all the previous VOCs, VOIs, including Omicron and its subvariants. The mutations in the NTD (N-terminal domain) and RBD (Receptor-binding domain) of the spike of these variants and subvariants are responsible for antibody escape. At the same time, it has been noted that spike RBD mutations have been increasing in the last few months. This review illustrates significant RBD mutations namely R346T, K417N/T, L452R, N460K E484A/K/Q, and N501Y found in the previous emerging SARS-CoV-2 variants, including Omicron and its subvariants in high frequency and their role in antibody evasion and immune evasion. The review also describes the different classes of nAb responsible for antibody escape in SARS-CoV-2 variants and the molecular perspective of the mutation in nAb escape. It will help the future researchers to develop efficient vaccines which can finally prevent the pandemic.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Srijan Chatterjee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata 700126, West Bengal, India.
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Tulsian NK, Palur RV, Qian X, Gu Y, D/O Shunmuganathan B, Samsudin F, Wong YH, Lin J, Purushotorman K, Kozma MM, Wang B, Lescar J, Wang CI, Gupta RK, Bond PJ, MacAry PA. Defining neutralization and allostery by antibodies against COVID-19 variants. Nat Commun 2023; 14:6967. [PMID: 37907459 PMCID: PMC10618280 DOI: 10.1038/s41467-023-42408-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023] Open
Abstract
The changing landscape of SARS-CoV-2 Spike protein is linked to the emergence of variants, immune-escape and reduced efficacy of the existing repertoire of anti-viral antibodies. The functional activity of neutralizing antibodies is linked to their quaternary changes occurring as a result of antibody-Spike trimer interactions. Here, we reveal the conformational dynamics and allosteric perturbations linked to binding of novel human antibodies and the viral Spike protein. We identified epitope hotspots, and associated changes in Spike dynamics that distinguish weak, moderate and strong neutralizing antibodies. We show the impact of mutations in Wuhan-Hu-1, Delta, and Omicron variants on differences in the antibody-induced conformational changes in Spike and illustrate how these render certain antibodies ineffective. Antibodies with similar binding affinities may induce destabilizing or stabilizing allosteric effects on Spike, with implications for neutralization efficacy. Our results provide mechanistic insights into the functional modes and synergistic behavior of human antibodies against COVID-19 and may assist in designing effective antiviral strategies.
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Affiliation(s)
- Nikhil Kumar Tulsian
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- Department of Biochemistry, National University of Singapore, Singapore, 117546, Singapore.
| | - Raghuvamsi Venkata Palur
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138761, Singapore
| | - Xinlei Qian
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
| | - Yue Gu
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
| | - Bhuvaneshwari D/O Shunmuganathan
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
| | - Firdaus Samsudin
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138761, Singapore
| | - Yee Hwa Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Experimental Medicine Building, Singapore, 636921, Singapore
| | - Jianqing Lin
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Experimental Medicine Building, Singapore, 636921, Singapore
| | - Kiren Purushotorman
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
| | - Mary McQueen Kozma
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
| | - Bei Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Experimental Medicine Building, Singapore, 636921, Singapore
| | - Cheng-I Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
| | - Ravindra Kumar Gupta
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Peter John Bond
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138761, Singapore.
| | - Paul Anthony MacAry
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore.
- Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore.
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129
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Peng S, Husnain Raza Shah S, Mei S, Gene Vong E, Sun Y, Zhan J. RBD-specific single-chain antibody protects against acute lung injury in mice. Int Immunopharmacol 2023; 124:111020. [PMID: 37812969 DOI: 10.1016/j.intimp.2023.111020] [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: 08/07/2023] [Revised: 09/24/2023] [Accepted: 10/01/2023] [Indexed: 10/11/2023]
Abstract
As SARS-CoV-2 variants continue spreading globally, the discovery of broad spectrum therapeutically active antibodies with retaining good protective activity is a global priority. It was reported that infection with SARS-CoV-2 could cause acute lung injury (ALI) in clinical investigations. Therefore, we discovered that anti-RBD scFv is effective against SARS-CoV-2-induced ALI. To begin, we utilized the receptor binding domain (RBD) of spike glycoprotein as a target to produce single-chain antibodies (scFvs) through an intensive phage display technology. The binding affinity and inhibitory effect of the scFvs were evaluated via ELISA and flow cytometry. Moreover, anti-RBD scFv No.35 significantly prevented ALI caused by LPS and SARS-CoV-2 spike RBD protein in mouse model. Thus, the anti-RBD scFv will aid the development of potential antibody treatments and reduce the inflammatory response of SARS-CoV-2.
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Affiliation(s)
- Shanshan Peng
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou 310056, China
| | - Syed Husnain Raza Shah
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou 310056, China
| | - Shengsheng Mei
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou 310056, China
| | - Eu Gene Vong
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou 310056, China
| | - Yisheng Sun
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Jinbiao Zhan
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), School of Medicine, Zhejiang University, Hangzhou 310056, China.
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130
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Sobhani K, Cheng S, Binder RA, Mantis NJ, Crawford JM, Okoye N, Braun JG, Joung S, Wang M, Lozanski G, King CL, Roback JD, Granger DA, Boppana SB, Karger AB. Clinical Utility of SARS-CoV-2 Serological Testing and Defining a Correlate of Protection. Vaccines (Basel) 2023; 11:1644. [PMID: 38005976 PMCID: PMC10674881 DOI: 10.3390/vaccines11111644] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/26/2023] Open
Abstract
Herein, we review established clinical use cases for SARS-CoV-2 antibody measures, which include diagnosis of recent prior infection, isolating high titer convalescent plasma, diagnosing multisystem inflammatory syndrome in children (MIS-C), and booster dosing in the immunosuppressed and other populations. We then address whether an antibody correlate of protection (CoP) for SARS-CoV-2 has been successfully defined with the following considerations: Antibody responses in the immunocompetent, vaccine type, variants, use of binding antibody tests vs. neutralization tests, and endpoint measures. In the transition from the COVID-19 pandemic to endemic, there has been much interest in defining an antibody CoP. Due to the high mutability of respiratory viruses and our current knowledge of SARS-CoV-2 variants defining a CoP for prevention of infection is unrealistic. However, a CoP may be defined for prevention of severe disease requiring hospitalization and/or death. Most SARS-CoV-2 CoP research has focused on neutralization measurements. However, there can be significant differences in neutralization test methods, and disparate responses to new variants depending on format. Furthermore, neutralization assays are often impractical for high throughput applications (e.g., assessing humoral immune response in populations or large cohorts). Nevertheless, CoP studies using neutralization measures are reviewed to determine where there is consensus. Alternatively, binding antibody tests could be used to define a CoP. Binding antibody assays tend to be highly automatable, high throughput, and therefore practical for large population applications. Again, we review studies for consensus on binding antibody responses to vaccines, focusing on standardized results. Binding antibodies directed against the S1 receptor binding domain (S1-RBD) of the viral spike protein can provide a practical, indirect measure of neutralization. Initially, a response for S1-RBD antibodies may be selected that reflects the peak response in immunocompetent populations and may serve as a target for booster dosing in the immunocompromised. From existing studies reporting peak S1-RBD responses in standardized units, an approximate range of 1372-2744 BAU/mL for mRNA and recombinant protein vaccines was extracted that could serve as an initial CoP target. This target would need to be confirmed and potentially adjusted for updated vaccines, and almost certainly for other vaccine formats (i.e., viral vector). Alternatively, a threshold or response could be defined based on outcomes over time (i.e., prevention of severe disease). We also discuss the precedent for clinical measurement of antibodies for vaccine-preventable diseases (e.g., hepatitis B). Lastly, cellular immunity is briefly addressed for its importance in the nature and durability of protection.
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Affiliation(s)
- Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA; (S.C.)
| | - Raquel A. Binder
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Nicholas J. Mantis
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY 12222, USA
| | - James M. Crawford
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Nkemakonam Okoye
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Jonathan G. Braun
- Department of Pathology and Laboratory Medicine, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sandy Joung
- Department of Cardiology, Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA; (S.C.)
| | - Minhao Wang
- Department of Cardiology, Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA; (S.C.)
| | - Gerard Lozanski
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Christopher L. King
- Department of Pathology, Case Western Reserve University and Veterans Affairs Research Service, Cleveland, OH 44106, USA
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Douglas A. Granger
- Institute for Interdisciplinary Salivary Bioscience Research, University of California Irvine, Irvine, CA 92697, USA
| | - Suresh B. Boppana
- Department of Pediatrics and Department of Microbiology, Heersink School of Medicine, UAB, Birmingham, AL 35233, USA
| | - Amy B. Karger
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA;
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131
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Gilliland T, Dunn M, Liu Y, Alcorn MD, Terada Y, Vasilatos S, Lundy J, Li R, Nambulli S, Larson D, Duprex P, Wu H, Luke T, Bausch C, Egland K, Sullivan E, Wang Z, Klimstra WB. Transchromosomic bovine-derived anti-SARS-CoV-2 polyclonal human antibodies protects hACE2 transgenic hamsters against multiple variants. iScience 2023; 26:107764. [PMID: 37736038 PMCID: PMC10509298 DOI: 10.1016/j.isci.2023.107764] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/24/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Abstract
Pandemic SARS-CoV-2 has undergone rapid evolution resulting in the emergence of many variants with mutations in the spike protein, some of which appear to evade antibody neutralization, transmit more efficiently, and/or exhibit altered virulence. This raises significant concerns regarding the efficacy of anti-S monoclonal antibody-based therapeutics which have failed against variant SARS-CoV-2 viruses. To address this concern, SAB-185, a human anti-SARS-CoV-2 polyclonal antibody was generated in the DiversitAb platform. SAB-185 exhibited equivalent, robust in vitro neutralization for Munich, Alpha, Beta, Gamma, and Δ144-146 variants and, although diminished, retained PRNT50 and PRNT80 neutralization endpoints for Delta and Omicron variants. Human ACE2 transgenic Syrian hamsters, which exhibit lethal SARS-CoV-2 disease, were protected from mortality after challenge with the Munich, Alpha, Beta, Delta, and Δ144-146 variants and clinical signs after non-lethal Omicron BA.1 infection. This suggests that SAB-185 may be an effective immunotherapy even in the presence of ongoing viral mutation.
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Affiliation(s)
- Theron Gilliland
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Matthew Dunn
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yanan Liu
- Department of Animal Dairy, Veterinary Sciences, Utah State University, Logan, UT 84341, USA
| | - Maria D.H. Alcorn
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yutaka Terada
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Shauna Vasilatos
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jeneveve Lundy
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Rong Li
- Department of Animal Dairy, Veterinary Sciences, Utah State University, Logan, UT 84341, USA
| | - Sham Nambulli
- Center for Vaccine Research and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Deanna Larson
- Department of Animal Dairy, Veterinary Sciences, Utah State University, Logan, UT 84341, USA
| | - Paul Duprex
- Center for Vaccine Research and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hua Wu
- SAb Biotherapeutics, Inc, Sioux Falls, SD 57104, USA
| | - Thomas Luke
- SAb Biotherapeutics, Inc, Sioux Falls, SD 57104, USA
| | | | - Kristi Egland
- SAb Biotherapeutics, Inc, Sioux Falls, SD 57104, USA
| | | | - Zhongde Wang
- Department of Animal Dairy, Veterinary Sciences, Utah State University, Logan, UT 84341, USA
| | - William B. Klimstra
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
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132
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Wu D, Cong J, Wei J, Hu J, Sun W, Ran W, Liao C, Zheng H, Ye L. A Naïve Phage Display Library-Derived Nanobody Neutralizes SARS-CoV-2 and Three Variants of Concern. Int J Nanomedicine 2023; 18:5781-5795. [PMID: 37869063 PMCID: PMC10588750 DOI: 10.2147/ijn.s427990] [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: 06/28/2023] [Accepted: 10/07/2023] [Indexed: 10/24/2023] Open
Abstract
Background The emergence of the coronavirus disease 2019 (COVID-19) pandemic and the new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs) requires the continuous development of safe, effective, and affordable prevention and therapeutics. Nanobodies have demonstrated antiviral activity against a variety of viruses, providing a new candidate for the prevention and treatment of SARS-CoV-2 and its variants. Methods SARS-CoV-2 glycoprotein spike 1 subunit (S1) was selected as the target antigen for nanobody screening of a naïve phage display library. We obtained a nanobody, named Nb-H6, and then determined its affinity, inhibition, and stability by ELISA, Competitive ELISA, and Biolayer Interferometry (BLI). Infection assays of authentic and pseudotyped SARS-CoV-2 were performed to evaluate the neutralization of Nb-H6. The structure and mechanism of action were investigated by AlphaFold, docking, and residue mutation assays. Results We isolated and characterized a nanobody, Nb-H6, which exhibits a broad affinity for S1 and the receptor binding domain (RBD) of SARS-CoV-2, or Alpha (B.1.1.7), Delta (B.1.617.2), Lambda (C.37), and Omicron (BA.2 and BA.5), and blocks receptor angiotensin-converting enzyme 2 (ACE2) binding. Moreover, Nb-H6 can retain its binding capability after pH or thermal treatment and effectively neutralize both pseudotyped and authentic SARS-CoV-2, as well as VOC Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (BA.2 and BA.5) pseudoviruses. We also confirmed that Nb-H6 binds two distinct amino acid residues of the RBD, preventing SARS-CoV-2 from interacting with the host receptor. Conclusion Our study highlights a novel nanobody, Nb-H6, that may be useful therapeutically in SARS-CoV-2 and VOC outbreaks and pandemics. These findings also provide a molecular foundation for further studies into how nanobodies neutralize SARS-CoV-2 and variants and imply potential therapeutic targets for the treatment of COVID-19.
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Affiliation(s)
- Dandan Wu
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Junxiao Cong
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Jiali Wei
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Jing Hu
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Wenhao Sun
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Wei Ran
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Chenghui Liao
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Housheng Zheng
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
| | - Liang Ye
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, People’s Republic of China
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133
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Liu L, Casner RG, Guo Y, Wang Q, Iketani S, Chan JFW, Yu J, Dadonaite B, Nair MS, Mohri H, Reddem ER, Yuan S, Poon VKM, Chan CCS, Yuen KY, Sheng Z, Huang Y, Bloom JD, Shapiro L, Ho DD. Antibodies targeting a quaternary site on SARS-CoV-2 spike glycoprotein prevent viral receptor engagement by conformational locking. Immunity 2023; 56:2442-2455.e8. [PMID: 37776849 PMCID: PMC10588992 DOI: 10.1016/j.immuni.2023.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/10/2023] [Accepted: 09/06/2023] [Indexed: 10/02/2023]
Abstract
SARS-CoV-2 continues to evolve, with many variants evading clinically authorized antibodies. To isolate monoclonal antibodies (mAbs) with broadly neutralizing capacities against the virus, we screened serum samples from convalescing COVID-19 patients. We isolated two mAbs, 12-16 and 12-19, which neutralized all SARS-CoV-2 variants tested, including the XBB subvariants, and prevented infection in hamsters challenged with Omicron BA.1 intranasally. Structurally, both antibodies targeted a conserved quaternary epitope located at the interface between the N-terminal domain and subdomain 1, uncovering a site of vulnerability on SARS-CoV-2 spike. These antibodies prevented viral receptor engagement by locking the receptor-binding domain (RBD) of spike in the down conformation, revealing a mechanism of virus neutralization for non-RBD antibodies. Deep mutational scanning showed that SARS-CoV-2 could mutate to escape 12-19, but such mutations are rarely found in circulating viruses. Antibodies 12-16 and 12-19 hold promise as prophylactic agents for immunocompromised persons who do not respond robustly to COVID-19 vaccines.
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Affiliation(s)
- Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Ryan G Casner
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Qian Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Hiroshi Mohri
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Eswar R Reddem
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Vincent Kwok-Man Poon
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Chris Chung-Sing Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Lawrence Shapiro
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
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Santos da Silva E, Servais JY, Kohnen M, Arendt V, Staub T, the CON-VINCE Consortium, the CoVaLux Consortium, Krüger R, Fagherazzi G, Wilmes P, Hübschen JM, Ollert M, Perez-Bercoff D, Seguin-Devaux C. Validation of a SARS-CoV-2 Surrogate Neutralization Test Detecting Neutralizing Antibodies against the Major Variants of Concern. Int J Mol Sci 2023; 24:14965. [PMID: 37834413 PMCID: PMC10573711 DOI: 10.3390/ijms241914965] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
SARS-CoV-2 infection and/or vaccination elicit a broad range of neutralizing antibody responses against the different variants of concern (VOC). We established a new variant-adapted surrogate virus neutralization test (sVNT) and assessed the neutralization activity against the ancestral B.1 (WT) and VOC Delta, Omicron BA.1, BA.2, and BA.5. Analytical performances were compared against the respective VOC to the reference virus neutralization test (VNT) and two CE-IVD labeled kits using three different cohorts collected during the COVID-19 waves. Correlation analyses showed moderate to strong correlation for Omicron sub-variants (Spearman's r = 0.7081 for BA.1, r = 0.7205 for BA.2, and r = 0.6042 for BA.5), and for WT (r = 0.8458) and Delta-sVNT (r = 0.8158), respectively. Comparison of the WT-sVNT performance with two CE-IVD kits, the "Icosagen SARS-CoV-2 Neutralizing Antibody ELISA kit" and the "Genscript cPass, kit" revealed an overall good correlation ranging from 0.8673 to -0.8773 and a midway profile between both commercial kits with 87.76% sensitivity and 90.48% clinical specificity. The BA.2-sVNT performance was similar to the BA.2 Genscript test. Finally, a correlation analysis revealed a strong association (r = 0.8583) between BA.5-sVNT and VNT sVNT using a double-vaccinated cohort (n = 100) and an Omicron-breakthrough infection cohort (n = 91). In conclusion, the sVNT allows for the efficient prediction of immune protection against the various VOCs.
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Affiliation(s)
- Eveline Santos da Silva
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Jean-Yves Servais
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Michel Kohnen
- National Service of Infectious Diseases, Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (V.A.); (T.S.)
| | - Vic Arendt
- National Service of Infectious Diseases, Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (V.A.); (T.S.)
| | - Therese Staub
- National Service of Infectious Diseases, Centre Hospitalier de Luxembourg, 4 Rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (V.A.); (T.S.)
| | | | | | - Rejko Krüger
- Transversal Translational Medicine, Luxembourg Institute of Health; Centre Hospitalier de Luxembourg, 4 rue Ernest Barblé, L-1210 Luxembourg, Luxembourg;
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Guy Fagherazzi
- Department of Precision Health, Luxembourg Institute of Health, 1AB Rue Thomas Edison, L-1445 Strassen, Luxembourg;
| | - Paul Wilmes
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, 7 Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg;
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Judith M. Hübschen
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Danielle Perez-Bercoff
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (J.M.H.); (M.O.); (D.P.-B.)
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135
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Yasugi M, Nakagama Y, Kaku N, Nitahara Y, Hatanaka N, Yamasaki S, Kido Y. Characteristics of epitope dominance pattern and cross-variant neutralisation in 16 SARS-CoV-2 mRNA vaccine sera. Vaccine 2023; 41:6248-6254. [PMID: 37673717 DOI: 10.1016/j.vaccine.2023.08.076] [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: 05/22/2023] [Revised: 08/09/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023]
Abstract
SARS-CoV-2 serological studies suggest that individual serum antibody repertoires can affect neutralisation breadth. Herein, we asked whether a BNT162b2 vaccine-induced epitope dominance pattern (i.e., predominant viral structural domain targeted by serum antibodies for virus neutralisation) affects cross-variant neutralisation. When a neutralisation assay against the ancestral strain was carried out using 16 vaccine sera preabsorbed with a recombinant receptor-binding domain (RBD) or an N-terminal domain (NTD) protein, three and 13 sera, respectively, showed lower neutralisation under NTD and RBD protein-preabsorbed conditions than under the other protein-preabsorbed conditions. This suggests that the NTD was responsible for virus neutralisation in three sera, whereas the other 13 sera elicited RBD-dominant neutralisation. The results also suggest the presence of infectivity-enhancing antibodies in four out of the 13 RBD-dominant sera. A neutralisation assay using SARS-CoV-2 variants revealed that NTD-dominant sera showed significantly reduced neutralising activity against the B.1.617.2 variant, whereas RBD-dominant sera retained neutralising activity even in the presence of infectivity-enhancing antibodies. Taken together, these results suggest the followings: (i) epitope dominance patterns are divided into at least two types: NTD-dominant and RBD-dominant; (ii) NTD-dominant sera have less potential to neutralise the B.1.617.2 variant than RBD-dominant sera; and (iii) infectivity-enhancing antibodies play a limited role in cross-variant neutralisation against the five variants tested.
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Affiliation(s)
- Mayo Yasugi
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan; Asian Health Science Research Institute, Osaka Metropolitan University, Izumisano, Osaka, Japan; Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan.
| | - Yu Nakagama
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan; Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Natsuko Kaku
- Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yuko Nitahara
- Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Noritoshi Hatanaka
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan; Asian Health Science Research Institute, Osaka Metropolitan University, Izumisano, Osaka, Japan; Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Shinji Yamasaki
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan; Asian Health Science Research Institute, Osaka Metropolitan University, Izumisano, Osaka, Japan; Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Yasutoshi Kido
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan; Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
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136
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Suryawanshi YR. An overview of protein-based SARS-CoV-2 vaccines. Vaccine 2023; 41:6174-6193. [PMID: 37699784 DOI: 10.1016/j.vaccine.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/10/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023]
Abstract
SARS-CoV-2 resulted in the COVID-19 pandemic which, to date, has resulted in an estimated loss of over 15 million human lives globally and continues to have negative social, and economic implications worldwide. Vaccine platforms that can be quickly updated to counter newly emerging SARS-CoV-2 variants are critical in combating the COVID-19 pandemic. Messenger RNA-based SARS-CoV-2 vaccines can be easily updated and have shown superior efficacy over other vaccine types, yet their high cost, reactogenicity, and stringent need for ultracold storage limit their accessibility. Global access to economic, safe, and effective SARS-CoV-2 vaccines is a critical step toward reducing COVID-19-associated mortality and ending the pandemic. Several protein-based SARS-CoV-2 vaccines targeting the spike protein (or its receptor-binding domain) have demonstrated safety and efficacy in clinical studies. Moreover, protein-based vaccines can be updated to immunize against new virus variants. Protein-based vaccines do not contain live viruses and are safe to use in immunocompromised and elderly populations, and can be optimized to improve the immune outcome in these poorly immunoresponsive individuals by using adjuvants. SARS-CoV-2 shows high genetic variability, similar to other RNA viruses, and protein-based vaccines are an economically feasible vaccine platform that can be used to design new vaccines with durable protective immunity, in addition to expanding the vaccine coverage.
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Affiliation(s)
- Yogesh R Suryawanshi
- Mayo Clinic Vaccine Research Group and Division of General Internal Medicine, Mayo Clinic, Rochester, MN, USA.
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137
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Ratswohl C, Vázquez García C, Ahmad AUW, Gonschior H, Lebedin M, Silvis CE, Spatt L, Gerhard C, Lehmann M, Sander LE, Kurth F, Olsson S, de la Rosa K. A design strategy to generate a SARS-CoV-2 RBD vaccine that abrogates ACE2 binding and improves neutralizing antibody responses. Eur J Immunol 2023; 53:e2350408. [PMID: 37435628 DOI: 10.1002/eji.202350408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/13/2023]
Abstract
The structure-based design of antigens holds promise for developing vaccines with higher efficacy and improved safety profiles. We postulate that abrogation of host receptor interaction bears potential for the improvement of vaccines by preventing antigen-induced modification of receptor function as well as the displacement or masking of the immunogen. Antigen modifications may yet destroy epitopes crucial for antibody neutralization. Here, we present a methodology that integrates deep mutational scans to identify and score SARS-CoV-2 receptor binding domain variants that maintain immunogenicity, but lack interaction with the widely expressed host receptor. Single point mutations were scored in silico, validated in vitro, and applied in vivo. Our top-scoring variant receptor binding domain-G502E prevented spike-induced cell-to-cell fusion, receptor internalization, and improved neutralizing antibody responses by 3.3-fold in rabbit immunizations. We name our strategy BIBAX for body-inert, B-cell-activating vaccines, which in the future may be applied beyond SARS-CoV-2 for the improvement of vaccines by design.
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Affiliation(s)
- Christoph Ratswohl
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, Germany
| | - Clara Vázquez García
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Ata Ul Wakeel Ahmad
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Hannes Gonschior
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Mikhail Lebedin
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Casper Ewijn Silvis
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Lisa Spatt
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Cathrin Gerhard
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Leif E Sander
- Charité - Universitätsmedizin, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, Berlin, Germany
| | | | - Simon Olsson
- Department of Computer Science and Engineering, Chalmers University of Technology, Göteborg, Västra Götalands län, Sweden
| | - Kathrin de la Rosa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, Berlin, Germany
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138
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Xu C, Han W, Cong Y. Cryo-EM and cryo-ET of the spike, virion, and antibody neutralization of SARS-CoV-2 and VOCs. Curr Opin Struct Biol 2023; 82:102664. [PMID: 37544111 DOI: 10.1016/j.sbi.2023.102664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/14/2023] [Accepted: 07/09/2023] [Indexed: 08/08/2023]
Abstract
Since the outbreak of the COVID-19 pandemic, cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) have been demonstrated to be powerful and efficient tools in structural studies of distinct conformational states of the trimeric spike protein of SARS-CoV-2 and the VOCs as well as the intact virion. Cryo-EM has also contributed greatly to revealing the molecular basis of receptor recognition and antibody neutralization of the S trimer. Additionally, it has provided structural insights into the enhanced transformation and immune evasion of the VOCs, thus facilitating antiviral antibody and drug discovery. In this review, we summarize the contributions of cryo-EM and cryo-ET in revealing the structures of SARS-CoV-2 S trimer and intact virion and the mechanisms of receptor binding and antibody neutralization. We also highlight their prospective utilities in the development of vaccines and future therapeutics against emerging SARS-CoV-2 variants and other epidemic viruses.
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Affiliation(s)
- Cong Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenyu Han
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yao Cong
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
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139
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Xia M, López K, Vago FS, Huang P, Auguste DI, Jiang W, Auguste AJ, Tan M. A bioengineered pseudovirus nanoparticle displaying SARS-CoV 2 RBD fully protects mice from mortality and weight loss caused by SARS-CoV 2 challenge. Biotechnol J 2023; 18:e2300130. [PMID: 37300425 PMCID: PMC10592332 DOI: 10.1002/biot.202300130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/25/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused considerable morbidity and mortality worldwide. Although authorized COVID-19 vaccines have been shown highly effective, their significantly lower efficacy against heterologous variants, and the rapid decrease of vaccine-elicited immunity raises serious concerns, calling for improved vaccine tactics. To this end, a pseudovirus nanoparticle (PVNP) displaying the receptor binding domains (RBDs) of SARS-CoV-2 spike, named S-RBD, was generated and shown it as a promising COVID-19 vaccine candidate. The S-RBD PVNP was produced using both prokaryotic and eukaryotic systems. A 3D structural model of the S-RBD PVNPs was built based on the known structures of the S60 particle and RBDs, revealing an S60 particle-based icosahedral symmetry with multiple surface-displayed RBDs that retain authentic conformations and receptor-binding functions. The PVNP is highly immunogenic, eliciting high titers of RBD-specific IgG and neutralizing antibodies in mice. The S-RBD PVNP demonstrated exceptional protective efficacy, and fully (100%) protected K18-hACE2 mice from mortality and weight loss after a lethal SARS-CoV-2 challenge, supporting the S-RBD PVNPs as a potent COVID-19 vaccine candidate. By contrast, a PVNP displaying the N-terminal domain (NTD) of SARS-CoV-2 spike exhibited only 50% protective efficacy. Since the RBD antigens of our PVNP vaccine are adjustable as needed to address the emergence of future variants, and various S-RBD PVNPs can be combined as a cocktail vaccine for broad efficacy, these non-replicating PVNPs offer a flexible platform for a safe, effective COVID-19 vaccine with minimal manufacturing cost and time.
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Affiliation(s)
- Ming Xia
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Krisangel López
- Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Frank S. Vago
- Department of Biological Sciences, Purdue Cryo-EM Facility, Purdue University, IN, USA
| | - Pengwei Huang
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Dawn I. Auguste
- Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Wen Jiang
- Department of Biological Sciences, Purdue Cryo-EM Facility, Purdue University, IN, USA
| | - Albert J. Auguste
- Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Ming Tan
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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140
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Onigbinde S, Reyes CDG, Fowowe M, Daramola O, Atashi M, Bennett AI, Mechref Y. Variations in O-Glycosylation Patterns Influence Viral Pathogenicity, Infectivity, and Transmissibility in SARS-CoV-2 Variants. Biomolecules 2023; 13:1467. [PMID: 37892149 PMCID: PMC10604390 DOI: 10.3390/biom13101467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
The highly glycosylated S protein plays a vital role in host cell invasion, making it the principal target for vaccine development. Differences in mutations observed on the spike (S) protein of SARS-CoV-2 variants may result in distinct glycosylation patterns, thus influencing immunological evasion, infectivity, and transmissibility. The glycans can mask key epitopes on the S1 protein and alter its structural conformation, allowing the virus to escape the immune system. Therefore, we comprehensively characterize O-glycosylation in eleven variants of SARS-CoV-2 S1 subunits to understand the differences observed in the biology of the variants. In-depth characterization was performed with a double digestion strategy and an efficient LC-MS/MS approach. We observed that O-glycosylation is highly conserved across all variants in the region between the NTD and RBD, whereas other domains and regions exhibit variation in O-glycosylation. Notably, omicron has the highest number of O-glycosylation sites on the S1 subunit. Also, omicron has the highest level of sialylation in the RBD and RBM functional motifs. Our findings may shed light on how differences in O-glycosylation impact viral pathogenicity in variants of SARS-CoV-2 and facilitate the development of a robust vaccine with high protective efficacy against the variants of concern.
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Affiliation(s)
| | | | | | | | | | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (S.O.); (C.D.G.R.); (M.F.); (O.D.); (M.A.); (A.I.B.)
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141
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Hu D, Irving AT. Massively-multiplexed epitope mapping techniques for viral antigen discovery. Front Immunol 2023; 14:1192385. [PMID: 37818363 PMCID: PMC10561112 DOI: 10.3389/fimmu.2023.1192385] [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: 03/23/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Following viral infection, viral antigens bind specifically to receptors on the surface of lymphocytes thereby activating adaptive immunity in the host. An epitope, the smallest structural and functional unit of an antigen, binds specifically to an antibody or antigen receptor, to serve as key sites for the activation of adaptive immunity. The complexity and diverse range of epitopes are essential to study and map for the diagnosis of disease, the design of vaccines and for immunotherapy. Mapping the location of these specific epitopes has become a hot topic in immunology and immune therapy. Recently, epitope mapping techniques have evolved to become multiplexed, with the advent of high-throughput sequencing and techniques such as bacteriophage-display libraries and deep mutational scanning. Here, we briefly introduce the principles, advantages, and disadvantages of the latest epitope mapping techniques with examples for viral antigen discovery.
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Affiliation(s)
- Diya Hu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Aaron T. Irving
- Department of Clinical Laboratory Studies, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Infection, Immunity & Cancer, Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
- Biomedical and Health Translational Research Centre of Zhejiang Province (BIMET), Haining, China
- College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
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142
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Vilibic-Cavlek T, Stevanovic V, Kovac S, Borko E, Bogdanic M, Miletic G, Hruskar Z, Ferenc T, Coric I, Vujica Ferenc M, Milasincic L, Antolasic L, Barbic L. Neutralizing Activity of SARS-CoV-2 Antibodies in Patients with COVID-19 and Vaccinated Individuals. Antibodies (Basel) 2023; 12:61. [PMID: 37873858 PMCID: PMC10594469 DOI: 10.3390/antib12040061] [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: 08/30/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Serological diagnosis of COVID-19 is complex due to the emergence of different SARS-CoV-2 variants. METHODS 164 serum samples from (I) patients who recovered from COVID-19 (n = 62) as well as (II) vaccinated individuals (n = 52) and (III) vaccinated individuals who were infected with different SARS-CoV-2 variants after vaccination (n = 50) were included. All samples were tested using EIA (binding antibodies) and a virus neutralization test (VNT) using the Wuhan strain (NT antibodies). Group III was further tested with a VNT using the Alpha/Delta/Omicron strains. RESULTS The highest antibody index (AI) was observed in vaccinated individuals infected with COVID-19 (median AI = 50, IQR = 27-71) and the lowest in vaccinated individuals (median AI = 19, IQR = 8-48). Similarly, NT antibody titer was highest in vaccinated individuals infected with COVID-19 (median 128; IQR = 32-256) compared to vaccinated individuals (median 32, IQR = 4-128) and patients with COVID-19 (median 32, IQR = 8-64). The correlation between AI and NT titer was strongly positive in vaccinated individuals and moderately positive in patients with COVID-19. No significant correlation was observed in vaccinated individuals infected with COVID-19. In patients infected with Alpha and Delta, the lowest VNT positivity rate was for the Omicron variant (85.0%/83.3%). Patients infected with the Alpha variant showed the lowest NT titer for the Omicron variant (median titer 32) compared to the Wuhan/Delta variants (64/128). Patients infected with the Delta variant had the lowest NT titer to the Omicron variant (median 32), compared to the Wuhan/Alpha variants (64/128). Patients infected with the Omicron variant showed similar titers to the Delta/Wuhan variants (128) and higher to the Alpha variant (256). CONCLUSIONS The cross-immunity to SARS-CoV-2 is lowest for the Omicron variant compared to the Alpha/Delta variants.
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Affiliation(s)
- Tatjana Vilibic-Cavlek
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (E.B.); (M.B.); (Z.H.); (L.M.); (L.A.)
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Vladimir Stevanovic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (S.K.); (G.M.); (I.C.); (L.B.)
| | - Snjezana Kovac
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (S.K.); (G.M.); (I.C.); (L.B.)
| | - Ema Borko
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (E.B.); (M.B.); (Z.H.); (L.M.); (L.A.)
| | - Maja Bogdanic
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (E.B.); (M.B.); (Z.H.); (L.M.); (L.A.)
| | - Gorana Miletic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (S.K.); (G.M.); (I.C.); (L.B.)
| | - Zeljka Hruskar
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (E.B.); (M.B.); (Z.H.); (L.M.); (L.A.)
| | - Thomas Ferenc
- Clinical Department of Diagnostic and Interventional Radiology, Merkur University Hospital, 10000 Zagreb, Croatia;
| | - Ivona Coric
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (S.K.); (G.M.); (I.C.); (L.B.)
| | - Mateja Vujica Ferenc
- Department of Obstetrics and Gynecology, University Hospital Center Zagreb, 10000 Zagreb, Croatia;
| | - Ljiljana Milasincic
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (E.B.); (M.B.); (Z.H.); (L.M.); (L.A.)
| | - Ljiljana Antolasic
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (E.B.); (M.B.); (Z.H.); (L.M.); (L.A.)
| | - Ljubo Barbic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (S.K.); (G.M.); (I.C.); (L.B.)
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143
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Connor RI, Sakharkar M, Rappazzo CG, Kaku CI, Curtis NC, Shin S, Wieland-Alter WF, Weiner JA, Ackerman ME, Walker LM, Lee J, Wright PF. Characteristics and functions of infection-enhancing antibodies to the N-terminal domain of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558444. [PMID: 37786672 PMCID: PMC10541592 DOI: 10.1101/2023.09.19.558444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Characterization of functional antibody responses to the N-terminal domain (NTD) of the SARS-CoV-2 spike (S) protein has included identification of both potent neutralizing activity and putative enhancement of infection. Fcγ-receptor (FcγR)-independent enhancement of SARS-CoV-2 infection mediated by NTD-binding monoclonal antibodies (mAbs) has been observed in vitro , but the functional significance of these antibodies in vivo is not clear. Here we studied 1,213 S-binding mAbs derived from longitudinal sampling of B-cells collected from eight COVID-19 convalescent patients and identified 72 (5.9%) mAbs that enhanced infection in a VSV-SARS-CoV-2-S-Wuhan pseudovirus (PV) assay. The majority (68%) of these mAbs recognized the NTD, were identified in patients with mild and severe disease, and persisted for at least five months post-infection. Enhancement of PV infection by NTD-binding mAbs was not observed using intestinal (Caco-2) and respiratory (Calu-3) epithelial cells as infection targets and was diminished or lost against SARS-CoV-2 variants of concern (VOC). Proteomic deconvolution of the serum antibody repertoire from two of the convalescent subjects identified, for the first time, NTD-binding, infection-enhancing mAbs among the circulating immunoglobulins directly isolated from serum ( i.e ., functionally secreted antibody). Functional analysis of these mAbs demonstrated robust activation of FcγRIIIa associated with antibody binding to recombinant S proteins. Taken together, these findings suggest functionally active NTD-specific mAbs arise frequently during natural infection and can last as major serum clonotypes during convalescence. These antibodies display diverse attributes that include FcγR activation, and may be selected against by mutations in NTD associated with SARS-CoV-2 VOC.
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144
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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145
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Cantoni D, Wilkie C, Bentley EM, Mayora-Neto M, Wright E, Scott S, Ray S, Castillo-Olivares J, Heeney JL, Mattiuzzo G, Temperton NJ. Correlation between pseudotyped virus and authentic virus neutralisation assays, a systematic review and meta-analysis of the literature. Front Immunol 2023; 14:1184362. [PMID: 37790941 PMCID: PMC10544934 DOI: 10.3389/fimmu.2023.1184362] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023] Open
Abstract
Background The virus neutralization assay is a principal method to assess the efficacy of antibodies in blocking viral entry. Due to biosafety handling requirements of viruses classified as hazard group 3 or 4, pseudotyped viruses can be used as a safer alternative. However, it is often queried how well the results derived from pseudotyped viruses correlate with authentic virus. This systematic review and meta-analysis was designed to comprehensively evaluate the correlation between the two assays. Methods Using PubMed and Google Scholar, reports that incorporated neutralisation assays with both pseudotyped virus, authentic virus, and the application of a mathematical formula to assess the relationship between the results, were selected for review. Our searches identified 67 reports, of which 22 underwent a three-level meta-analysis. Results The three-level meta-analysis revealed a high level of correlation between pseudotyped viruses and authentic viruses when used in an neutralisation assay. Reports that were not included in the meta-analysis also showed a high degree of correlation, with the exception of lentiviral-based pseudotyped Ebola viruses. Conclusion Pseudotyped viruses identified in this report can be used as a surrogate for authentic virus, though care must be taken in considering which pseudotype core to use when generating new uncharacterised pseudotyped viruses.
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Affiliation(s)
- Diego Cantoni
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Craig Wilkie
- School of Mathematics & Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Emma M. Bentley
- Medicines and Healthcare Products Regulatory Agency, South Mimms, United Kingdom
| | - Martin Mayora-Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Chatham, United Kingdom
| | - Edward Wright
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Simon Scott
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Chatham, United Kingdom
| | - Surajit Ray
- School of Mathematics & Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Javier Castillo-Olivares
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge University, Cambridge, United Kingdom
| | - Jonathan Luke Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge University, Cambridge, United Kingdom
- DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - Giada Mattiuzzo
- Medicines and Healthcare Products Regulatory Agency, South Mimms, United Kingdom
| | - Nigel James Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Chatham, United Kingdom
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146
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Mihalič F, Benz C, Kassa E, Lindqvist R, Simonetti L, Inturi R, Aronsson H, Andersson E, Chi CN, Davey NE, Överby AK, Jemth P, Ivarsson Y. Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets. Nat Commun 2023; 14:5636. [PMID: 37704626 PMCID: PMC10499821 DOI: 10.1038/s41467-023-41312-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
The virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 interactions involving eight SARS-CoV-2 protein domains were determined (KD ∼ 7-300 μM). Key specificity residues of the peptides were established for six of the interactions. Two of the peptides, binding Nsp9 and Nsp16, respectively, inhibited viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously identify potential host-virus interactions and peptides with antiviral properties. Furthermore, the high number of low-affinity interactions suggest that overexpression of viral proteins during infection may perturb multiple cellular pathways.
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Affiliation(s)
- Filip Mihalič
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eszter Kassa
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Hanna Aronsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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147
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Buchholz U, Kaiser J, Nelson C, Liu X, Park HS, Matsuoka Y, Luongo C, Santos C, Ahlers L, Herbert R, Moore I, Wilder-Kofie T, Moore R, Walker A, Lijuan Y, Munir S, Teng IT, Kwong P, Dowdell K, Nguyen H, Kim J, Cohen J, Johnson RF, Garza N, Via L, Barber D, LE Nouen C. Mucosal prime-boost immunization with live murine pneumonia virus-vectored SARS-CoV-2 vaccine is protective in macaques. RESEARCH SQUARE 2023:rs.3.rs-3278289. [PMID: 37790295 PMCID: PMC10543296 DOI: 10.21203/rs.3.rs-3278289/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Immunization via the respiratory route is predicted to increase the effectiveness of a SARS-CoV-2 vaccine. We evaluated the immunogenicity and protective efficacy of one or two doses of a live-attenuated murine pneumonia virus vector expressing SARS-CoV-2 prefusion-stabilized spike protein (MPV/S-2P), delivered intranasally/intratracheally to rhesus macaques. A single dose of MPV/S-2P was highly immunogenic, and a second dose increased the magnitude and breadth of the mucosal and systemic anti-S antibody responses and increased levels of dimeric anti-S IgA in the airways. MPV/S-2P also induced S-specific CD4+ and CD8+ T-cells in the airways that differentiated into large populations of tissue-resident memory cells within a month after the boost. One dose induced substantial protection against SARS-CoV-2 challenge, and two doses of MPV/S-2P were fully protective against SARS-CoV-2 challenge virus replication in the airways. A prime/boost immunization with a mucosally-administered live-attenuated MPV vector could thus be highly effective in preventing SARS-CoV-2 infection and replication.
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Affiliation(s)
| | | | - Christine Nelson
- National Institutes of Health, National Institute of Allergy and Infectious Diseases
| | - Xueqiao Liu
- Laboratory of Infectious Diseases, NIAID, NIH
| | | | | | | | | | | | | | | | | | | | | | | | - Shirin Munir
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH
| | | | | | | | | | | | | | | | | | | | - Daniel Barber
- National Institutes of Health/National Institute of Allergy and Infectious Diseases
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148
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Colom MS, Vucinic J, Adolf-Bryfogle J, Bowman JW, Verel S, Moczygemba I, Schiex T, Simoncini D, Bahl CD. Complete Combinatorial Mutational Enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity. RESEARCH SQUARE 2023:rs.3.rs-2248327. [PMID: 36482980 PMCID: PMC9727770 DOI: 10.21203/rs.3.rs-2248327/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Understanding how proteins evolve under selective pressure is a longstanding challenge. The immensity of the search space has limited efforts to systematically evaluate the impact of multiple simultaneous mutations, so mutations have typically been assessed individually. However, epistasis, or the way in which mutations interact, prevents accurate prediction of combinatorial mutations based on measurements of individual mutations. Here, we use artificial intelligence to define the entire functional sequence landscape of a protein binding site in silico, and we call this approach Complete Combinatorial Mutational Enumeration (CCME). By leveraging CCME, we are able to construct a comprehensive map of the evolutionary connectivity within this functional sequence landscape. As a proof of concept, we applied CCME to the ACE2 binding site of the SARS-CoV-2 spike protein receptor binding domain. We selected representative variants from across the functional sequence landscape for testing in the laboratory. We identified variants that retained functionality to bind ACE2 despite changing over 40% of evaluated residue positions, and the variants now escape binding and neutralization by monoclonal antibodies. This work represents a crucial initial stride towards achieving precise predictions of pathogen evolution, opening avenues for proactive mitigation.
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Affiliation(s)
- Mireia Solà Colom
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- current address: AI Proteins; Boston, Massachusetts, 02215, USA
| | - Jelena Vucinic
- Université Fédérale de Toulouse; ANITI, IRIT-CNRS UMR 5505, Université Toulouse Capitole, 31000 Toulouse, France
| | - Jared Adolf-Bryfogle
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - James W. Bowman
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- current address: AI Proteins; Boston, Massachusetts, 02215, USA
| | - Sébastien Verel
- Université Littoral Côte d’Opale; UR 4491, LISIC, F-62100 Calais, France
| | - Isabelle Moczygemba
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- current address: AI Proteins; Boston, Massachusetts, 02215, USA
| | - Thomas Schiex
- Université Fédérale de Toulouse; ANITI, INRAE-UR 875, 31000 Toulouse, France
| | - David Simoncini
- Université Fédérale de Toulouse; ANITI, IRIT-CNRS UMR 5505, Université Toulouse Capitole, 31000 Toulouse, France
| | - Christopher D. Bahl
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- current address: AI Proteins; Boston, Massachusetts, 02215, USA
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149
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Yang L, Wang Z. Bench-to-bedside: Innovation of small molecule anti-SARS-CoV-2 drugs in China. Eur J Med Chem 2023; 257:115503. [PMID: 37229831 PMCID: PMC10193775 DOI: 10.1016/j.ejmech.2023.115503] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/19/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
The ongoing COVID-19 pandemic has resulted in millions of deaths globally, highlighting the need to develop potent prophylactic and therapeutic strategies against SARS-CoV-2. Small molecule inhibitors (remdesivir, Paxlovid, and molnupiravir) are essential complements to vaccines and play important roles in clinical treatment of SARS-CoV-2. Many advances have been made in development of anti-SARS-CoV-2 inhibitors in China, but progress in discovery and characterization of pharmacological activity, antiviral mechanisms, and clinical efficacy are limited. We review development of small molecule anti-SARS-CoV-2 drugs (azvudine [approved by the NMPA of China on July 25, 2022], VV116 [approved by the NMPA of China on January 29, 2023], FB2001, WPV01, pentarlandir, and cepharanthine) in China and summarize their pharmacological activity, potential mechanisms of action, clinical trials and use, and important milestones in their discovery. The role of structural biology in drug development is also reviewed. Future studies should focus on development of diverse second-generation inhibitors with excellent oral bioavailability, superior plasma half-life, increased antiviral activity against SARS-CoV-2 and its variants, high target specificity, minimal side effects, reduced drug-drug interactions, and improved lung histopathology.
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Affiliation(s)
- Liyan Yang
- School of Physics and Physical Engineering, Qufu Normal University, Qufu, 273165, PR China; Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Zhonglei Wang
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, 273165, PR China; School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus, Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, PR China.
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150
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Guo M, Xiong M, Peng J, Guan T, Su H, Huang Y, Yang CG, Li Y, Boraschi D, Pillaiyar T, Wang G, Yi C, Xu Y, Chen C. Multi-omics for COVID-19: driving development of therapeutics and vaccines. Natl Sci Rev 2023; 10:nwad161. [PMID: 37936830 PMCID: PMC10627145 DOI: 10.1093/nsr/nwad161] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 11/09/2023] Open
Abstract
The ongoing COVID-19 pandemic caused by SARS-CoV-2 has raised global concern for public health and economy. The development of therapeutics and vaccines to combat this virus is continuously progressing. Multi-omics approaches, including genomics, transcriptomics, proteomics, metabolomics, epigenomics and metallomics, have helped understand the structural and molecular features of the virus, thereby assisting in the design of potential therapeutics and accelerating vaccine development for COVID-19. Here, we provide an up-to-date overview of the latest applications of multi-omics technologies in strategies addressing COVID-19, in order to provide suggestions towards the development of highly effective knowledge-based therapeutics and vaccines.
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Affiliation(s)
- Mengyu Guo
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Tong Guan
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyi Huang
- Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 528107, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Li
- Laboratory of Immunology and Nanomedicine, and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Diana Boraschi
- Laboratory of Immunology and Nanomedicine, and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Institute of Biochemistry and Cell Biology, National Research Council, Napoli 80131, Italy
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Guanbo Wang
- Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 528107, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunying Chen
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
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