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Benlarbi M, Ding S, Bélanger É, Tauzin A, Poujol R, Medjahed H, El Ferri O, Bo Y, Bourassa C, Hussin J, Fafard J, Pazgier M, Levade I, Abrams C, Côté M, Finzi A. Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission. mBio 2024:e0090724. [PMID: 38953636 DOI: 10.1128/mbio.00907-24] [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: 03/26/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
The continued evolution of severe acute respiratory syndrome 2 (SARS-CoV-2) requires persistent monitoring of its subvariants. Omicron subvariants are responsible for the vast majority of SARS-CoV-2 infections worldwide, with XBB and BA.2.86 sublineages representing more than 90% of circulating strains as of January 2024. To better understand parameters involved in viral transmission, we characterized the functional properties of Spike glycoproteins from BA.2.75, CH.1.1, DV.7.1, BA.4/5, BQ.1.1, XBB, XBB.1, XBB.1.16, XBB.1.5, FD.1.1, EG.5.1, HK.3, BA.2.86 and JN.1. We tested their capacity to evade plasma-mediated recognition and neutralization, binding to angiotensin-converting enzyme 2 (ACE2), their susceptibility to cold inactivation, Spike processing, as well as the impact of temperature on Spike-ACE2 interaction. We found that compared to the early wild-type (D614G) strain, most Omicron subvariants' Spike glycoproteins evolved to escape recognition and neutralization by plasma from individuals who received a fifth dose of bivalent (BA.1 or BA.4/5) mRNA vaccine and improve ACE2 binding, particularly at low temperatures. Moreover, BA.2.86 had the best affinity for ACE2 at all temperatures tested. We found that Omicron subvariants' Spike processing is associated with their susceptibility to cold inactivation. Intriguingly, we found that Spike-ACE2 binding at low temperature was significantly associated with growth rates of Omicron subvariants in humans. Overall, we report that Spikes from newly emerged Omicron subvariants are relatively more stable and resistant to plasma-mediated neutralization, present improved affinity for ACE2 which is associated, particularly at low temperatures, with their growth rates.IMPORTANCEThe persistent evolution of SARS-CoV-2 gave rise to a wide range of variants harboring new mutations in their Spike glycoproteins. Several factors have been associated with viral transmission and fitness such as plasma-neutralization escape and ACE2 interaction. To better understand whether additional factors could be of importance in SARS-CoV-2 variants' transmission, we characterize the functional properties of Spike glycoproteins from several Omicron subvariants. We found that the Spike glycoprotein of Omicron subvariants presents an improved escape from plasma-mediated recognition and neutralization, Spike processing, and ACE2 binding which was further improved at low temperature. Intriguingly, Spike-ACE2 interaction at low temperature is strongly associated with viral growth rate, as such, low temperatures could represent another parameter affecting viral transmission.
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Affiliation(s)
- Mehdi Benlarbi
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, Montréal, Québec, Canada
| | - Étienne Bélanger
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Alexandra Tauzin
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Raphaël Poujol
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
| | | | - Omar El Ferri
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Julie Hussin
- Montreal Heart Institute, Research Center, Montreal, Quebec, Canada
- Département de Médecine, Université de Montréal, Montréal, Québec, Canada
- Mila-Quebec AI institute, Montreal, Quebec, Canada
| | - Judith Fafard
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine of Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Inès Levade
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Cameron Abrams
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
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2
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Bajracharya D, Jansen RJ. Observations of COVID-19 vaccine coverage and vaccine hesitancy on COVID-19 outbreak: An American ecological study. Vaccine 2024; 42:246-254. [PMID: 38103963 PMCID: PMC10842854 DOI: 10.1016/j.vaccine.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/10/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023]
Abstract
In this ecological study, we aim to establish the role vaccines play in bringing the pandemic under control, as well as the impact of pathogen variants, vaccine hesitancy, and medical resource availability during the process by utilizing publicly available data. The study spans a three-year data collection period for daily hospital admissions due to COVID-19 and the daily reported cases of COVID-19 across all 50 states in the USA. In doing so, we aim to demonstrate the difference in severity of the SARS-CoV-2 pathogen among vaccinated and unvaccinated populations in the USA. The study assesses the correlation of COVID-19 vaccines (e.g., Pfizer, Moderna, and Janssen) and disease outcomes (transmissibility, severity, and deaths) caused by different strains of SARS-CoV-2 and establishes a negative correlation between COVID-19 vaccine and disease outcomes. By considering potential confounders in vaccine hesitancy, medical resource availability and vaccine dosage, we demonstrate the aforementioned to be insubstantial in predicting disease outcomes while the latter displays a contrasting significance in terms of disease outcomes. Between all the major variants of concern, the Delta and Omicron variants in particular have been associated with higher virulence and transmissibility factors respectively. Hence, the CDC continues to encourage the US population to get vaccinated since vaccines are one of the most effective ways to protect the community from potential outbreaks and prevent severe disease manifestations.
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Affiliation(s)
- Deewan Bajracharya
- Genomics, Phenomics, and Bioinformatics Program, North Dakota State University, Fargo, ND, USA.
| | - Rick J Jansen
- Genomics, Phenomics, and Bioinformatics Program, North Dakota State University, Fargo, ND, USA; Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
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3
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de Souza AS, de Souza RF, Guzzo CR. Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1). J Comput Aided Mol Des 2023; 37:585-606. [PMID: 37792106 DOI: 10.1007/s10822-023-00534-0] [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: 03/22/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023]
Abstract
Herein, we conducted simulations of trimeric Spike from several SARS-CoV-2 variants of concern (Delta and Omicron sub-variants BA.2, BA.5, and BQ.1) and investigated the mechanisms by which specific mutations confer resistance to neutralizing antibodies. We observed that the mutations primarily affect the cooperation between protein domains within and between protomers. The substitutions K417N and L452R expand hydrogen bonding interactions, reducing their interaction with neutralizing antibodies. By interacting with nearby residues, the K444T and N460K mutations in the SpikeBQ.1 variant potentially reduces solvent exposure, thereby promoting resistance to antibodies. We also examined the impact of D614G, P681R, and P681H substitutions on Spike protein structure that may be related to infectivity. The D614G substitution influences communication between a glycine residue and neighboring domains, affecting the transition between up- and -down RBD states. The P681R mutation, found in the Delta variant, enhances correlations between protein subunits, while the P681H mutation in Omicron sub-variants weakens long-range interactions that may be associated with reduced fusogenicity. Using a multiple linear regression model, we established a connection between inter-protomer communication and loss of sensitivity to neutralizing antibodies. Our findings underscore the importance of structural communication between protein domains and provide insights into potential mechanisms of immune evasion by SARS-CoV-2. Overall, this study deepens our understanding of how specific mutations impact SARS-CoV-2 infectivity and shed light on how the virus evades the immune system.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
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4
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Zhao F, Yuan M, Keating C, Shaabani N, Limbo O, Joyce C, Woehl J, Barman S, Burns A, Tran Q, Zhu X, Ricciardi M, Peng L, Smith J, Huang D, Briney B, Sok D, Nemazee D, Teijaro JR, Wilson IA, Burton DR, Jardine JG. Broadening a SARS-CoV-1-neutralizing antibody for potent SARS-CoV-2 neutralization through directed evolution. Sci Signal 2023; 16:eabk3516. [PMID: 37582161 DOI: 10.1126/scisignal.abk3516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 07/27/2023] [Indexed: 08/17/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for strategies to rapidly develop neutralizing monoclonal antibodies that can function as prophylactic and therapeutic agents and to help guide vaccine design. Here, we demonstrate that engineering approaches can be used to refocus an existing antibody that neutralizes one virus but not a related virus. Through a rapid affinity maturation strategy, we engineered CR3022, a SARS-CoV-1-neutralizing antibody, to bind to the receptor binding domain of SARS-CoV-2 with >1000-fold increased affinity. The engineered CR3022 neutralized SARS-CoV-2 and provided prophylactic protection from viral challenge in a small animal model of SARS-CoV-2 infection. Deep sequencing throughout the engineering process paired with crystallographic analysis of engineered CR3022 elucidated the molecular mechanisms by which the antibody can accommodate sequence differences in the epitopes between SARS-CoV-1 and SARS-CoV-2. This workflow provides a blueprint for the rapid broadening of neutralization of an antibody from one virus to closely related but resistant viruses.
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Affiliation(s)
- Fangzhu Zhao
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Celina Keating
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Namir Shaabani
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oliver Limbo
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Collin Joyce
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jordan Woehl
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Shawn Barman
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alison Burns
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Quoc Tran
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Ricciardi
- Department of Pathology, George Washington University, Washington, DC 20052, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jessica Smith
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Deli Huang
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
- Center for Viral Systems Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - David Nemazee
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Teijaro
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Joseph G Jardine
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
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5
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Adin DB, Spalla M, Walden H, Gruntmeir J, Hernandez JA, Long M. Angiotensin-converting enzyme 2 in dogs with Dirofilaria immitis. Parasit Vectors 2023; 16:145. [PMID: 37106412 PMCID: PMC10139826 DOI: 10.1186/s13071-023-05649-9] [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: 12/06/2022] [Accepted: 01/03/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND Infection by the canine heartworm, Dirofilaria immitis, causes significant cardiopulmonary disease, with progression impacted by increasing parasite numbers and duration of infection. The renin-angiotensin-aldosterone system (RAAS) is an important mediator of cardiac and pulmonary disease. Angiotensin-converting enzyme 2 (ACE2) mitigates the maladaptive effects of angiotensin II by converting it to angiotensin (1-7). We hypothesized that circulating ACE2 activity would be altered in dogs with high heartworm infection intensities relative to dogs without heartworms. METHODS Frozen serum samples (-80 °C) from 30 dogs euthanized at Florida shelters were analyzed for ACE2 activity using liquid chromatography-mass spectrometry/mass spectroscopy and a kinetics approach with and without an ACE2 inhibitor. A convenience sample of 15 dogs without heartworms (HW0) and 15 dogs with > 50 heartworms (HW>50) was included. Heartworm number and microfilariae presence were determined at necropsy. The effects of heartworm status, body weight, and sex on ACE2 were evaluated using regression analysis. Values of P < 0.05 were considered significant. RESULTS All HW0 dogs were D. immitis microfilariae-negative and all HW>50 dogs were D. immitis microfilariae-positive with a median adult worm count of 74 (minimum = 63, maximum = 137). The ACE2 activity of HW>50 dogs (median = 28.2 ng/ml; minimum = 13.6, maximum = 76.2) was not different from HW0 dogs (median 31.9 ng/ml; minimum = 14.1, maximum = 139.1; P = 0.53). The ACE2 activity was higher in dogs with high body weight (median 34.2 ng/ml minimum = 14.1, maximum = 76.2) than in dogs with low weight (median 27.5 ng/ml; minimum = 16.4, maximum = 139.1; P = .044). CONCLUSIONS Heartworm infection did not impact ACE2 activity in shelter dogs with or without heartworms, but heavier dogs had higher ACE2 activity compared to lighter dogs. Comprehensive RAAS evaluation and additional clinical information would aid in understanding how ACE2 activity relates to the entire cascade and clinical status in dogs with heartworm disease.
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Affiliation(s)
- Darcy B Adin
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA.
| | - Meaghan Spalla
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Heather Walden
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Jeff Gruntmeir
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Jorge A Hernandez
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Maureen Long
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
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6
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Chen Y, Prévost J, Ullah I, Romero H, Lisi V, Tolbert WD, Grover JR, Ding S, Gong SY, Beaudoin-Bussières G, Gasser R, Benlarbi M, Vézina D, Anand SP, Chatterjee D, Goyette G, Grunst MW, Yang Z, Bo Y, Zhou F, Béland K, Bai X, Zeher AR, Huang RK, Nguyen DN, Sherburn R, Wu D, Piszczek G, Paré B, Matthies D, Xia D, Richard J, Kumar P, Mothes W, Côté M, Uchil PD, Lavallée VP, Smith MA, Pazgier M, Haddad E, Finzi A. Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD. iScience 2023; 26:105783. [PMID: 36514310 PMCID: PMC9733284 DOI: 10.1016/j.isci.2022.105783] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/07/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Neutralizing antibodies (NAbs) hold great promise for clinical interventions against SARS-CoV-2 variants of concern (VOCs). Understanding NAb epitope-dependent antiviral mechanisms is crucial for developing vaccines and therapeutics against VOCs. Here we characterized two potent NAbs, EH3 and EH8, isolated from an unvaccinated pediatric patient with exceptional plasma neutralization activity. EH3 and EH8 cross-neutralize the early VOCs and mediate strong Fc-dependent effector activity in vitro. Structural analyses of EH3 and EH8 in complex with the receptor-binding domain (RBD) revealed the molecular determinants of the epitope-driven protection and VOC evasion. While EH3 represents the prevalent IGHV3-53 NAb whose epitope substantially overlaps with the ACE2 binding site, EH8 recognizes a narrow epitope exposed in both RBD-up and RBD-down conformations. When tested in vivo, a single-dose prophylactic administration of EH3 fully protected stringent K18-hACE2 mice from lethal challenge with Delta VOC. Our study demonstrates that protective NAbs responses converge in pediatric and adult SARS-CoV-2 patients.
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Affiliation(s)
- Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Jérémie Prévost
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hugo Romero
- Centre de Recherche du CHU Ste-Justine, Montreal, QC H3T 1C5, Canada
| | - Veronique Lisi
- Centre de Recherche du CHU Ste-Justine, Montreal, QC H3T 1C5, Canada
| | - William D. Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Jonathan R. Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shilei Ding
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Shang Yu Gong
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Mehdi Benlarbi
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Dani Vézina
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | | | - Michael W. Grunst
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ziwei Yang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Fei Zhou
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathie Béland
- Centre de Recherche du CHU Ste-Justine, Montreal, QC H3T 1C5, Canada
| | - Xiaoyun Bai
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Allison R. Zeher
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rick K. Huang
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dung N. Nguyen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Rebekah Sherburn
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bastien Paré
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Doreen Matthies
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan Richard
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Pradeep D. Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Vincent-Philippe Lavallée
- Centre de Recherche du CHU Ste-Justine, Montreal, QC H3T 1C5, Canada
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire (CHU) Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Université de Montréal, Montreal, QC H3T 1C5, Canada
| | - Martin A. Smith
- Centre de Recherche du CHU Ste-Justine, Montreal, QC H3T 1C5, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Elie Haddad
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
- Département de Pédiatrie, Université de Montréal, Montreal, QC H3T 1C5, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
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7
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Gong SY, Ding S, Benlarbi M, Chen Y, Vézina D, Marchitto L, Beaudoin-Bussières G, Goyette G, Bourassa C, Bo Y, Medjahed H, Levade I, Pazgier M, Côté M, Richard J, Prévost J, Finzi A. Temperature Influences the Interaction between SARS-CoV-2 Spike from Omicron Subvariants and Human ACE2. Viruses 2022; 14:2178. [PMID: 36298733 PMCID: PMC9607596 DOI: 10.3390/v14102178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 continues to infect millions of people worldwide. The subvariants arising from the variant-of-concern (VOC) Omicron include BA.1, BA.1.1, BA.2, BA.2.12.1, BA.4, and BA.5. All possess multiple mutations in their Spike glycoprotein, notably in its immunogenic receptor-binding domain (RBD), and present enhanced viral transmission. The highly mutated Spike glycoproteins from these subvariants present different degrees of resistance to recognition and cross-neutralisation by plasma from previously infected and/or vaccinated individuals. We have recently shown that the temperature affects the interaction between the Spike and its receptor, the angiotensin converting enzyme 2 (ACE2). The affinity of RBD for ACE2 is significantly increased at lower temperatures. However, whether this is also observed with the Spike of Omicron and sub-lineages is not known. Here we show that, similar to other variants, Spikes from Omicron sub-lineages bind better the ACE2 receptor at lower temperatures. Whether this translates into enhanced transmission during the fall and winter seasons remains to be determined.
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Affiliation(s)
- Shang Yu Gong
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
| | - Mehdi Benlarbi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine of Uniformed Services, University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Dani Vézina
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Lorie Marchitto
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | | | | | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | | | - Inès Levade
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine of Uniformed Services, University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
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8
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Daniell H, Nair SK, Shi Y, Wang P, Montone KT, Shaw PA, Choi GH, Ghani D, Weaver J, Rader DJ, Margulies KB, Collman RG, Laudanski K, Bar KJ. Decrease in Angiotensin-Converting Enzyme activity but not concentration in plasma/lungs in COVID-19 patients offers clues for diagnosis/treatment. Mol Ther Methods Clin Dev 2022; 26:266-278. [PMID: 35818571 PMCID: PMC9258412 DOI: 10.1016/j.omtm.2022.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 07/03/2022] [Indexed: 12/12/2022]
Abstract
Although several therapeutics are used to treat coronavirus disease 2019 (COVID-19) patients, there is still no definitive metabolic marker to evaluate disease severity and recovery or a quantitative test to end quarantine. Because severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infects human cells via the angiotensin-converting-enzyme 2 (ACE2) receptor and COVID-19 is associated with renin-angiotensin system dysregulation, we evaluated soluble ACE2 (sACE2) activity in the plasma/saliva of 80 hospitalized COVID-19 patients and 27 non-COVID-19 volunteers, and levels of ACE2/Ang (1-7) in plasma or membrane (mACE2) in lung autopsy samples. sACE2 activity was markedly reduced (p < 0.0001) in COVID-19 plasma (n = 59) compared with controls (n = 27). Nadir sACE2 activity in early hospitalization was restored during disease recovery, irrespective of patient age, demographic variations, or comorbidity; in convalescent plasma-administered patients (n = 45), restoration was statistically higher than matched controls (n = 22, p = 0.0021). ACE2 activity was also substantially reduced in the saliva of COVID-19 patients compared with controls (p = 0.0065). There is a strong inverse correlation between sACE2 concentration and sACE2 activity and Ang (1-7) levels in participant plasmas. However, there were no difference in membrane ACE2 levels in lungs of autopsy tissues of COVID-19 (n = 800) versus other conditions (n = 300). These clinical observations suggest sACE2 activity as a potential biomarker and therapeutic target for COVID-19.
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Affiliation(s)
- Henry Daniell
- W. D. Miller Professor & Director of Translational Research, Vice Chair, Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, 240 South 40th Street, 547 Levy Building, Philadelphia, PA 19104-6030, USA
| | - Smruti K. Nair
- W. D. Miller Professor & Director of Translational Research, Vice Chair, Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, 240 South 40th Street, 547 Levy Building, Philadelphia, PA 19104-6030, USA
| | - Yao Shi
- W. D. Miller Professor & Director of Translational Research, Vice Chair, Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, 240 South 40th Street, 547 Levy Building, Philadelphia, PA 19104-6030, USA
| | - Ping Wang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathleen T. Montone
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pamela A. Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Kaiser Permanente Washington Health Research Group, Seattle, WA, USA
| | - Grace H. Choi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Danyal Ghani
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - JoEllen Weaver
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel J. Rader
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenneth B. Margulies
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronald G. Collman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Krzysztof Laudanski
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katharine J. Bar
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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Ding S, Ullah I, Gong SY, Grover JR, Mohammadi M, Chen Y, Vézina D, Beaudoin-Bussières G, Verma VT, Goyette G, Gaudette F, Richard J, Yang D, Smith AB, Pazgier M, Côté M, Abrams C, Kumar P, Mothes W, Uchil PD, Finzi A, Baron C. VE607 stabilizes SARS-CoV-2 Spike in the "RBD-up" conformation and inhibits viral entry. iScience 2022; 25:104528. [PMID: 35677392 PMCID: PMC9164512 DOI: 10.1016/j.isci.2022.104528] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/11/2022] [Accepted: 05/30/2022] [Indexed: 10/26/2022] Open
Abstract
SARS-CoV-2 infection of host cells starts by binding the Spike glycoprotein (S) to the ACE2 receptor. The S-ACE2 interaction is a potential target for therapies against COVID-19 as demonstrated by the development of immunotherapies blocking this interaction. VE607 - a commercially available compound composed of three stereoisomers - was described as an inhibitor of SARS-CoV-1. Here, we show that VE607 broadly inhibits pseudoviral particles bearing the Spike from major VOCs (D614G, Alpha, Beta, Gamma, Delta, Omicron - BA.1, and BA.2) as well as authentic SARS-CoV-2 at low micromolar concentrations. In silico docking, mutational analysis, and smFRET revealed that VE607 binds to the receptor binding domain (RBD)-ACE2 interface and stabilizes RBD in its "up" conformation. Prophylactic treatment with VE607 did not prevent SARS-CoV-2-induced mortality in K18-hACE2 mice, but it did reduce viral replication in the lungs by 37-fold. Thus, VE607 is an interesting lead for drug development for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Shilei Ding
- Centre de recherche du CHUM, Montréal, QC, Canada
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shang Yu Gong
- Centre de recherche du CHUM, Montréal, QC, Canada,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Jonathan R. Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Mohammadjavad Mohammadi
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Dani Vézina
- Centre de recherche du CHUM, Montréal, QC, Canada,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de recherche du CHUM, Montréal, QC, Canada,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Vijay Tailor Verma
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada
| | | | | | - Jonathan Richard
- Centre de recherche du CHUM, Montréal, QC, Canada,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Derek Yang
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Amos B. Smith
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Cameron Abrams
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pradeep D. Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Andrés Finzi
- Centre de recherche du CHUM, Montréal, QC, Canada,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada,Corresponding author
| | - Christian Baron
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada,Corresponding author
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10
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Li T, Zhou B, Li Y, Huang S, Luo Z, Zhou Y, Lai Y, Gautam A, Bourgeau S, Wang S, Bao J, Tan J, Lavillette D, Li D. Isolation, characterization, and structure-based engineering of a neutralizing nanobody against SARS-CoV-2. Int J Biol Macromol 2022; 209:1379-1388. [PMID: 35460753 PMCID: PMC9020654 DOI: 10.1016/j.ijbiomac.2022.04.096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 11/29/2022]
Abstract
SARS-CoV-2 engages with human cells through the binding of its Spike receptor-binding domain (S-RBD) to the receptor ACE2. Molecular blocking of this engagement represents a proven strategy to treat COVID-19. Here, we report a single-chain antibody (nanobody, DL4) isolated from immunized alpaca with picomolar affinity to RBD. DL4 neutralizes SARS-CoV-2 pseudoviruses with an IC50 of 0.101 μg mL-1 (6.2 nM). A crystal structure of the DL4-RBD complex at 1.75-Å resolution unveils the interaction detail and reveals a direct competition mechanism for DL4's ACE2-blocking and hence neutralizing activity. The structural information allows us to rationally design a mutant with higher potency. Our work adds diversity of neutralizing nanobodies against SARS-CoV-2 and should encourage protein engineering to improve antibody affinities in general.
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Affiliation(s)
- Tingting Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China
| | - Bingjie Zhou
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China
| | - Yaning Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China,University of CAS, Beijing 101408, China
| | - Suqiong Huang
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China,College of Pharmacy, Chongqing Medical University, China
| | - Zhipu Luo
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Yuanze Zhou
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Yanling Lai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China,University of CAS, Beijing 101408, China
| | - Anupriya Gautam
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China
| | - Salome Bourgeau
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China,Institut National de la Santé et de la Recherche Médicale, École des Hautes Etudes en Santé Publique, Institut de Recherche en Santé, Environnement et Travail, Université de Rennes, F-35000 Rennes, France
| | - Shurui Wang
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Juan Bao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China
| | - Jingquan Tan
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Dimitri Lavillette
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China; Pasteurien College, Soochow University, Jiangsu, China.
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China.
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11
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Daniell H, Nair SK, Esmaeili N, Wakade G, Shahid N, Ganesan PK, Islam MR, Shepley-McTaggart A, Feng S, Gary EN, Ali AR, Nuth M, Cruz SN, Graham-Wooten J, Streatfield SJ, Montoya-Lopez R, Kaznica P, Mawson M, Green BJ, Ricciardi R, Milone M, Harty RN, Wang P, Weiner DB, Margulies KB, Collman RG. Debulking SARS-CoV-2 in saliva using angiotensin converting enzyme 2 in chewing gum to decrease oral virus transmission and infection. Mol Ther 2022; 30:1966-1978. [PMID: 34774754 PMCID: PMC8580552 DOI: 10.1016/j.ymthe.2021.11.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/03/2021] [Accepted: 11/07/2021] [Indexed: 12/29/2022] Open
Abstract
To advance a novel concept of debulking virus in the oral cavity, the primary site of viral replication, virus-trapping proteins CTB-ACE2 were expressed in chloroplasts and clinical-grade plant material was developed to meet FDA requirements. Chewing gum (2 g) containing plant cells expressed CTB-ACE2 up to 17.2 mg ACE2/g dry weight (11.7% leaf protein), have physical characteristics and taste/flavor like conventional gums, and no protein was lost during gum compression. CTB-ACE2 gum efficiently (>95%) inhibited entry of lentivirus spike or VSV-spike pseudovirus into Vero/CHO cells when quantified by luciferase or red fluorescence. Incubation of CTB-ACE2 microparticles reduced SARS-CoV-2 virus count in COVID-19 swab/saliva samples by >95% when evaluated by microbubbles (femtomolar concentration) or qPCR, demonstrating both virus trapping and blocking of cellular entry. COVID-19 saliva samples showed low or undetectable ACE2 activity when compared with healthy individuals (2,582 versus 50,126 ΔRFU; 27 versus 225 enzyme units), confirming greater susceptibility of infected patients for viral entry. CTB-ACE2 activity was completely inhibited by pre-incubation with SARS-CoV-2 receptor-binding domain, offering an explanation for reduced saliva ACE2 activity among COVID-19 patients. Chewing gum with virus-trapping proteins offers a general affordable strategy to protect patients from most oral virus re-infections through debulking or minimizing transmission to others.
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Affiliation(s)
- Henry Daniell
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Smruti K Nair
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nardana Esmaeili
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Geetanjali Wakade
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Naila Shahid
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Prem Kumar Ganesan
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Md Reyazul Islam
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ariel Shepley-McTaggart
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sheng Feng
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ebony N Gary
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Ali R Ali
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Manunya Nuth
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Selene Nunez Cruz
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jevon Graham-Wooten
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | | | - Paul Kaznica
- Fraunhofer USA, Center Mid-Atlantic, Newark, DE 19711, USA
| | | | - Brian J Green
- Fraunhofer USA, Center Mid-Atlantic, Newark, DE 19711, USA
| | - Robert Ricciardi
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Milone
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ronald N Harty
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ping Wang
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - David B Weiner
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Kenneth B Margulies
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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12
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Georgas A, Lampas E, Houhoula D, Skoufias A, Patsilinakos S, Tsafaridis I, Patrinos G, Adamopoulos N, Ferraro A, Hristoforou E. ACE2-based capacitance sensor for rapid native SARS-CoV-2 detection in biological fluids and its correlation with real-time PCR. Biosens Bioelectron 2022; 202:114021. [PMID: 35092924 PMCID: PMC8776344 DOI: 10.1016/j.bios.2022.114021] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/14/2022]
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13
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Pak AJ, Yu A, Ke Z, Briggs JAG, Voth GA. Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core. Nat Commun 2022; 13:1002. [PMID: 35194049 PMCID: PMC8863989 DOI: 10.1038/s41467-022-28654-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 02/03/2022] [Indexed: 12/29/2022] Open
Abstract
The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes dissociation of the S1 domains and exposure of the fusion machinery, although the molecular details of this process have yet to be observed. We report the development of bottom-up coarse-grained (CG) models consistent with cryo-electron tomography data, and the use of CG molecular dynamics simulations to investigate viral binding and S2 core exposure. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces in a manner distinct from binding between soluble proteins, which processively induces S1 dissociation. We also simulate possible variant behavior using perturbed CG models, and find that ACE2-induced S1 dissociation is primarily sensitive to conformational state populations and the extent of S1/S2 cleavage, rather than ACE2 binding affinity. These simulations reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.
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Affiliation(s)
- Alexander J Pak
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, USA
| | - Alvin Yu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Zunlong Ke
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - John A G Briggs
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Gregory A Voth
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- James Franck Institute, The University of Chicago, Chicago, IL, USA.
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14
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Ahmad W, Shabbiri K. Two years of SARS-CoV-2 infection (2019-2021): structural biology, vaccination, and current global situation. THE EGYPTIAN JOURNAL OF INTERNAL MEDICINE 2022; 34:5. [PMID: 35043040 PMCID: PMC8759062 DOI: 10.1186/s43162-021-00092-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/03/2021] [Indexed: 11/10/2022] Open
Abstract
The deadly SARS-CoV-2 virus has infected more than 259,502,031 confirmed cases with 5,183,003 deaths in 223 countries during the last 22 months (Dec 2019-Nov 2021), whereas approximately 7,702,859,718, vaccine doses have been administered (WHO: https://covid19.who.int/) as of the 24th of Nov 2021. Recent announcements of test trial completion of several new vaccines resulted in the launching of immunization for the common person around the globe highlighting a ray of hope to cope with this infection. Meanwhile, genetic variations in SARS-CoV-2 and third layer of infection spread in numerous countries emerged as a stronger prototype than the parental. New and parental SARS-CoV-2 strains appeared as a risk factor for other pre-existing diseases like cancer, diabetes, neurological disorders, kidney, liver, heart, and eye injury. This situation requires more attention and re-structuring of the currently developed vaccines and/or drugs against SARS-CoV-2 infection. Although a decline in COVID-19 infection has been reported globally, an increase in COVID-19 cases in the subcontinent and east Mediterranean area could be alarming. In this review, we have summarized the current information about the SARS-CoV-2 biology, its interaction and possible infection pathways within the host, epidemiology, risk factors, economic collapse, and possible vaccine and drug development.
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Affiliation(s)
- Waqar Ahmad
- Department of Biochemistry, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
- The University of Queensland, Brisbane, Australia
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15
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Chatterjee D, Tauzin A, Laumaea A, Gong SY, Bo Y, Guilbault A, Goyette G, Bourassa C, Gendron-Lepage G, Medjahed H, Richard J, Moreira S, Côté M, Finzi A. Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. Viruses 2022; 14:v14010144. [PMID: 35062348 PMCID: PMC8780535 DOI: 10.3390/v14010144] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
The rapid emergence of SARS-CoV-2 variants is fueling the recent waves of the COVID-19 pandemic. Here, we assessed ACE2 binding and antigenicity of Mu (B.1.621) and A.2.5 Spikes. Both these variants carry some mutations shared by other emerging variants. Some of the pivotal mutations such as N501Y and E484K in the receptor-binding domain (RBD) detected in B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) are now present within the Mu variant. Similarly, the L452R mutation of B.1.617.2 (Delta) variant is present in A.2.5. In this study, we observed that these Spike variants bound better to the ACE2 receptor in a temperature-dependent manner. Pseudoviral particles bearing the Spike of Mu were similarly neutralized by plasma from vaccinated individuals than those carrying the Beta (B.1.351) and Delta (B.1.617.2) Spikes. Altogether, our results indicate the importance of measuring critical parameters such as ACE2 interaction, plasma recognition and neutralization ability of each emerging variant.
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Affiliation(s)
- Debashree Chatterjee
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
| | - Alexandra Tauzin
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Annemarie Laumaea
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Shang Yu Gong
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (Y.B.); (M.C.)
| | - Aurélie Guilbault
- Laboratoire de Santé Publique du Québec, Institut Nationale de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; (A.G.); (S.M.)
| | - Guillaume Goyette
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
| | - Catherine Bourassa
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
| | - Gabrielle Gendron-Lepage
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
| | - Halima Medjahed
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Sandrine Moreira
- Laboratoire de Santé Publique du Québec, Institut Nationale de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; (A.G.); (S.M.)
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (Y.B.); (M.C.)
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; (D.C.); (A.T.); (A.L.); (S.Y.G.); (G.G.); (C.B.); (G.G.-L.); (H.M.); (J.R.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G4, Canada
- Correspondence:
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16
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Li W, Chen Y, Prévost J, Ullah I, Lu M, Gong SY, Tauzin A, Gasser R, Vézina D, Anand SP, Goyette G, Chaterjee D, Ding S, Tolbert WD, Grunst MW, Bo Y, Zhang S, Richard J, Zhou F, Huang RK, Esser L, Zeher A, Côté M, Kumar P, Sodroski J, Xia D, Uchil PD, Pazgier M, Finzi A, Mothes W. Structural basis and mode of action for two broadly neutralizing antibodies against SARS-CoV-2 emerging variants of concern. Cell Rep 2022; 38:110210. [PMID: 34971573 PMCID: PMC8673750 DOI: 10.1016/j.celrep.2021.110210] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/26/2021] [Accepted: 12/13/2021] [Indexed: 01/15/2023] Open
Abstract
Emerging variants of concern for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transmit more efficiently and partially evade protective immune responses, thus necessitating continued refinement of antibody therapies and immunogen design. Here, we elucidate the structural basis and mode of action for two potent SARS-CoV-2 spike (S)-neutralizing monoclonal antibodies, CV3-1 and CV3-25, which remain effective against emerging variants of concern in vitro and in vivo. CV3-1 binds to the (485-GFN-487) loop within the receptor-binding domain (RBD) in the "RBD-up" position and triggers potent shedding of the S1 subunit. In contrast, CV3-25 inhibits membrane fusion by binding to an epitope in the stem helix region of the S2 subunit that is highly conserved among β-coronaviruses. Thus, vaccine immunogen designs that incorporate the conserved regions in the RBD and stem helix region are candidates to elicit pan-coronavirus protective immune responses.
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Affiliation(s)
- Wenwei Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Jérémie Prévost
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shang Yu Gong
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alexandra Tauzin
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Dani Vézina
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | | | - Shilei Ding
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - William D Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Michael W Grunst
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Richard
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Fei Zhou
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rick K Huang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lothar Esser
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Allison Zeher
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pradeep D Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA.
| | - Andrés Finzi
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA.
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17
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Amini MA, Karimi J, Talebi SS, Piri H. The Association of COVID-19 and Reactive Oxygen Species Modulator 1 (ROMO1) with Oxidative Stress. Chonnam Med J 2022; 58:1-5. [PMID: 35169552 PMCID: PMC8813649 DOI: 10.4068/cmj.2022.58.1.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 12/04/2022] Open
Abstract
There is no denying that the massive spread of COVID-19 around the world has worried everyone. The virus can cause mild to severe symptoms in various organs, especially the lungs. The virus affects oxidative stress in the cells. Reactive Oxygen Species modulator 1 (ROMO1) is one of the most important mitochondrial proteins that plays a critical regulatory role in the production of Reactive Oxygen Species (ROS). According to the studies, COVID-19 can promote oxidative stress through some important pathways, for instance, TNF-α and NF-κB routes. Furthermore, ROMO1 is closely related to these pathways and its dysfunction may affect these routes, then promote oxidative stress, and ultimately cause tissue damage, especially in the lungs. Another factor to consider is that the TNF-α and NF-κB pathways are associated with ROMO1, COVID-19, and oxidative stress. To summarize, it is hypothesized that COVID-19 may increase oxidative stress by affecting ROMO1. Understanding the exact molecular mechanisms of ROMO1 in the pathogenesis of COVID-19 can pave the way to find better therapeutic strategies.
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Affiliation(s)
- Mohammad Amin Amini
- Department of Clinical Biochemistry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Jamshid Karimi
- Department of Clinical Biochemistry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Seyed Saman Talebi
- Department of Internal Medicine, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hosein Piri
- Department of Biochemistry and Nutrition, School of Medicine, Qazvin University of Medical Science, Qazvin, Iran
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18
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Brought to Light: How Ultraviolet Disinfection Can Prevent the Nosocomial Transmission of COVID-19 and Other Infectious Diseases. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1030035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The novel coronavirus disease 2019 (COVID-19) pandemic has brought to light the role of environmental hygiene in controlling disease transmission. Healthcare facilities are hot spots for infectious pathogens where physical distancing and personal protective equipment (PPE) are not always sufficient to prevent disease transmission. Healthcare facilities need to consider adjunct strategies to prevent transmission of infectious pathogens. In combination with current infection control procedures, many healthcare facilities are incorporating ultraviolet (UV) disinfection into their routines. This review considers how pathogens are transmitted in healthcare facilities, the mechanism of UV microbial inactivation and the documented activity of UV against clinical pathogens. Emphasis is placed on the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) as well as multidrug resistant organisms (MDROs) that are commonly transmitted in healthcare facilities. The potential benefits and limitations of UV technologies are discussed to help inform healthcare workers, including clinical studies where UV technology is used in healthcare facilities.
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19
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Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Sci Rep 2021; 11:22195. [PMID: 34773067 PMCID: PMC8589851 DOI: 10.1038/s41598-021-01690-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/02/2021] [Indexed: 12/24/2022] Open
Abstract
To initiate SARS-CoV-2 infection, the Receptor Binding Domain (RBD) on the viral spike protein must first bind to the host receptor ACE2 protein on pulmonary and other ACE2-expressing cells. We hypothesized that cardiac glycoside drugs might block the binding reaction between ACE2 and the Spike (S) protein, and thus block viral penetration into target cells. To test this hypothesis we developed a biochemical assay for ACE2:Spike binding, and tested cardiac glycosides as inhibitors of binding. Here we report that ouabain, digitoxin, and digoxin, as well as sugar-free derivatives digitoxigenin and digoxigenin, are high-affinity competitive inhibitors of ACE2 binding to the Original [D614] S1 and the α/β/γ [D614G] S1 proteins. These drugs also inhibit ACE2 binding to the Original RBD, as well as to RBD proteins containing the β [E484K], Mink [Y453F] and α/β/γ [N501Y] mutations. As hypothesized, we also found that ouabain, digitoxin and digoxin blocked penetration by SARS-CoV-2 Spike-pseudotyped virus into human lung cells, and infectivity by native SARS-CoV-2. These data indicate that cardiac glycosides may block viral penetration into the target cell by first inhibiting ACE2:RBD binding. Clinical concentrations of ouabain and digitoxin are relatively safe for short term use for subjects with normal hearts. It has therefore not escaped our attention that these common cardiac medications could be deployed worldwide as inexpensive repurposed drugs for anti-COVID-19 therapy.
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Gong SY, Chatterjee D, Richard J, Prévost J, Tauzin A, Gasser R, Bo Y, Vézina D, Goyette G, Gendron-Lepage G, Medjahed H, Roger M, Côté M, Finzi A. Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Virology 2021. [PMID: 34536797 DOI: 10.1101/2021.08.04.455140v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Towards the end of 2020, multiple variants of concern (VOCs) and variants of interest (VOIs) have arisen from the original SARS-CoV-2 Wuhan-Hu-1 strain. Mutations in the Spike protein are highly scrutinized for their impact on transmissibility, pathogenesis and vaccine efficacy. Here, we contribute to the growing body of literature on emerging variants by evaluating the impact of single mutations on the overall antigenicity of selected variants and their binding to the ACE2 receptor. We observe a differential contribution of single mutants to the global variants phenotype related to ACE2 interaction and antigenicity. Using biolayer interferometry, we observe that enhanced ACE2 interaction is mostly modulated by a decrease in off-rate. Finally, we made the interesting observation that the Spikes from tested emerging variants bind better to ACE2 at 37°C compared to the D614G variant. Whether improved ACE2 binding at higher temperature facilitates emerging variants transmission remain to be demonstrated.
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Affiliation(s)
- Shang Yu Gong
- Centre de Recherche du CHUM, QC, H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, H3A 0G4, Canada
| | | | - Jonathan Richard
- Centre de Recherche du CHUM, QC, H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, H2X 0A9, Canada
| | - Jérémie Prévost
- Centre de Recherche du CHUM, QC, H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, H2X 0A9, Canada
| | - Alexandra Tauzin
- Centre de Recherche du CHUM, QC, H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, H2X 0A9, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM, QC, H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, H2X 0A9, Canada
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Dani Vézina
- Centre de Recherche du CHUM, QC, H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, H2X 0A9, Canada
| | | | | | | | - Michel Roger
- Centre de Recherche du CHUM, QC, H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, H2X 0A9, Canada; Laboratoire de Santé Publique du Québec, Institut Nationale de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, H9X 3R5, Canada
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM, QC, H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, H3A 0G4, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, H2X 0A9, Canada.
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21
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Prévost J, Richard J, Gasser R, Ding S, Fage C, Anand SP, Adam D, Gupta Vergara N, Tauzin A, Benlarbi M, Gong SY, Goyette G, Privé A, Moreira S, Charest H, Roger M, Mothes W, Pazgier M, Brochiero E, Boivin G, Abrams CF, Schön A, Finzi A. Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. J Biol Chem 2021; 297:101151. [PMID: 34478710 PMCID: PMC8406544 DOI: 10.1016/j.jbc.2021.101151] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 12/29/2022] Open
Abstract
The seasonal nature of outbreaks of respiratory viral infections with increased transmission during low temperatures has been well established. Accordingly, temperature has been suggested to play a role on the viability and transmissibility of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. The receptor-binding domain (RBD) of the Spike glycoprotein is known to bind to its host receptor angiotensin-converting enzyme 2 (ACE2) to initiate viral fusion. Using biochemical, biophysical, and functional assays to dissect the effect of temperature on the receptor-Spike interaction, we observed a significant and stepwise increase in RBD-ACE2 affinity at low temperatures, resulting in slower dissociation kinetics. This translated into enhanced interaction of the full Spike glycoprotein with the ACE2 receptor and higher viral attachment at low temperatures. Interestingly, the RBD N501Y mutation, present in emerging variants of concern (VOCs) that are fueling the pandemic worldwide (including the B.1.1.7 (α) lineage), bypassed this requirement. This data suggests that the acquisition of N501Y reflects an adaptation to warmer climates, a hypothesis that remains to be tested.
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Affiliation(s)
- Jérémie Prévost
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Jonathan Richard
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada
| | - Clément Fage
- Centre de Recherche du CHU de Québec, Université Laval, Quebec City, Quebec, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Damien Adam
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Médicine, Université de Montréal, Montréal, Quebec, Canada
| | - Natasha Gupta Vergara
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Alexandra Tauzin
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Mehdi Benlarbi
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada
| | - Shang Yu Gong
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Guillaume Goyette
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada
| | - Anik Privé
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada
| | - Sandrine Moreira
- Laboratoire de Santé Publique du Québec, Institut Nationale de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Hugues Charest
- Laboratoire de Santé Publique du Québec, Institut Nationale de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Michel Roger
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada; Laboratoire de Santé Publique du Québec, Institut Nationale de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Emmanuelle Brochiero
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Médicine, Université de Montréal, Montréal, Quebec, Canada
| | - Guy Boivin
- Centre de Recherche du CHU de Québec, Université Laval, Quebec City, Quebec, Canada
| | - Cameron F Abrams
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Arne Schön
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, axe Immunopathologie, Montreal, Quebec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada; Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.
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22
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Li W, Chen Y, Prévost J, Ullah I, Lu M, Gong SY, Tauzin A, Gasser R, Vézina D, Anand SP, Goyette G, Chaterjee D, Ding S, Tolbert WD, Grunst MW, Bo Y, Zhang S, Richard J, Zhou F, Huang RK, Esser L, Zeher A, Côté M, Kumar P, Sodroski J, Xia D, Uchil PD, Pazgier M, Finzi A, Mothes W. Structural Basis and Mode of Action for Two Broadly Neutralizing Antibodies Against SARS-CoV-2 Emerging Variants of Concern. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.02.454546. [PMID: 34373853 PMCID: PMC8351775 DOI: 10.1101/2021.08.02.454546] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Emerging variants of concern for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transmit more efficiently and partially evade protective immune responses, thus necessitating continued refinement of antibody therapies and immunogen design. Here we elucidate the structural basis and mode of action for two potent SARS-CoV-2 Spike (S) neutralizing monoclonal antibodies CV3-1 and CV3-25 that remained effective against emerging variants of concern in vitro and in vivo. CV3-1 bound to the (485-GFN-487) loop within the receptor-binding domain (RBD) in the "RBD-up" position and triggered potent shedding of the S1 subunit. In contrast, CV3-25 inhibited membrane fusion by binding to an epitope in the stem helix region of the S2 subunit that is highly conserved among β-coronaviruses. Thus, vaccine immunogen designs that incorporate the conserved regions in RBD and stem helix region are candidates to elicit pan-coronavirus protective immune responses.
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Affiliation(s)
- Wenwei Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Jérémie Prévost
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Shang Yu Gong
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alexandra Tauzin
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Dani Vézina
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | | | - Shilei Ding
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - William D. Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Michael W. Grunst
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Jonathan Richard
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Fei Zhou
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rick K. Huang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lothar Esser
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Allison Zeher
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pradeep D. Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
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23
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Pak AJ, Yu A, Ke Z, Briggs JAG, Voth GA. Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.05.24.445443. [PMID: 34127973 PMCID: PMC8202425 DOI: 10.1101/2021.05.24.445443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind, fuse, and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes the preparation of the fusion machinery by dissociation of the S1 domains. We report the development of bottom-up coarse-grained (CG) models validated with cryo-electron tomography (cryo-ET) data, and the use of CG molecular dynamics simulations to investigate the dynamical mechanisms involved in viral binding and exposure of the S2 trimeric core. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces. The multivalent interaction cyclically and processively induces S1 dissociation, thereby exposing the S2 core containing the fusion machinery. Our simulations thus reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.
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24
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Li T, Huang T, Guo C, Wang A, Shi X, Mo X, Lu Q, Sun J, Hui T, Tian G, Wang L, Yang J. Genomic variation, origin tracing, and vaccine development of SARS-CoV-2: A systematic review. Innovation (N Y) 2021; 2:100116. [PMID: 33997827 PMCID: PMC8110321 DOI: 10.1016/j.xinn.2021.100116] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 04/30/2021] [Indexed: 02/07/2023] Open
Abstract
COVID-19 has spread globally to over 200 countries with more than 40 million confirmed cases and one million deaths as of November 1, 2020. The SARS-CoV-2 virus, leading to COVID-19, shows extremely high rates of infectivity and replication, and can result in pneumonia, acute respiratory distress, or even mortality. SARS-CoV-2 has been found to continue to rapidly evolve, with several genomic variants emerging in different regions throughout the world. In addition, despite intensive study of the spike protein, its origin, and molecular mechanisms in mediating host invasion are still only partially resolved. Finally, the repertoire of drugs for COVID-19 treatment is still limited, with several candidates still under clinical trial and no effective therapeutic yet reported. Although vaccines based on either DNA/mRNA or protein have been deployed, their efficacy against emerging variants requires ongoing study, with multivalent vaccines supplanting the first-generation vaccines due to their low efficacy against new strains. Here, we provide a systematic review of studies on the epidemiology, immunological pathogenesis, molecular mechanisms, and structural biology, as well as approaches for drug or vaccine development for SARS-CoV-2.
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Affiliation(s)
- Tianbao Li
- Genetic Testing Center, Academician Workstation, Changsha Medical University, Changsha 410219, China
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cheng Guo
- Center for Infection and Immunity, School of Public Health, Columbia University, New York, NY 10032, USA
| | - Ailan Wang
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
| | - Xiaoli Shi
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
| | - Xiaofei Mo
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
| | - Qingqing Lu
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
| | - Jing Sun
- Department of Pathology, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Tingting Hui
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
- Corresponding author
| | - Jialiang Yang
- Genetic Testing Center, Academician Workstation, Changsha Medical University, Changsha 410219, China
- Geneis (Beijing) Co., Ltd, Beijing 100102, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao 266000, China
- Corresponding author
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25
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Souza PFN, Mesquita FP, Amaral JL, Landim PGC, Lima KRP, Costa MB, Farias IR, Lima LB, Montenegro RC. The human pandemic coronaviruses on the show: The spike glycoprotein as the main actor in the coronaviruses play. Int J Biol Macromol 2021; 179:1-19. [PMID: 33667553 PMCID: PMC7921731 DOI: 10.1016/j.ijbiomac.2021.02.203] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 01/28/2023]
Abstract
Three coronaviruses (CoVs) have threatened the world population by causing outbreaks in the last two decades. In late 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged and caused the coronaviruses to disease 2019 (COVID-19), leading to the ongoing global outbreak. The other pandemic coronaviruses, SARS-CoV and Middle East respiratory syndrome CoV (MERS-CoV), share a considerable level of similarities at genomic and protein levels. However, the differences between them lead to distinct behaviors. These differences result from the accumulation of mutations in the sequence and structure of spike (S) glycoprotein, which plays an essential role in coronavirus infection, pathogenicity, transmission, and evolution. In this review, we brought together many studies narrating a sequence of events and highlighting the differences among S proteins from SARS-CoV, MERS-CoV, and SARS-CoV-2. It was performed here, analysis of S protein sequences and structures from the three pandemic coronaviruses pointing out the mutations among them and what they come through. Additionally, we investigated the receptor-binding domain (RBD) from all S proteins explaining the mutation and biological importance of all of them. Finally, we discuss the mutation in the S protein from several new isolates of SARS-CoV-2, reporting their difference and importance. This review brings into detail how the variations in S protein that make SARS-CoV-2 more aggressive than its relatives coronaviruses and other differences between coronaviruses.
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Affiliation(s)
- Pedro F N Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Brazil.
| | - Felipe P Mesquita
- Drug research and Development Center, Department of Medicine, Federal University of Ceara, Brazil
| | - Jackson L Amaral
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Brazil
| | - Patrícia G C Landim
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Brazil
| | - Karollyny R P Lima
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Brazil
| | - Marília B Costa
- Drug research and Development Center, Department of Medicine, Federal University of Ceara, Brazil
| | - Izabelle R Farias
- Drug research and Development Center, Department of Medicine, Federal University of Ceara, Brazil
| | - Luina B Lima
- Drug research and Development Center, Department of Medicine, Federal University of Ceara, Brazil
| | - Raquel C Montenegro
- Drug research and Development Center, Department of Medicine, Federal University of Ceara, Brazil
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26
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Govind Kumar V, Ogden DS, Isu U, Polasa A, Losey J, Moradi M. Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33398271 DOI: 10.1101/2020.12.25.424008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The coronavirus spike protein, which binds to the same human receptor in both SARS-CoV-1 and 2, has been implied to be a potential source of their differential transmissibility. However, the mechanistic details of spike protein binding to its human receptor remain elusive at the molecular level. Here, we have used an extensive set of unbiased and biased microsecond-level all-atom molecular dynamics (MD) simulations of SARS-CoV-1 and 2 spike proteins to determine the differential dynamic behavior of prefusion spike protein structure in the two viruses. Our results indicate that the active form of the SARS-CoV-2 spike protein is more stable than that of SARS-CoV-1 and the energy barrier associated with the activation is higher in SARS-CoV-2. Our results also suggest that not only the receptor binding domain (RBD) but also other domains such as the N-terminal domain (NTD) could play a role in the differential binding behavior of SARS-CoV-1 and 2 spike proteins.
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27
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Multicenter Evaluation of the Clinical Performance and the Neutralizing Antibody Activity Prediction Properties of 10 High-Throughput Serological Assays Used in Clinical Laboratories. J Clin Microbiol 2021; 59:JCM.02511-20. [PMID: 33303562 PMCID: PMC8106733 DOI: 10.1128/jcm.02511-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/08/2020] [Indexed: 02/08/2023] Open
Abstract
As the coronavirus disease 2019 (COVID-19) pandemic second wave is emerging, it is of the upmost importance to screen the population immunity in order to keep track of infected individuals. Consequently, immunoassays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high specificity and positive predictive values are needed to obtain an accurate epidemiological picture. As more data accumulate about the immune responses and the kinetics of neutralizing-antibody (nAb) production in SARS-CoV-2-infected individuals, new applications are forecast for serological assays such as nAb activity prediction in convalescent-phase plasma from recovered patients. This multicenter study, involving six hospital centers, determined the baseline clinical performances, reproducibility, and nAb level correlations of 10 commercially available immunoassays. In addition, three lateral-flow chromatography assays were evaluated, as these devices can be used in logistically challenged areas. All assays were evaluated using the same patient panels in duplicate, thus enabling accurate comparison of the tests. Seven immunoassays examined in this study were shown to have excellent specificity (98 to 100%) and good to excellent positive predictive values (82 to 100%) when used in a low (5%)-seroprevalence setting. We observed sensitivities as low as 74% and as high as 95% at ≥15 days after symptom onset. The determination of optimized cutoff values through receiver operating characteristic (ROC) curve analyses had a significant impact on the diagnostic resolution of several enzyme immunoassays by increasing the sensitivity significantly without a large trade-off in specificity. We found that spike-based immunoassays seem to be better correlates of nAb activity. Finally, the results reported here will add to the general knowledge of the interlaboratory reproducibility of clinical performance parameters of immunoassays and provide new evidence about nAb activity prediction.
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28
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Liu W, Guan WJ, Zhong NS. Strategies and Advances in Combating COVID-19 in China. ENGINEERING (BEIJING, CHINA) 2020; 6:1076-1084. [PMID: 33078078 PMCID: PMC7558233 DOI: 10.1016/j.eng.2020.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 05/02/2023]
Abstract
Coronavirus disease 2019 (COVID-19)-the third in a series of coronavirus infections-has caused a global public health event in the 21st century, resulting in substantial global morbidity and mortality. Building on its legacy of managing severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), China has played a key role in the scientific community by revealing the viral transmission routes and clinical characteristics of COVID-19 and developing novel therapeutic interventions and vaccines. Despite these rapid scientific and technological advances, uncertainties remain in tracing the original sources of infection, determining the routes of transmission and pathogenesis, and addressing the lack of targeted clinical management of COVID-19. Here, we summarize the major COVID-19 research advances in China in order to provide useful information for global pandemic control.
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Affiliation(s)
- Wei Liu
- 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 510120, China
| | - Wei-Jie Guan
- 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 510120, China
| | - Nan-Shan Zhong
- 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 510120, China
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