1
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Lei R, Qing E, Odle A, Yuan M, Gunawardene CD, Tan TJC, So N, Ouyang WO, Wilson IA, Gallagher T, Perlman S, Wu NC, Wong LYR. Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning. Nat Commun 2024; 15:4056. [PMID: 38744813 PMCID: PMC11094058 DOI: 10.1038/s41467-024-48104-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we perform a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identify mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we show that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Abby Odle
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Chaminda D Gunawardene
- Center for Virus-Host Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Natalie So
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Wenhao O Ouyang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA.
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA.
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA.
- Center for Virus-Host Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
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2
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Yagüe Relimpio A, Fink A, Bui DT, Fabritz S, Schröter M, Ruggieri A, Platzman I, Spatz JP. Bottom-up Assembled Synthetic SARS-CoV-2 Miniviruses Reveal Lipid Membrane Affinity of Omicron Variant Spike Glycoprotein. ACS NANO 2023; 17:23913-23923. [PMID: 37976416 PMCID: PMC10722588 DOI: 10.1021/acsnano.3c08323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
The ongoing COVID-19 pandemic has been brought on by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike glycoprotein (S), which decorates the viral envelope forming a corona, is responsible for the binding to the angiotensin-converting enzyme 2 (ACE2) receptor and initiating the infection. In comparison to previous variants, Omicron S presents additional binding sites as well as a more positive surface charge. These changes hint at additional molecular targets for interactions between virus and cell, such as the cell membrane or proteoglycans on the cell surface. Herein, bottom-up assembled synthetic SARS-CoV-2 miniviruses (MiniVs), with a lipid composition similar to that of infectious particles, are implemented to study and compare the binding properties of Omicron and Alpha variants. Toward this end, a systematic functional screening is performed to study the binding ability of Omicron and Alpha S proteins to ACE2-functionalized and nonfunctionalized planar supported lipid bilayers. Moreover, giant unilamellar vesicles are used as a cell membrane model to perform competitive interaction assays of the two variants. Finally, two cell lines with and without presentation of the ACE2 receptor are used to confirm the binding properties of the Omicron and Alpha MiniVs to the cellular membrane. Altogether, the results reveal a significantly higher affinity of Omicron S toward both the lipid membrane and ACE2 receptor. The research presented here highlights the advantages of creating and using bottom-up assembled SARS-CoV-2 viruses to understand the impact of changes in the affinity of S for ACE2 in infection studies.
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Affiliation(s)
- Ana Yagüe Relimpio
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Andreas Fink
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Duc Thien Bui
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Sebastian Fabritz
- Department
for Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Martin Schröter
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Alessia Ruggieri
- Heidelberg
University, Medical Faculty, Centre for Integrative Infectious Disease Research (CIID), Department
of Infectious Diseases, Molecular Virology, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Ilia Platzman
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
- Max
Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard’s Close, Bristol BS8 1TD, U.K.
| | - Joachim P. Spatz
- Department
for Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering and Advanced Materials (IMSEAM), Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
- Max
Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard’s Close, Bristol BS8 1TD, U.K.
- Max Planck
School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany
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3
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Hu X, Liao M, Ding K, Wang J, Xu H, Tao K, Zhou F, Lu JR. Neutron reflection and scattering in characterising peptide assemblies. Adv Colloid Interface Sci 2023; 322:103033. [PMID: 37931380 DOI: 10.1016/j.cis.2023.103033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023]
Abstract
Self-assemblies of de novo designed short peptides at interface and in bulk solution provide potential platforms for developing applications in many medical and technological areas. However, characterising how bioinspired supramolecular nanostructures evolve with dynamic self-assembling processes and respond to different stimuli remains challenging. Neutron scattering technologies including small angle neutron scattering (SANS) and neutron reflection (NR) can be advantageous and complementary to other state-of-the-art techniques in tracing structural changes under different conditions. With more neutron sources now available, SANS and NR are becoming increasingly popular in studying self-assembling processes of diverse peptide and protein systems, but the difficulty in experimental manipulation and data analysis can deter beginners. This review will introduce the basic theory, general experimental setup and data analysis of SANS and NR, followed by provision of their applications in characterising interfacial and solution self-assemblies of representative peptides and proteins. SANS and NR are remarkably effective in determining the morphological features self-assembled short peptides, especially size and shape transitions as a result of either sequence changes or in response to environmental stimuli, demonstrating the unique capability of NR and SANS in unravelling the interactive processes. These examples highlight the potential of NR and SANS in supporting the development of novel short peptides and proteins as biopharmaceutical candidates in the fight against many diseases and infections that share common features of membrane interactive processes.
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Affiliation(s)
- Xuzhi Hu
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, UK.; Lanzhou Institute of Chemical Physics, Tianshui Middle Road, Lanzhou 730000, Gansu, China
| | - Mingrui Liao
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Ke Ding
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Jiqian Wang
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Hai Xu
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Kai Tao
- State Key Laboratory of Fluid Power and Mechatronic Systems, Key Laboratory of Advanced Manufacturing Technology of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, Hangzhou 310058, China; Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Zhejiang University, Hangzhou 311215, China
| | - Feng Zhou
- Lanzhou Institute of Chemical Physics, Tianshui Middle Road, Lanzhou 730000, Gansu, China
| | - Jian R Lu
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, UK..
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4
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Lei R, Qing E, Odle A, Yuan M, Tan TJ, So N, Ouyang WO, Wilson IA, Gallagher T, Perlman S, Wu NC, Wong LYR. Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569051. [PMID: 38076875 PMCID: PMC10705381 DOI: 10.1101/2023.11.28.569051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we performed a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identified mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we showed that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Abby Odle
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Natalie So
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wenhao O. Ouyang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Center for Virus-Host-Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
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5
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Niort K, Dancourt J, Boedec E, Al Amir Dache Z, Lavieu G, Tareste D. Cholesterol and Ceramide Facilitate Membrane Fusion Mediated by the Fusion Peptide of the SARS-CoV-2 Spike Protein. ACS OMEGA 2023; 8:32729-32739. [PMID: 37720777 PMCID: PMC10500581 DOI: 10.1021/acsomega.3c03610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/17/2023] [Indexed: 09/19/2023]
Abstract
SARS-CoV-2 entry into host cells is mediated by the Spike (S) protein of the viral envelope. The S protein is composed of two subunits: S1 that induces binding to the host cell via its interaction with the ACE2 receptor of the cell surface and S2 that triggers fusion between viral and cellular membranes. Fusion by S2 depends on its heptad repeat domains that bring membranes close together and its fusion peptide (FP) that interacts with and perturbs the membrane structure to trigger fusion. Recent studies have suggested that cholesterol and ceramide lipids from the cell surface may facilitate SARS-CoV-2 entry into host cells, but their exact mode of action remains unknown. We have used a combination of in vitro liposome-liposome and in situ cell-cell fusion assays to study the lipid determinants of S-mediated membrane fusion. Our findings reveal that both cholesterol and ceramide lipids facilitate fusion, suggesting that targeting these lipids could be effective against SARS-CoV-2. As a proof of concept, we examined the effect of chlorpromazine (CPZ), an antipsychotic drug known to perturb membrane structure. Our results show that CPZ effectively inhibits S-mediated membrane fusion, thereby potentially impeding SARS-CoV-2 entry into the host cell.
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Affiliation(s)
- Kristina Niort
- Université
Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and
Neuroscience of Paris (IPNP), Paris 75014, France
| | - Julia Dancourt
- Université
Paris Cité, Inserm U 1316, CNRS UMR 7057, Laboratoire Matières
et Systèmes Complexes (MSC), Paris 75006, France
| | - Erwan Boedec
- Université
Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and
Neuroscience of Paris (IPNP), Paris 75014, France
| | - Zahra Al Amir Dache
- Université
Paris Cité, Inserm U 1316, CNRS UMR 7057, Laboratoire Matières
et Systèmes Complexes (MSC), Paris 75006, France
| | - Grégory Lavieu
- Université
Paris Cité, Inserm U 1316, CNRS UMR 7057, Laboratoire Matières
et Systèmes Complexes (MSC), Paris 75006, France
| | - David Tareste
- Université
Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and
Neuroscience of Paris (IPNP), Paris 75014, France
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6
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Siebert HC, Eckert T, Bhunia A, Klatte N, Mohri M, Siebert S, Kozarova A, Hudson JW, Zhang R, Zhang N, Li L, Gousias K, Kanakis D, Yan M, Jiménez-Barbero J, Kožár T, Nifantiev NE, Vollmer C, Brandenburger T, Kindgen-Milles D, Haak T, Petridis AK. Blood pH Analysis in Combination with Molecular Medical Tools in Relation to COVID-19 Symptoms. Biomedicines 2023; 11:biomedicines11051421. [PMID: 37239092 DOI: 10.3390/biomedicines11051421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
The global outbreak of SARS-CoV-2/COVID-19 provided the stage to accumulate an enormous biomedical data set and an opportunity as well as a challenge to test new concepts and strategies to combat the pandemic. New research and molecular medical protocols may be deployed in different scientific fields, e.g., glycobiology, nanopharmacology, or nanomedicine. We correlated clinical biomedical data derived from patients in intensive care units with structural biology and biophysical data from NMR and/or CAMM (computer-aided molecular modeling). Consequently, new diagnostic and therapeutic approaches against SARS-CoV-2 were evaluated. Specifically, we tested the suitability of incretin mimetics with one or two pH-sensitive amino acid residues as potential drugs to prevent or cure long-COVID symptoms. Blood pH values in correlation with temperature alterations in patient bodies were of clinical importance. The effects of biophysical parameters such as temperature and pH value variation in relation to physical-chemical membrane properties (e.g., glycosylation state, affinity of certain amino acid sequences to sialic acids as well as other carbohydrate residues and lipid structures) provided helpful hints in identifying a potential Achilles heel against long COVID. In silico CAMM methods and in vitro NMR experiments (including 31P NMR measurements) were applied to analyze the structural behavior of incretin mimetics and SARS-CoV fusion peptides interacting with dodecylphosphocholine (DPC) micelles. These supramolecular complexes were analyzed under physiological conditions by 1H and 31P NMR techniques. We were able to observe characteristic interaction states of incretin mimetics, SARS-CoV fusion peptides and DPC membranes. Novel interaction profiles (indicated, e.g., by 31P NMR signal splitting) were detected. Furthermore, we evaluated GM1 gangliosides and sialic acid-coated silica nanoparticles in complex with DPC micelles in order to create a simple virus host cell membrane model. This is a first step in exploring the structure-function relationship between the SARS-CoV-2 spike protein and incretin mimetics with conserved pH-sensitive histidine residues in their carbohydrate recognition domains as found in galectins. The applied methods were effective in identifying peptide sequences as well as certain carbohydrate moieties with the potential to protect the blood-brain barrier (BBB). These clinically relevant observations on low blood pH values in fatal COVID-19 cases open routes for new therapeutic approaches, especially against long-COVID symptoms.
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Affiliation(s)
- Hans-Christian Siebert
- RI-B-NT-Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr. 116, 24118 Kiel, Germany
| | - Thomas Eckert
- Department of Chemistry and Biology, University of Applied Sciences Fresenius, Limburger Str. 2, 65510 Idstein, Germany
- RISCC-Research Institute for Scientific Computing and Consulting, Ludwig-Schunk-Str. 15, 35452 Heuchelheim, Germany
- Institut für Veterinärphysiologie und Biochemie, Fachbereich Veterinärmedizin, Justus-Liebig Universität Gießen, Frankfurter Str. 100, 35392 Gießen, Germany
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Nele Klatte
- Department of Chemistry and Biology, University of Applied Sciences Fresenius, Limburger Str. 2, 65510 Idstein, Germany
| | - Marzieh Mohri
- RI-B-NT-Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr. 116, 24118 Kiel, Germany
| | - Simone Siebert
- RI-B-NT-Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr. 116, 24118 Kiel, Germany
| | - Anna Kozarova
- Department of Biomedical Sciences, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - John W Hudson
- Department of Biomedical Sciences, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Ruiyan Zhang
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China
| | - Ning Zhang
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China
| | - Lan Li
- Klinik für Neurochirurgie, Alfried Krupp Krankenhaus, Rüttenscheid, Alfried-Krupp-Straße 21, 45131 Essen, Germany
| | - Konstantinos Gousias
- Klinik für Neurochirurgie, Klinikum Lünen, St.-Marien-Hospital, Akad. Lehrkrankenhaus der Westfälische Wilhelms-Universität Münster, 44534 Lünen, Germany
| | - Dimitrios Kanakis
- Institute of Pathology, University of Nicosia Medical School, 2408 Egkomi, Cyprus
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
| | | | - Tibor Kožár
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University, Jesenná 5, 04001 Košice, Slovakia
| | - Nikolay E Nifantiev
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia
| | - Christian Vollmer
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Timo Brandenburger
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Detlef Kindgen-Milles
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Thomas Haak
- Diabetes Klinik Bad Mergentheim, Theodor-Klotzbücher-Str. 12, 97980 Bad Mergentheim, Germany
| | - Athanasios K Petridis
- Medical School, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
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7
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Functional Peptides from SARS-CoV-2 Binding with Cell Membrane: From Molecular Dynamics Simulations to Cell Demonstration. Cells 2022; 11:cells11111738. [PMID: 35681433 PMCID: PMC9179371 DOI: 10.3390/cells11111738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/17/2022] [Accepted: 05/21/2022] [Indexed: 12/03/2022] Open
Abstract
Herein, we have verified the interaction between the functional peptides from the SARS-CoV-2 and cell membrane, and we further proved that peptides exhibit little membrane disruption. The specific amino acids (Lys, Ile, Glu, Asn, Gln, etc.) with charge or hydrophobic residues play a significant role during the functional-peptide binding to membrane. The findings could provide the hints related to viral infection and also might pave the way for development of new materials based on peptides with membrane-binding activity, which would enable functional peptides further as peptide adjuvants, in order to help deliver the cancer drug into tumor cells for the efficient tumor therapy.
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8
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Samara A, Khalil A, Brien PO, Herlenius E. The effect of the Delta SARS-CoV-2 variant in maternal infection and pregnancy. iScience 2022; 25:104295. [PMID: 35492217 PMCID: PMC9040522 DOI: 10.1016/j.isci.2022.104295] [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] [Indexed: 12/29/2022] Open
Abstract
A greater proportion of pregnant women with COVID-19 have mild disease compared with their non-pregnant counterparts. Paradoxically, however, they are at higher risk of developing severe disease, requiring respiratory support and admission to intensive care. The delta SARS-Cov-2 variant is associated with increased risk of hospitalization and morbidity in unvaccinated pregnant populations. However, it is not known whether the worse pregnancy outcomes associated with the delta variant are due to a direct effect of the virus on the pregnancy, or whether this effect is mediated through more severe maternal infection. Here, we synthesize studies of COVID-19 pregnancies, focusing on the different routes of SARS-CoV-2 infection of lung and placenta, and the mechanisms of syncytial formation for each SARS-CoV-2 variant. To delineate COVID-19 complications in pregnant women, future studies should explore whether the delta variant causes greater placental infection compared to other variants and contributes to increased syncytial formation.
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Affiliation(s)
- Athina Samara
- Division of Clinical Paediatrics, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Asma Khalil
- The Royal College of Obstetricians and Gynaecologists, London, UK.,University College London Hospitals NHS Foundation Trust, London, UK.,Fetal Medicine Unit, St George's Hospital, St George's University of London, London, UK
| | - Patrick O' Brien
- Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK.,Fetal Medicine Unit, Liverpool Women's Hospital, University of Liverpool, Liverpool, UK
| | - Eric Herlenius
- Division of Clinical Paediatrics, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
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9
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Exosomal mediated signal transduction through artificial microRNA (amiRNA): A potential target for inhibition of SARS-CoV-2. Cell Signal 2022; 95:110334. [PMID: 35461900 PMCID: PMC9022400 DOI: 10.1016/j.cellsig.2022.110334] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 12/27/2022]
Abstract
Exosome trans-membrane signals provide cellular communication between the cells through transport and/or receiving the signal by molecule, change the functional metabolism, and stimulate and/or inhibit receptor signal complexes. COVID19 genetic transformations are varied in different geographic positions, and single nucleotide polymorphic lineages were reported in the second waves due to the fast mutational rate and adaptation. Several vaccines were developed and in treatment practice, but effective control has yet to reach in cent presence. It was initially a narrow immune-modulating protein target. Controlling these diverse viral strains may inhibit their transuding mechanisms primarily to target RNA genes responsible for COVID19 transcription. Exosomal miRNAs are the main sources of transmembrane signals, and trans-located miRNAs can directly target COVID19 mRNA transcription. This review discussed targeted viral transcription by delivering the artificial miRNA (amiRNA) mediated exosomes in the infected cells and significant resources of exosome and their efficacy.
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10
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Santamaria A, Batchu KC, Matsarskaia O, Prévost SF, Russo D, Natali F, Seydel T, Hoffmann I, Laux V, Haertlein M, Darwish TA, Russell RA, Corucci G, Fragneto G, Maestro A, Zaccai NR. Strikingly Different Roles of SARS-CoV-2 Fusion Peptides Uncovered by Neutron Scattering. J Am Chem Soc 2022; 144:2968-2979. [PMID: 35157798 PMCID: PMC8862744 DOI: 10.1021/jacs.1c09856] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Indexed: 02/02/2023]
Abstract
Coronavirus disease-2019 (COVID-19), a potentially lethal respiratory illness caused by the coronavirus SARS-CoV-2, emerged in the end of 2019 and has since spread aggressively across the globe. A thorough understanding of the molecular mechanisms of cellular infection by coronaviruses is therefore of utmost importance. A critical stage in infection is the fusion between viral and host membranes. Here, we present a detailed investigation of the role of selected SARS-CoV-2 Spike fusion peptides, and the influence of calcium and cholesterol, in this fusion process. Structural information from specular neutron reflectometry and small angle neutron scattering, complemented by dynamics information from quasi-elastic and spin-echo neutron spectroscopy, revealed strikingly different functions encoded in the Spike fusion domain. Calcium drives the N-terminal of the Spike fusion domain to fully cross the host plasma membrane. Removing calcium, however, reorients the peptide back to the lipid leaflet closest to the virus, leading to significant changes in lipid fluidity and rigidity. In conjunction with other regions of the fusion domain, which are also positioned to bridge and dehydrate viral and host membranes, the molecular events leading to cell entry by SARS-CoV-2 are proposed.
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Affiliation(s)
- Andreas Santamaria
- Institut
Laue-Langevin, 38042 Grenoble, France
- Departamento
de Química Física, Universidad
Complutense de Madrid, 28040 Madrid, Spain
| | | | | | | | - Daniela Russo
- Institut
Laue-Langevin, 38042 Grenoble, France
- CNR-IOM
& INSIDE@ILL, 38042 Grenoble, France
| | - Francesca Natali
- Institut
Laue-Langevin, 38042 Grenoble, France
- CNR-IOM
& INSIDE@ILL, 38042 Grenoble, France
| | - Tilo Seydel
- Institut
Laue-Langevin, 38042 Grenoble, France
| | | | | | | | - Tamim A. Darwish
- National
Deuteration Facility, ANSTO-Sidney, Lucas Heights, NSW 2234, Australia
| | - Robert A. Russell
- National
Deuteration Facility, ANSTO-Sidney, Lucas Heights, NSW 2234, Australia
| | - Giacomo Corucci
- Institut
Laue-Langevin, 38042 Grenoble, France
- École
Doctorale de Physique, Université
Grenoble Alpes, 38400 Saint-Martin-d’Héres, France
| | - Giovanna Fragneto
- Institut
Laue-Langevin, 38042 Grenoble, France
- École
Doctorale de Physique, Université
Grenoble Alpes, 38400 Saint-Martin-d’Héres, France
| | - Armando Maestro
- Institut
Laue-Langevin, 38042 Grenoble, France
- Centro
de Física de Materiales (CSIC, UPV/EHU) − Materials
Physics Center MPC, Paseo
Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- IKERBASQUE
− Basque Foundation for Science, Plaza Euskadi 5, E-48009 Bilbao, Spain
| | - Nathan R. Zaccai
- Cambridge
Institute for Medical Research, University
of Cambridge, Cambridge CB22 7QQ, United Kingdom
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11
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Abstract
This review discusses peptide epitopes used as antigens in the development of vaccines in clinical trials as well as future vaccine candidates. It covers peptides used in potential immunotherapies for infectious diseases including SARS-CoV-2, influenza, hepatitis B and C, HIV, malaria, and others. In addition, peptides for cancer vaccines that target examples of overexpressed proteins are summarized, including human epidermal growth factor receptor 2 (HER-2), mucin 1 (MUC1), folate receptor, and others. The uses of peptides to target cancers caused by infective agents, for example, cervical cancer caused by human papilloma virus (HPV), are also discussed. This review also provides an overview of model peptide epitopes used to stimulate non-specific immune responses, and of self-adjuvanting peptides, as well as the influence of other adjuvants on peptide formulations. As highlighted in this review, several peptide immunotherapies are in advanced clinical trials as vaccines, and there is great potential for future therapies due the specificity of the response that can be achieved using peptide epitopes.
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Affiliation(s)
- Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, U.K
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12
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Castelletto V, Hamley IW. Amyloid
and Hydrogel Formation of a Peptide Sequence
from a Coronavirus Spike Protein. ACS NANO 2022; 16:1857-1867. [PMCID: PMC8867915 DOI: 10.1021/acsnano.1c10658] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/29/2021] [Indexed: 05/28/2023]
Abstract
![]()
We demonstrate that
a conserved coronavirus spike protein peptide
forms amyloid structures, differing from the native helical conformation
and not predicted by amyloid aggregation algorithms. We investigate
the conformation and aggregation of peptide RSAIEDLLFDKV,
which is a sequence common to many animal and human coronavirus spike
proteins. This sequence is part of a native α-helical S2 glycoprotein
domain, close to and partly spanning the fusion sequence. This peptide
aggregates into β-sheet amyloid nanotape structures close to
the calculated pI = 4.2, but forms disordered monomers at high and
low pH. The β-sheet conformation revealed by FTIR and circular
dichroism (CD) spectroscopy leads to peptide nanotape structures,
imaged using transmission electron microscopy (TEM) and probed by
small-angle X-ray scattering (SAXS). The nanotapes comprise arginine-coated
bilayers. A Congo red dye UV–vis assay is used to probe the
aggregation of the peptide into amyloid structures, which enabled
the determination of a critical aggregation concentration (CAC). This
peptide also forms hydrogels under precisely defined conditions of
pH and concentration, the rheological properties of which were probed.
The observation of amyloid formation by a coronavirus spike has relevance
to the stability of the spike protein conformation (or its destabilization via pH change), and the peptide may have potential utility
as a functional material. Hydrogels formed by coronavirus peptides
may also be of future interest in the development of slow-release
systems, among other applications.
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Affiliation(s)
- Valeria Castelletto
- Department
of Chemistry, University of Reading, Reading RG6 6AD, United Kingdom
| | - Ian W. Hamley
- Department
of Chemistry, University of Reading, Reading RG6 6AD, United Kingdom
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13
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Salvador-Pinos CA, Martinez EZ, Dueñas-Matute SE, Aguinaga RRD, Jácome JC, Michelena-Tupiza S, Cárdenas-Morales V. Health of the Newborn and Breastfeeding during the COVID-19 Pandemic: A Literature Review. REVISTA BRASILEIRA DE GINECOLOGIA E OBSTETRICIA : REVISTA DA FEDERACAO BRASILEIRA DAS SOCIEDADES DE GINECOLOGIA E OBSTETRICIA 2022; 44:311-318. [PMID: 35100631 PMCID: PMC9948297 DOI: 10.1055/s-0041-1741449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE The present article presents a literature review concerning the microbiota of breast milk and the influence of epigenetics in the susceptibility to COVID-19. METHODS A literature review. RESULTS Breastfeeding transfers microbiota, nutrients, diverse white blood cells, prebiotics, hormones, and antibodies to the baby, which provide short- and long-term immunological protection against several infectious, gastrointestinal, and respiratory illnesses. The little evidence available shows that breast milk very rarely carries the SARS-CoV-2 virus, and even in those cases, it has been discarded as the source of contagion. CONCLUSION The reviewed studies show evidence of a beneficial effect of breastfeeding and highlights its importance on the current pandemic due to the immune reinforcement that it provides. Breastfed individuals showed better clinical response due to the influence on the microbiota and to the nutritional and immune contribution provided by breast milk, compared with those who were not breastfed.
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Affiliation(s)
| | - Edson Zangiacomi Martinez
- Department of Social Medicine, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Susana Eulalia Dueñas-Matute
- Facultad de Ciencias Médicas, Universidad Central del Ecuador, Quito, Ecuador.,Department of Social Medicine, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Juan Carlos Jácome
- Facultad de Ciencias Médicas, Universidad Central del Ecuador, Quito, Ecuador
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14
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Nature of viruses and pandemics: Coronaviruses. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:151-158. [PMID: 35966177 PMCID: PMC9359481 DOI: 10.1016/j.crimmu.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
Coronaviruses (CoVs) have the largest genome among RNA viruses and store large amounts of information without genome integration as they replicate in the cell cytoplasm. The replication of the virus is a continuous process, whereas the transcription of the subgenomic mRNAs is a discontinuous one, involving a template switch, which resembles a high frequency recombination mechanism that may favor virus genome variability. The origin of the three deadly human CoVs SARS-CoV, MERS-CoV and SARS-CoV-2 are zoonotic events. SARS-CoV-2 has incorporated in its spike protein a furine proteolytic site that facilitates the activation of the virus in any tissue, making this CoV strain highly polytropic and pathogenic. Using MERS-CoV as a model, a propagation-deficient RNA replicon was generated by removing E protein gene (essential for viral morphogenesis and involved in virulence), and accessory genes 3, 4a, 4b and 5 (responsible for antagonism of the innate immune response) to attenuate the virus: MERS-CoV-Δ[3,4a,4b,5,E]. This RNA replicon is strongly attenuated and elicits sterilizing protection after a single immunization in transgenic mice with the receptor for MERS-CoV, making it a promising vaccine candidate for this virus and an interesting platform for vector-based vaccine development. A strategy could be developed for the design of RNA replicon vaccines for other human pathogenic coronaviruses. CoV RNA transcription is a discontinuous high-frequency recombination process. Human CoVs have a zoonotic origin. Replication-competent propagation-defective CoVs are the bases for vaccines. Single immunization with CoV RNA replicon vaccines elicits sterilizing immunity.
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15
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Hsueh FC, Wu CN, Lin MYC, Hsu FY, Lin CF, Chang HW, Lin JH, Liu HF, Chiou MT, Chan KR, Lin CN. Phylodynamic analysis and spike protein mutations in porcine deltacoronavirus with a new variant introduction in Taiwan. Virus Evol 2021; 7:veab096. [PMID: 34858636 PMCID: PMC8634457 DOI: 10.1093/ve/veab096] [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: 08/28/2021] [Revised: 11/08/2021] [Accepted: 11/23/2021] [Indexed: 11/12/2022] Open
Abstract
Porcine deltacoronavirus (PDCoV) is a highly transmissible intestinal pathogen that causes mild to severe clinical symptoms, such as anorexia, vomiting, and watery diarrhea in pigs. By comparing the genetic sequences of the spike glycoprotein between historical and current Taiwanese PDCoV strains, we identified a novel PDCoV variant that displaced the PDCoV responsible for the 2015 epidemic. This PDCoV variant belongs to a young population within the US lineage, and infected pigs carry high concentrations of the virus. It also has several critical point mutations and an amino acid insertion at position 52 that may enhance the affinity between the B-cell epitopes located in the N-terminal domain with its complementarity regions, consequently facilitating binding or penetration between the fusion peptide and cellular membrane. Furthermore, viral protein structure prediction demonstrated that these amino acid changes may change the ability of the virus to bind to the receptor, which may consequently alter virus infectivity. Our results hence suggest the emergence of new PDCoV strains in Taiwan with the potential for greater transmission and pathogenesis.
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Affiliation(s)
- Fu-Chun Hsueh
- Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Scienceand Technology, Pingtung 912301, Taiwan
| | - Cheng-Nan Wu
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung 406053, Taiwan
| | | | - Feng-Yang Hsu
- Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Scienceand Technology, Pingtung 912301, Taiwan
| | - Chuen-Fu Lin
- Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Scienceand Technology, Pingtung 912301, Taiwan
| | - Hui-Wen Chang
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Jih-Hui Lin
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei 11561, Taiwan
| | - Hsin-Fu Liu
- Department of Medical Research, Mackay Memorial Hospital, Taipei 10449, Taiwan
| | - Ming-Tang Chiou
- Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Scienceand Technology, Pingtung 912301, Taiwan
| | - Kuan Rong Chan
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Chao-Nan Lin
- Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Scienceand Technology, Pingtung 912301, Taiwan
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16
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Gutiérrez-Álvarez J, Honrubia JM, Sanz-Bravo A, González-Miranda E, Fernández-Delgado R, Rejas MT, Zúñiga S, Sola I, Enjuanes L. Middle East respiratory syndrome coronavirus vaccine based on a propagation-defective RNA replicon elicited sterilizing immunity in mice. Proc Natl Acad Sci U S A 2021; 118:e2111075118. [PMID: 34686605 PMCID: PMC8639359 DOI: 10.1073/pnas.2111075118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2021] [Indexed: 12/11/2022] Open
Abstract
Self-amplifying RNA replicons are promising platforms for vaccine generation. Their defects in one or more essential functions for viral replication, particle assembly, or dissemination make them highly safe as vaccines. We previously showed that the deletion of the envelope (E) gene from the Middle East respiratory syndrome coronavirus (MERS-CoV) produces a replication-competent propagation-defective RNA replicon (MERS-CoV-ΔE). Evaluation of this replicon in mice expressing human dipeptidyl peptidase 4, the virus receptor, showed that the single deletion of the E gene generated an attenuated mutant. The combined deletion of the E gene with accessory open reading frames (ORFs) 3, 4a, 4b, and 5 resulted in a highly attenuated propagation-defective RNA replicon (MERS-CoV-Δ[3,4a,4b,5,E]). This RNA replicon induced sterilizing immunity in mice after challenge with a lethal dose of a virulent MERS-CoV, as no histopathological damage or infectious virus was detected in the lungs of challenged mice. The four mutants lacking the E gene were genetically stable, did not recombine with the E gene provided in trans during their passage in cell culture, and showed a propagation-defective phenotype in vivo. In addition, immunization with MERS-CoV-Δ[3,4a,4b,5,E] induced significant levels of neutralizing antibodies, indicating that MERS-CoV RNA replicons are highly safe and promising vaccine candidates.
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MESH Headings
- Animals
- Antibodies, Neutralizing/biosynthesis
- Antibodies, Viral/biosynthesis
- Coronavirus Infections/genetics
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/virology
- Defective Viruses/genetics
- Defective Viruses/immunology
- Female
- Gene Deletion
- Genes, env
- Humans
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Middle East Respiratory Syndrome Coronavirus/genetics
- Middle East Respiratory Syndrome Coronavirus/immunology
- Middle East Respiratory Syndrome Coronavirus/pathogenicity
- RNA, Viral/administration & dosage
- RNA, Viral/genetics
- RNA, Viral/immunology
- Replicon
- Vaccines, DNA
- Vaccines, Virus-Like Particle/administration & dosage
- Vaccines, Virus-Like Particle/genetics
- Vaccines, Virus-Like Particle/immunology
- Viral Vaccines/administration & dosage
- Viral Vaccines/genetics
- Viral Vaccines/immunology
- Virulence/genetics
- Virulence/immunology
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Affiliation(s)
- J Gutiérrez-Álvarez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - J M Honrubia
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - A Sanz-Bravo
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - E González-Miranda
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - R Fernández-Delgado
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - M T Rejas
- Electron Microscopy Service, Centro de Biología Molecular "Severo Ochoa" (CBMSO-CSIC-UAM), Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - S Zúñiga
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - I Sola
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain
| | - L Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Universidad Autónoma de Madrid 28049 Madrid, Spain;
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17
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Abstract
The high SARS-CoV-2 reproductive number driving the COVID-19 pandemic has been a mystery. Our recent in vitro, and in vivo coronaviral pathogenesis studies involving Mouse Hepatitis Virus (MHV-A59) suggest a crucial role for a small host membrane-virus contact initiator region of the Spike protein, called the fusion peptide that enhances the virus fusogenicity and infectivity. Here I study the Spike from five human β-coronaviruses (HCoV) including the SARS-CoV-2, and MHV-A59 for comparison. The structural and dynamics analyses of the Spike show that its fusion loop spatially organizes three fusion peptides contiguous to each other to synergistically trigger the virus-host membrane fusion process. I propose a Contact Initiation Model based on the architecture of the Spike quaternary structure that explains the obligatory participation of the fusion loop in the initiation of the host membrane contact for the virus fusion process. Among all the HCoV Spikes in this study, SARS-CoV-2 has the most hydrophobic surface and the extent of hydrophobicity correlates with the reproductive number and infectivity of the other HCoV. Comparison between results from standard and replica exchange molecular dynamics reveal the unique physicochemical properties of the SARS-CoV-2 fusion peptides, accrued in part from the presence of consecutive prolines that impart backbone rigidity which aids the virus fusogenicity. The priming of the Spike by its cleavage and subsequent fusogenic conformational transition steered by the fusion loop may be critical for the SARS-CoV-2 spread. The importance of the fusion loop makes it an apt target for anti-virals and vaccine candidates.
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Affiliation(s)
- Debnath Pal
- Indian Institute of Science, Bengaluru 560012, India.
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18
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Killed whole-genome reduced-bacteria surface-expressed coronavirus fusion peptide vaccines protect against disease in a porcine model. Proc Natl Acad Sci U S A 2021; 118:2025622118. [PMID: 33858942 PMCID: PMC8106328 DOI: 10.1073/pnas.2025622118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
As the coronavirus disease 2019 (COVID-19) pandemic rages on, it is important to explore new evolution-resistant vaccine antigens and new vaccine platforms that can produce readily scalable, inexpensive vaccines with easier storage and transport. We report here a synthetic biology-based vaccine platform that employs an expression vector with an inducible gram-negative autotransporter to express vaccine antigens on the surface of genome-reduced bacteria to enhance interaction of vaccine antigen with the immune system. As a proof-of-principle, we utilized genome-reduced Escherichia coli to express SARS-CoV-2 and porcine epidemic diarrhea virus (PEDV) fusion peptide (FP) on the cell surface, and evaluated their use as killed whole-cell vaccines. The FP sequence is highly conserved across coronaviruses; the six FP core amino acid residues, along with the four adjacent residues upstream and the three residues downstream from the core, are identical between SARS-CoV-2 and PEDV. We tested the efficacy of PEDV FP and SARS-CoV-2 FP vaccines in a PEDV challenge pig model. We demonstrated that both vaccines induced potent anamnestic responses upon virus challenge, potentiated interferon-γ responses, reduced viral RNA loads in jejunum tissue, and provided significant protection against clinical disease. However, neither vaccines elicited sterilizing immunity. Since SARS-CoV-2 FP and PEDV FP vaccines provided similar clinical protection, the coronavirus FP could be a target for a broadly protective vaccine using any platform. Importantly, the genome-reduced bacterial surface-expressed vaccine platform, when using a vaccine-appropriate bacterial vector, has potential utility as an inexpensive, readily manufactured, and rapid vaccine platform for other pathogens.
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19
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Pal D. Spike protein fusion loop controls SARS-CoV-2 fusogenicity and infectivity. J Struct Biol 2021; 213:107713. [PMID: 33662570 PMCID: PMC7919542 DOI: 10.1016/j.jsb.2021.107713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 01/30/2023]
Abstract
The high SARS-CoV-2 reproductive number driving the COVID-19 pandemic has been a mystery. Our recent in vitro, and in vivo coronaviral pathogenesis studies involving Mouse Hepatitis Virus (MHV-A59) suggest a crucial role for a small host membrane-virus contact initiator region of the Spike protein, called the fusion peptide that enhances the virus fusogenicity and infectivity. Here I study the Spike from five human β-coronaviruses (HCoV) including the SARS-CoV-2, and MHV-A59 for comparison. The structural and dynamics analyses of the Spike show that its fusion loop spatially organizes three fusion peptides contiguous to each other to synergistically trigger the virus-host membrane fusion process. I propose a Contact Initiation Model based on the architecture of the Spike quaternary structure that explains the obligatory participation of the fusion loop in the initiation of the host membrane contact for the virus fusion process. Among all the HCoV Spikes in this study, SARS-CoV-2 has the most hydrophobic surface and the extent of hydrophobicity correlates with the reproductive number and infectivity of the other HCoV. Comparison between results from standard and replica exchange molecular dynamics reveal the unique physicochemical properties of the SARS-CoV-2 fusion peptides, accrued in part from the presence of consecutive prolines that impart backbone rigidity which aids the virus fusogenicity. The priming of the Spike by its cleavage and subsequent fusogenic conformational transition steered by the fusion loop may be critical for the SARS-CoV-2 spread. The importance of the fusion loop makes it an apt target for anti-virals and vaccine candidates.
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Affiliation(s)
- Debnath Pal
- Indian Institute of Science, Bengaluru 560012, India.
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20
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Soleimanpour S, Yaghoubi A. COVID-19 vaccine: where are we now and where should we go? Expert Rev Vaccines 2021; 20:23-44. [PMID: 33435774 PMCID: PMC7898300 DOI: 10.1080/14760584.2021.1875824] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 01/11/2021] [Indexed: 01/12/2023]
Abstract
INTRODUCTION The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has currently caused the pandemic with a high progressive speed and has been considered as the global public health crisis in 2020. This new member of the coronavirus family has created a potentially fatal disease, called coronavirus disease-2019 (COVID-19). Despite the continuous efforts of researchers to find effective vaccines and drugs for COVID-19, there is still no success in this matter. AREAS COVERED Here, the literature regarding the COVID-19 vaccine candidates currently in the clinical trials, as well as main candidates in pre-clinical stages for development and research, were reviewed. These candidates have been developed under five different major platforms, including live-attenuated vaccine, mRNA-based vaccine, DNA vaccines, inactivated virus, and viral-vector-based vaccine. EXPERT OPINION There are several limitations in the field of the rapid vaccine development against SARS-CoV-2, and other members of the coronavirus family such as SARS-CoV and MERS-CoV. The key challenges of designing an effective vaccine within a short time include finding the virulence ability of an emerging virus and potential antigen, choosing suitable experimental models and efficient route of administration, the immune-response study, designing the clinical trials, and determining the safety, as well as efficacy.
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Affiliation(s)
- Saman Soleimanpour
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atieh Yaghoubi
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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21
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Singh SP, Pritam M, Pandey B, Yadav TP. Microstructure, pathophysiology, and potential therapeutics of COVID-19: A comprehensive review. J Med Virol 2021; 93:275-299. [PMID: 32617987 PMCID: PMC7361355 DOI: 10.1002/jmv.26254] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/14/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023]
Abstract
There have been over seven million cases and almost 413 372 deaths globally due to the novel coronavirus (2019-nCoV) associated disease COVID-19, as of 11 June 2020. Phylogenetic analysis suggests that there is a common source for these infections. The overall sequence similarities between the spike protein of 2019-nCoV and that of SARS-CoV are known to be around 76% to 78% and 73% to 76% for the whole protein and receptor-binding domain (RBD), respectively. Thus, they have the potential to serve as the drug and/or vaccine candidate. However, the individual response against 2019-nCoV differs due to genetic variations in the human population. Understanding the variations in angiotensin-converting enzyme 2 (ACE2) and human leukocyte antigen (HLA) that may affect the severity of 2019-nCoV infection could help in identifying individuals at a higher risk from the COVID-19. A number of potential drugs/vaccines as well as antibody/cytokine-based therapeutics are in various developmental stages of preclinical/clinical trials against SARS-CoV, MERS-CoV, and 2019-nCoV with substantial cross-reactivity, and may be used against COVID-19. For diagnosis, the reverse-transcription polymerase chain reaction is the gold standard test for initial diagnosis of COVID-19. A kit based on serological tests are also recommended for investigating the spread of COVID-19 but this is challenging due to the antibodies cross-reactivity. This review comprehensively summarizes the recent reports available regarding the host-pathogen interaction, morphological and genomic structure of the virus, and the diagnostic techniques as well as the available potential therapeutics against COVID-19.
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Affiliation(s)
| | - Manisha Pritam
- Amity Institute of BiotechnologyAmity University Uttar PradeshLucknowIndia
| | - Brijesh Pandey
- Department of BiotechnologyMahatma Gandhi Central UniversityMotihariIndia
| | - Thakur Prasad Yadav
- Department of Physics, Institute of ScienceBanaras Hindu UniversityVaranasiIndia
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22
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Sarwar Z, Ahmad T, Kakar S. Potential approaches to combat COVID-19: a mini-review. Mol Biol Rep 2020; 47:9939-9949. [PMID: 33185828 PMCID: PMC7662020 DOI: 10.1007/s11033-020-05988-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/12/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023]
Abstract
The outbreak of a novel coronavirus namely SARS-CoV-2, which first emerged from Wuhan, China, has wreaked havoc not only in China but the whole world that now has been engulfed in its wrath. In a short lapse of time, this virus was successful in spreading at a blistering pace throughout the globe, hence raising the flag of pandemic status. The mounting number of deaths with each elapsing day has summoned researchers from all around the world to play their part in driving this SARS-CoV-2 pandemic to an end. As of now, multiple research teams are immersed in either scrutinizing various antiviral drugs for their efficacy or developing different types of vaccines that will be capable of providing long-term immunity against this deadly virus. The mini-review sheds light on the possible approaches that can be undertaken to curb the COVID-19 spread. Possible strategies comprise viral vector-based, nucleic acid-based, protein-based, inactivated and weakened virus vaccines; COVID-19 vaccine being developed by deploying Hyleukin-7 technology; plant-based chimeric protein and subunit vaccines; humanized nano-bodies and human antibodies; intravenous immunoglobulin (IVIG) infusion therapy; inhibitors for ACE-2, Angiotensin 1 receptor (AT1R), complement system, viral proteins, host cell protease and endocytosis; shield immunity; IL-6R, NKG2A and hACE2-SARS-CoV-2-RBD interaction blocking monoclonal antibodies; SARS-CoV RdRp-based drugs, traditional Chinese medicine, repositioned and anti-viral drugs. These vaccines and drugs are currently being screened in the clinical trials as several of them have manifested positive results, hence increasing the probability of becoming one of the potential treatments for this disease.
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Affiliation(s)
- Zainab Sarwar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Tahir Ahmad
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.
| | - Salik Kakar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
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23
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Chaudhry SN, Hazafa A, Mumtaz M, Kalsoom U, Abbas S, Kainaat A, Bilal S, Zafar N, Siddique A, Zafar A. New insights on possible vaccine development against SARS-CoV-2. Life Sci 2020; 260:118421. [PMID: 32926920 PMCID: PMC7484811 DOI: 10.1016/j.lfs.2020.118421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023]
Abstract
In December 2019, a novel virus, namely COVID-19 caused by SARS-CoV-2, developed from Wuhan, (Hubei territory of China) used its viral spike glycoprotein receptor-binding domain (RBD) for the entrance into a host cell by binding with ACE-2 receptor and cause acute respiratory distress syndrome (ARDS). Data revealed that the newly emerged SARS-CoV-2 affected more than 24,854,140 people with 838,924 deaths worldwide. Until now, no licensed immunization or drugs are present for the medication of SARS-CoV-2. The present review aims to investigate the latest developments and discuss the candidate antibodies in different vaccine categories to develop a reliable and efficient vaccine against SARS-CoV-2 in a short time duration. Besides, the review focus on the present challenges and future directions, structure, and mechanism of SARS-CoV-2 for a better understanding. Based on data, we revealed that most of the vaccines are focus on targeting the spike protein (S) of COVID-19 to neutralized viral infection and develop long-lasting immunity. Up to phase-1 clinical trials, some vaccines showed the specific antigen-receptor T-cell response, elicit the humoral and immune response, displayed tight binding with human-leukocytes-antigen (HLA), and recognized specific antibodies to provoke long-lasting immunity against SARS-CoV-2.
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Affiliation(s)
- Sundas Nasir Chaudhry
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Abu Hazafa
- Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Muhummad Mumtaz
- Department of Chemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Ume Kalsoom
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54000, Pakistan
| | - Saima Abbas
- Department of Biochemistry, Kinnaird College for Women Lahore, 54000, Pakistan
| | - Amna Kainaat
- School of Biological Sciences, University of the Punjab, Lahore 54000, Pakistan
| | - Shahid Bilal
- Department of Agronomy, Faculty of Agriculture, University of Agriculture, Faisalabad 38000, Pakistan
| | - Nauman Zafar
- Department of Chemistry, Faculty of Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Aleena Siddique
- MBBS, Rashid Latif Medical and Dental College, Lahore 54000, Pakistan
| | - Ayesha Zafar
- Institute of Biochemistry and Biotechnology, Faculty of Biosciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
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24
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Tohidinia M, Sefid F. Identification B and T-Cell epitopes and functional exposed amino acids of S protein as a potential vaccine candidate against SARS-CoV-2/COVID-19. Microb Pathog 2020; 148:104459. [PMID: 32835775 PMCID: PMC7441888 DOI: 10.1016/j.micpath.2020.104459] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/31/2020] [Accepted: 08/17/2020] [Indexed: 01/01/2023]
Abstract
Coronavirus disease (COVID-19) is an infectious disease caused by a newly discovered coronavirus that it disease spreads in over the world. Coronaviruses are single-stranded, positive-sense RNA viruses with a genome of approximately 30 KD, the largest genome among RNA viruses. Most people infected with the COVID-19 virus will experience mild to moderate respiratory illness and recover without requiring special treatment. Older people and those with underlying medical problems like cardiovascular disease, diabetes, chronic respiratory disease, and cancer are more likely to develop serious illness. At this time, there are no specific vaccines or treatments for COVID-19. So, there is an emergency need for vaccines and antiviral strategies. The spike protein is the major surface protein that it uses to bind to a receptor of another protein that acts as a doorway into a human cell. The putative antigenic epitopes may prove effective as novel vaccines for eradication and combating of COV19 infection. A combination of available bioinformatics tools are used to synthesis of such peptides that are important for the development of a vaccine. In conclusion, amino acids 250-800 were selected as effective B cell epitopes, T cell epitopes, and functional exposed amino acids in order to a recombinant vaccine against coronavirus.
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MESH Headings
- Binding Sites
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19/virology
- COVID-19 Vaccines/immunology
- Drug Design
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Epitopes, B-Lymphocyte/isolation & purification
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/isolation & purification
- Humans
- Models, Molecular
- Protein Conformation
- SARS-CoV-2/immunology
- Sequence Alignment
- Sequence Homology, Amino Acid
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Maryam Tohidinia
- Department of Biology, Faculty of Science, Yazd University, Yazd, Iran.
| | - Fatemeh Sefid
- Department of Medical Genetics, Shahid Sadoughi University of Medical Science, Yazd, Iran; Department of Biology, Science and Art University, Yazd, Iran.
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25
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Identification of a Membrane Binding Peptide in the Envelope Protein of MHV Coronavirus. Viruses 2020; 12:v12091054. [PMID: 32971895 PMCID: PMC7551300 DOI: 10.3390/v12091054] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
Coronaviruses (CoVs) are enveloped, positive sense, single strand RNA viruses that cause respiratory, intestinal and neurological diseases in mammals and birds. Following replication, CoVs assemble on intracellular membranes including the endoplasmic reticulum Golgi intermediate compartment (ERGIC) where the envelope protein (E) functions in virus assembly and release. In consequence, E potentially contains membrane-modifying peptides. To search for such peptides, the E coding sequence of Mouse Hepatitis Virus (MHV) was inspected for its amino acid conservation, proximity to the membrane and/or predicted amphipathic helices. Peptides identified in silico were synthesized and tested for membrane-modifying activity in the presence of giant unilamellar vesicles (GUVs) consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), sphingomyelin and cholesterol. To confirm the presence of membrane binding peptides identified in the context of a full-length E protein, the wild type and a number of mutants in the putative membrane binding peptide were expressed in Lenti-X-293T mammalian and insect cells, and the distribution of E antigen within the expressing cell was assessed. Our data identify a role for the post-transmembrane region of MHV E in membrane binding.
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26
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Farrera-Soler L, Daguer JP, Barluenga S, Vadas O, Cohen P, Pagano S, Yerly S, Kaiser L, Vuilleumier N, Winssinger N. Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma. PLoS One 2020; 15:e0238089. [PMID: 32903266 PMCID: PMC7480855 DOI: 10.1371/journal.pone.0238089] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/10/2020] [Indexed: 01/09/2023] Open
Abstract
A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) is the source of a current pandemic (COVID-19) with devastating consequences in public health and economic stability. Using a peptide array to map the antibody response of plasma from healing patients (12) and heathy patients (6), we identified three immunodominant linear epitopes, two of which correspond to key proteolytic sites on the spike protein (S1/S2 and S2') known to be critical for cellular entry. We show biochemical evidence that plasma positive for the epitope adjacent to the S1/S2 cleavage site inhibits furin-mediated proteolysis of spike.
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Affiliation(s)
- Lluc Farrera-Soler
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Jean-Pierre Daguer
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Oscar Vadas
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Patrick Cohen
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Sabrina Pagano
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Sabine Yerly
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Laurent Kaiser
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Division of Infectious Diseases¸ Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nicolas Vuilleumier
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
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27
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Poh CM, Carissimo G, Wang B, Amrun SN, Lee CYP, Chee RSL, Fong SW, Yeo NKW, Lee WH, Torres-Ruesta A, Leo YS, Chen MIC, Tan SY, Chai LYA, Kalimuddin S, Kheng SSG, Thien SY, Young BE, Lye DC, Hanson BJ, Wang CI, Renia L, Ng LFP. Two linear epitopes on the SARS-CoV-2 spike protein that elicit neutralising antibodies in COVID-19 patients. Nat Commun 2020; 11:2806. [PMID: 32483236 PMCID: PMC7264175 DOI: 10.1038/s41467-020-16638-2] [Citation(s) in RCA: 286] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/17/2020] [Indexed: 12/12/2022] Open
Abstract
Given the ongoing SARS-CoV-2 pandemic, identification of immunogenic targets against the coronavirus spike glycoprotein will provide crucial advances towards the development of sensitive diagnostic tools and potential vaccine candidate targets. In this study, using pools of overlapping linear B-cell peptides, we report two IgG immunodominant regions on SARS-CoV-2 spike glycoprotein that are recognised by sera from COVID-19 convalescent patients. Notably, one is specific to SARS-CoV-2, which is located in close proximity to the receptor binding domain. The other region, which is localised at the fusion peptide, could potentially function as a pan-SARS target. Functionally, antibody depletion assays demonstrate that antibodies targeting these immunodominant regions significantly alter virus neutralisation capacities. Taken together, identification and validation of these neutralising B-cell epitopes will provide insights towards the design of diagnostics and vaccine candidates against this high priority coronavirus.
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Affiliation(s)
- Chek Meng Poh
- Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore, 138648, Singapore
| | - Guillaume Carissimo
- Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore, 138648, Singapore
| | - Bei Wang
- Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore, 138648, Singapore
| | - Siti Naqiah Amrun
- Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore, 138648, Singapore
| | - Cheryl Yi-Pin Lee
- Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore, 138648, Singapore
| | - Rhonda Sin-Ling Chee
- Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore, 138648, Singapore
| | - Siew-Wai Fong
- Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore, 138648, Singapore
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Nicholas Kim-Wah Yeo
- Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore, 138648, Singapore
| | - Wen-Hsin Lee
- Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore, 138648, Singapore
| | - Anthony Torres-Ruesta
- Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore, 138648, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore, 308442, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, 10 Medical Drive, Singapore, 117597, Singapore
| | - Mark I-Cheng Chen
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore, 308442, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, 12 Science Drive 2, #10-01, Singapore, 117549, Singapore
| | - Seow-Yen Tan
- Department of Infectious Diseases, Changi General Hospital, 2 Simei Street 3, Singapore, 529889, Singapore
| | - Louis Yi Ann Chai
- Department of Infectious Diseases, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
- Department of Medicine, National University Hospital, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Shirin Kalimuddin
- Department of Infectious Diseases, Singapore General Hospital, 31 Third Hospital Ave, #03-03 Bowyer Block C, Singapore, 168753, Singapore
- Emerging Infectious Disease Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Shirley Seah Gek Kheng
- Biological Defence Program, DSO National Laboratories, 27 Medical Drive, Singapore, 117510, Singapore
| | - Siew-Yee Thien
- Department of Infectious Diseases, Singapore General Hospital, 31 Third Hospital Ave, #03-03 Bowyer Block C, Singapore, 168753, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore, 308442, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - David C Lye
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore, 308442, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, 10 Medical Drive, Singapore, 117597, Singapore
| | - Brendon John Hanson
- Biological Defence Program, DSO National Laboratories, 27 Medical Drive, Singapore, 117510, Singapore
| | - Cheng-I Wang
- Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore, 138648, Singapore
| | - Laurent Renia
- Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore, 138648, Singapore
| | - Lisa F P Ng
- Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore, 138648, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, 8 West Derby Street, Liverpool, L7 3EA, United Kingdom.
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28
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Tang T, Bidon M, Jaimes JA, Whittaker GR, Daniel S. Coronavirus membrane fusion mechanism offers a potential target for antiviral development. Antiviral Res 2020. [PMID: 32272173 DOI: 10.1016/j.antiviral.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has focused attention on the need to develop effective therapies against the causative agent, SARS-CoV-2, and also against other pathogenic coronaviruses (CoV) that have emerged in the past or might appear in future. Researchers are therefore focusing on steps in the CoV replication cycle that may be vulnerable to inhibition by broad-spectrum or specific antiviral agents. The conserved nature of the fusion domain and mechanism across the CoV family make it a valuable target to elucidate and develop pan-CoV therapeutics. In this article, we review the role of the CoV spike protein in mediating fusion of the viral and host cell membranes, summarizing the results of research on SARS-CoV, MERS-CoV, and recent peer-reviewed studies of SARS-CoV-2, and suggest that the fusion mechanism be investigated as a potential antiviral target. We also provide a supplemental file containing background information on the biology, epidemiology, and clinical features of all human-infecting coronaviruses, along with a phylogenetic tree of these coronaviruses.
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Affiliation(s)
- Tiffany Tang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Miya Bidon
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Javier A Jaimes
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, 14853, USA
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, 14853, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA.
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29
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Tang T, Bidon M, Jaimes JA, Whittaker GR, Daniel S. Coronavirus membrane fusion mechanism offers a potential target for antiviral development. Antiviral Res 2020; 178:104792. [PMID: 32272173 PMCID: PMC7194977 DOI: 10.1016/j.antiviral.2020.104792] [Citation(s) in RCA: 515] [Impact Index Per Article: 128.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/05/2020] [Accepted: 04/05/2020] [Indexed: 12/14/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has focused attention on the need to develop effective therapies against the causative agent, SARS-CoV-2, and also against other pathogenic coronaviruses (CoV) that have emerged in the past or might appear in future. Researchers are therefore focusing on steps in the CoV replication cycle that may be vulnerable to inhibition by broad-spectrum or specific antiviral agents. The conserved nature of the fusion domain and mechanism across the CoV family make it a valuable target to elucidate and develop pan-CoV therapeutics. In this article, we review the role of the CoV spike protein in mediating fusion of the viral and host cell membranes, summarizing the results of research on SARS-CoV, MERS-CoV, and recent peer-reviewed studies of SARS-CoV-2, and suggest that the fusion mechanism be investigated as a potential antiviral target. We also provide a supplemental file containing background information on the biology, epidemiology, and clinical features of all human-infecting coronaviruses, along with a phylogenetic tree of these coronaviruses.
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Affiliation(s)
- Tiffany Tang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Miya Bidon
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Javier A Jaimes
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, 14853, USA
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, 14853, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA.
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30
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Pruimboom L. Methylation Pathways and SARS-CoV-2 Lung Infiltration and Cell Membrane-Virus Fusion Are Both Subject to Epigenetics. Front Cell Infect Microbiol 2020; 10:290. [PMID: 32574283 PMCID: PMC7265211 DOI: 10.3389/fcimb.2020.00290] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022] Open
Abstract
The recent pandemic SARS-CoV-2 outbreak affects all kinds of individuals worldwide. The health, social, and economic impacts of the pandemic are dramatic, and vaccines or specific treatment options are not yet available. The only approaches that we currently have available to stop the epidemic are those of classical epidemic control, such as case isolation, contact tracing and quarantine, physical distancing, and hygiene measures. It is therefore essential to find further preventive measures and possible interventions that can slow down the number of infected individuals and decrease the severity of disease when affected by SARS-CoV-2. It seems that epigenetic mechanisms are an important part of the pathophysiology and illness severity of COVID-19. These mechanisms have been identified in SARS-CoV-2 but also in other viral infections. If and when these mechanisms are confirmed, then epigenetic interventions influencing DNA methylation could be indicated as primary and/or secondary preventive options.
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Affiliation(s)
- Leo Pruimboom
- Facultad de Enfermería y Fisioterapia Salus Infirmorum, Pontifice University of Salamanca, Madrid, Spain.,PNI Europe, The Hague, Netherlands
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31
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Zhang J, Zeng H, Gu J, Li H, Zheng L, Zou Q. Progress and Prospects on Vaccine Development against SARS-CoV-2. Vaccines (Basel) 2020; 8:E153. [PMID: 32235387 PMCID: PMC7349596 DOI: 10.3390/vaccines8020153] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 12/15/2022] Open
Abstract
In December 2019, the outbreak of pneumonia caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a serious pandemic in China and other countries worldwide. So far, more than 460,000 confirmed cases were diagnosed in nearly 190 countries, causing globally over 20,000 deaths. Currently, the epidemic is still spreading and there is no effective means to prevent the infection. Vaccines are proved to be the most effective and economical means to prevent and control infectious diseases. Several countries, companies, and institutions announced their programs and progress on vaccine development against the virus. While most of the vaccines are under design and preparation, there are some that have entered efficacy evaluation in animals and initial clinical trials. This review mainly focused on the progress and our prospects on field of vaccine development against SARS-CoV-2.
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Affiliation(s)
- Jinyong Zhang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy and Laboratory Medicine, Third Military Medical University, Chongqing 400038, China; (J.Z.); (H.Z.); (J.G.); (H.L.)
| | - Hao Zeng
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy and Laboratory Medicine, Third Military Medical University, Chongqing 400038, China; (J.Z.); (H.Z.); (J.G.); (H.L.)
| | - Jiang Gu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy and Laboratory Medicine, Third Military Medical University, Chongqing 400038, China; (J.Z.); (H.Z.); (J.G.); (H.L.)
| | - Haibo Li
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy and Laboratory Medicine, Third Military Medical University, Chongqing 400038, China; (J.Z.); (H.Z.); (J.G.); (H.L.)
| | - Lixin Zheng
- Laboratory of the Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Quanming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy and Laboratory Medicine, Third Military Medical University, Chongqing 400038, China; (J.Z.); (H.Z.); (J.G.); (H.L.)
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Abrahão JS, de Arruda LB. Special Issue "Emerging Viruses: Surveillance, Prevention, Evolution, and Control". Viruses 2020; 12:v12030306. [PMID: 32168932 PMCID: PMC7150905 DOI: 10.3390/v12030306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 03/09/2020] [Indexed: 12/14/2022] Open
Abstract
Emerging viruses represent a major concern for public health offices. Climate changes, the international migration of people and products, deforestation, and other anthropogenic activities (and their consequences) have been historically and continuously related to the emerging and re-emerging of new viruses, triggering an increasing number of notified outbreaks, epidemics, and pandemics. [...].
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Affiliation(s)
- Jônatas Santos Abrahão
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
- Correspondence: (J.S.A.); (L.B.d.A.)
| | - Luciana Barros de Arruda
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
- Correspondence: (J.S.A.); (L.B.d.A.)
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