851
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Bouwman KM, Tomris I, Turner HL, van der Woude R, Shamorkina TM, Bosman GP, Rockx B, Herfst S, Snijder J, Haagmans BL, Ward AB, Boons GJ, de Vries RP. Multimerization- and glycosylation-dependent receptor binding of SARS-CoV-2 spike proteins. PLoS Pathog 2021; 17:e1009282. [PMID: 33556147 PMCID: PMC7895411 DOI: 10.1371/journal.ppat.1009282] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/19/2021] [Accepted: 01/06/2021] [Indexed: 01/16/2023] Open
Abstract
Receptor binding studies on sarbecoviruses would benefit from an available toolkit of recombinant spike proteins, or domains thereof, that recapitulate receptor binding properties of native viruses. We hypothesized that trimeric Receptor Binding Domain (RBD) proteins would be suitable candidates to study receptor binding properties of SARS-CoV-1 and -2. Here we created monomeric and trimeric fluorescent RBD proteins, derived from adherent HEK293T, as well as in GnTI-/- mutant cells, to analyze the effect of complex vs high mannose glycosylation on receptor binding. The results demonstrate that trimeric, complex glycosylated proteins are superior in receptor binding compared to monomeric and immaturely glycosylated variants. Although differences in binding to commonly used cell lines were minimal between the different RBD preparations, substantial differences were observed when respiratory tissues of experimental animals were stained. The RBD trimers demonstrated distinct ACE2 expression profiles in bronchiolar ducts and confirmed the higher binding affinity of SARS-CoV-2 over SARS-CoV-1. Our results show that complex glycosylated trimeric RBD proteins are attractive to analyze sarbecovirus receptor binding and explore ACE2 expression profiles in tissues.
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Affiliation(s)
- Kim M Bouwman
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Ilhan Tomris
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Roosmarijn van der Woude
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Tatiana M Shamorkina
- Biomolecular Mass Spectrometry and Proteomics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Gerlof P Bosman
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Geert-Jan Boons
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
- Department of Chemistry, University of Georgia, Athens, Georgia, United States of America
| | - Robert P de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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852
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Nguyen N, Strnad O, Klein T, Luo D, Alharbi R, Wonka P, Maritan M, Mindek P, Autin L, Goodsell DS, Viola I. Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2021; 27:722-732. [PMID: 33055034 PMCID: PMC8642830 DOI: 10.1109/tvcg.2020.3030415] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/31/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
We present a new technique for the rapid modeling and construction of scientifically accurate mesoscale biological models. The resulting 3D models are based on a few 2D microscopy scans and the latest knowledge available about the biological entity, represented as a set of geometric relationships. Our new visual-programming technique is based on statistical and rule-based modeling approaches that are rapid to author, fast to construct, and easy to revise. From a few 2D microscopy scans, we determine the statistical properties of various structural aspects, such as the outer membrane shape, the spatial properties, and the distribution characteristics of the macromolecular elements on the membrane. This information is utilized in the construction of the 3D model. Once all the imaging evidence is incorporated into the model, additional information can be incorporated by interactively defining the rules that spatially characterize the rest of the biological entity, such as mutual interactions among macromolecules, and their distances and orientations relative to other structures. These rules are defined through an intuitive 3D interactive visualization as a visual-programming feedback loop. We demonstrate the applicability of our approach on a use case of the modeling procedure of the SARS-CoV-2 virion ultrastructure. This atomistic model, which we present here, can steer biological research to new promising directions in our efforts to fight the spread of the virus.
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Affiliation(s)
- Ngan Nguyen
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | - Ondřej Strnad
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | | | - Deng Luo
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | - Ruwayda Alharbi
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | - Peter Wonka
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
| | | | | | | | | | - Ivan Viola
- King Abdullah University of Science and Technology (KAUST)Saudi Arabia
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853
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Johari YB, Jaffé SRP, Scarrott JM, Johnson AO, Mozzanino T, Pohle TH, Maisuria S, Bhayat-Cammack A, Lambiase G, Brown AJ, Tee KL, Jackson PJ, Wong TS, Dickman MJ, Sargur RB, James DC. Production of trimeric SARS-CoV-2 spike protein by CHO cells for serological COVID-19 testing. Biotechnol Bioeng 2021; 118:1013-1021. [PMID: 33128388 DOI: 10.1002/bit.27615] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/14/2020] [Accepted: 10/27/2020] [Indexed: 12/27/2022]
Abstract
We describe scalable and cost-efficient production of full length, His-tagged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein trimer by Chinese hamster ovary (CHO) cells that can be used to detect SARS-CoV-2 antibodies in patient sera at high specificity and sensitivity. Transient production of spike in both human embryonic kidney (HEK) and CHO cells mediated by polyethyleneimine was increased significantly (up to 10.9-fold) by a reduction in culture temperature to 32°C to permit extended duration cultures. Based on these data GS-CHO pools stably producing spike trimer under the control of a strong synthetic promoter were cultured in hypothermic conditions with combinations of bioactive small molecules to increase yield of purified spike product 4.9-fold to 53 mg/L. Purification of recombinant spike by Ni-chelate affinity chromatography initially yielded a variety of co-eluting protein impurities identified as host cell derived by mass spectrometry, which were separated from spike trimer using a modified imidazole gradient elution. Purified CHO spike trimer antigen was used in enzyme-linked immunosorbent assay format to detect immunoglobulin G antibodies against SARS-CoV-2 in sera from patient cohorts previously tested for viral infection by polymerase chain reaction, including those who had displayed coronavirus disease 2019 (COVID-19) symptoms. The antibody assay, validated to ISO 15189 Medical Laboratories standards, exhibited a specificity of 100% and sensitivity of 92.3%. Our data show that CHO cells are a suitable host for the production of larger quantities of recombinant SARS-CoV-2 trimer which can be used as antigen for mass serological testing.
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Affiliation(s)
- Yusuf B Johari
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, UK
| | - Stephen R P Jaffé
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, UK
| | - Joseph M Scarrott
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, UK
| | - Abayomi O Johnson
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, UK
| | - Théo Mozzanino
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, UK
| | - Thilo H Pohle
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, UK
| | - Sheetal Maisuria
- Department of Immunology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Amina Bhayat-Cammack
- Department of Immunology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Giulia Lambiase
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, UK
| | - Adam J Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, UK
| | - Kang Lan Tee
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, UK
| | - Philip J Jackson
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, UK
| | - Tuck Seng Wong
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, UK
| | - Ravishankar B Sargur
- Department of Immunology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - David C James
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, UK
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854
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Prates ET, Garvin MR, Pavicic M, Jones P, Shah M, Demerdash O, Amos BK, Geiger A, Jacobson D. Potential Pathogenicity Determinants Identified from Structural Proteomics of SARS-CoV and SARS-CoV-2. Mol Biol Evol 2021; 38:702-715. [PMID: 32941612 PMCID: PMC7543629 DOI: 10.1093/molbev/msaa231] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Despite SARS-CoV and SARS-CoV-2 being equipped with highly similar protein arsenals, the corresponding zoonoses have spread among humans at extremely different rates. The specific characteristics of these viruses that led to such distinct outcomes remain unclear. Here, we apply proteome-wide comparative structural analysis aiming to identify the unique molecular elements in the SARS-CoV-2 proteome that may explain the differing consequences. By combining protein modeling and molecular dynamics simulations, we suggest nonconservative substitutions in functional regions of the spike glycoprotein (S), nsp1, and nsp3 that are contributing to differences in virulence. Particularly, we explain why the substitutions at the receptor-binding domain of S affect the structure–dynamics behavior in complexes with putative host receptors. Conservation of functional protein regions within the two taxa is also noteworthy. We suggest that the highly conserved main protease, nsp5, of SARS-CoV and SARS-CoV-2 is part of their mechanism of circumventing the host interferon antiviral response. Overall, most substitutions occur on the protein surfaces and may be modulating their antigenic properties and interactions with other macromolecules. Our results imply that the striking difference in the pervasiveness of SARS-CoV-2 and SARS-CoV among humans seems to significantly derive from molecular features that modulate the efficiency of viral particles in entering the host cells and blocking the host immune response.
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Affiliation(s)
- Erica T Prates
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN.,National Virtual Biotechnology Laboratory, US Department of Energy, TN
| | - Michael R Garvin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN.,National Virtual Biotechnology Laboratory, US Department of Energy, TN
| | - Mirko Pavicic
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN.,National Virtual Biotechnology Laboratory, US Department of Energy, TN
| | - Piet Jones
- National Virtual Biotechnology Laboratory, US Department of Energy, TN.,The Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee Knoxville, Knoxville, TN
| | - Manesh Shah
- Genome Science and Technology, The University of Tennessee Knoxville, Knoxville, TN
| | - Omar Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - B Kirtley Amos
- Department of Horticulture, N-318 Ag Sciences Center, University of Kentucky, Lexington, KY
| | - Armin Geiger
- National Virtual Biotechnology Laboratory, US Department of Energy, TN.,The Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee Knoxville, Knoxville, TN
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN.,National Virtual Biotechnology Laboratory, US Department of Energy, TN.,The Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee Knoxville, Knoxville, TN.,Genome Science and Technology, The University of Tennessee Knoxville, Knoxville, TN.,Department of Psychology, The University of Tennessee Knoxville, Knoxville, TN
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855
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Wang J, Wang D, Zhang Y, Dong J. Synthesis and Biopharmaceutical Applications of Sugar-Based Polymers: New Advances and Future Prospects. ACS Biomater Sci Eng 2021; 7:963-982. [PMID: 33523642 DOI: 10.1021/acsbiomaterials.0c01710] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The rapid rise in research interest in carbohydrate-based polymers is undoubtedly due to the nontoxic nature of such materials in an in vivo environment and the versatile roles that the polymers can play in cellular functions. Such polymers have served as therapeutic tools for drug delivery, including antigens, proteins, and genes, as well as diagnostic devices. Our focus in the first half of this Review is on synthetic methods based on ring-opening polymerization and enzyme-catalyzed polymerization, along with controlled radical polymerization. In the second half of this Review, sugar-based polymers are discussed on the basis of their remarkable success in competitive receptor binding, as multifunctional nanocarriers of targeting inhibitors for cancer treatment, in genome-editing delivery, in immunotherapy based on endogenous antibody recruitment, and in treatment of respiratory diseases, including influenza A. Particular emphasis is put on the synthesis and biopharmaceutical applications of sugar-based polymers published in the most recent 5 years. A noticeable attribute of carbohydrate-based polymers is that the sugar-receptor interactions can be facilitated by the cooperative effect of multiple sugar units. Their diversified topology and structures will drive the development of new synthetic strategies and bring about important applications, including coronavirus-related drug therapy.
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Affiliation(s)
- Jie Wang
- College of Chemistry and Chemical Engineering, Shaoxing University, 508 Huancheng West Road, Shaoxing, Zhejiang Province 312000, China
| | - Dong Wang
- College of Chemistry and Chemical Engineering, Shaoxing University, 508 Huancheng West Road, Shaoxing, Zhejiang Province 312000, China
| | - Yixian Zhang
- College of Chemistry and Chemical Engineering, Shaoxing University, 508 Huancheng West Road, Shaoxing, Zhejiang Province 312000, China
| | - Jian Dong
- College of Chemistry and Chemical Engineering, Shaoxing University, 508 Huancheng West Road, Shaoxing, Zhejiang Province 312000, China
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856
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Abstract
Vaccines are urgently needed to control the coronavirus disease 2019 (COVID-19) pandemic and to help the return to pre-pandemic normalcy. A great many vaccine candidates are being developed, several of which have completed late-stage clinical trials and are reporting positive results. In this Progress article, we discuss which viral elements are used in COVID-19 vaccine candidates, why they might act as good targets for the immune system and the implications for protective immunity.
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Affiliation(s)
- Lianpan Dai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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857
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Rihn SJ, Merits A, Bakshi S, Turnbull ML, Wickenhagen A, Alexander AJT, Baillie C, Brennan B, Brown F, Brunker K, Bryden SR, Burness KA, Carmichael S, Cole SJ, Cowton VM, Davies P, Davis C, De Lorenzo G, Donald CL, Dorward M, Dunlop JI, Elliott M, Fares M, da Silva Filipe A, Freitas JR, Furnon W, Gestuveo RJ, Geyer A, Giesel D, Goldfarb DM, Goodman N, Gunson R, Hastie CJ, Herder V, Hughes J, Johnson C, Johnson N, Kohl A, Kerr K, Leech H, Lello LS, Li K, Lieber G, Liu X, Lingala R, Loney C, Mair D, McElwee MJ, McFarlane S, Nichols J, Nomikou K, Orr A, Orton RJ, Palmarini M, Parr YA, Pinto RM, Raggett S, Reid E, Robertson DL, Royle J, Cameron-Ruiz N, Shepherd JG, Smollett K, Stewart DG, Stewart M, Sugrue E, Szemiel AM, Taggart A, Thomson EC, Tong L, Torrie LS, Toth R, Varjak M, Wang S, Wilkinson SG, Wyatt PG, Zusinaite E, Alessi DR, Patel AH, Zaid A, Wilson SJ, Mahalingam S. A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLoS Biol 2021; 19:e3001091. [PMID: 33630831 PMCID: PMC7906417 DOI: 10.1371/journal.pbio.3001091] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/05/2021] [Indexed: 12/30/2022] Open
Abstract
The recent emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the underlying cause of Coronavirus Disease 2019 (COVID-19), has led to a worldwide pandemic causing substantial morbidity, mortality, and economic devastation. In response, many laboratories have redirected attention to SARS-CoV-2, meaning there is an urgent need for tools that can be used in laboratories unaccustomed to working with coronaviruses. Here we report a range of tools for SARS-CoV-2 research. First, we describe a facile single plasmid SARS-CoV-2 reverse genetics system that is simple to genetically manipulate and can be used to rescue infectious virus through transient transfection (without in vitro transcription or additional expression plasmids). The rescue system is accompanied by our panel of SARS-CoV-2 antibodies (against nearly every viral protein), SARS-CoV-2 clinical isolates, and SARS-CoV-2 permissive cell lines, which are all openly available to the scientific community. Using these tools, we demonstrate here that the controversial ORF10 protein is expressed in infected cells. Furthermore, we show that the promising repurposed antiviral activity of apilimod is dependent on TMPRSS2 expression. Altogether, our SARS-CoV-2 toolkit, which can be directly accessed via our website at https://mrcppu-covid.bio/, constitutes a resource with considerable potential to advance COVID-19 vaccine design, drug testing, and discovery science.
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Affiliation(s)
- Suzannah J. Rihn
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Siddharth Bakshi
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Matthew L. Turnbull
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Arthur Wickenhagen
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | - Carla Baillie
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Benjamin Brennan
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Fiona Brown
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Steven R. Bryden
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Kerry A. Burness
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Stephen Carmichael
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Sarah J. Cole
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Vanessa M. Cowton
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Claire L. Donald
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Mark Dorward
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - James I. Dunlop
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Matthew Elliott
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mazigh Fares
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Joseph R. Freitas
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Rommel J. Gestuveo
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- Division of Biological Sciences, College of Arts and Sciences, University of the Philippines Visayas, Miagao, Iloilo, Philippines
| | - Anna Geyer
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Daniel Giesel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Daniel M. Goldfarb
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Nicola Goodman
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Glasgow, United Kingdom
| | - C. James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Vanessa Herder
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Clare Johnson
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Natasha Johnson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Karen Kerr
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Hannah Leech
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | | | - Kathy Li
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Gauthier Lieber
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Xiang Liu
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Rajendra Lingala
- Indian Immunologicals Ltd (IIL), Rakshapuram, Gachibowli Post, Hyderabad Telangana, India
| | - Colin Loney
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Daniel Mair
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Marion J. McElwee
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Steven McFarlane
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Anne Orr
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Richard J. Orton
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Yasmin A. Parr
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Rute Maria Pinto
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Samantha Raggett
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Elaine Reid
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Jamie Royle
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Natalia Cameron-Ruiz
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - James G. Shepherd
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Douglas G. Stewart
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Meredith Stewart
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Elena Sugrue
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Agnieszka M. Szemiel
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Aislynn Taggart
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Emma C. Thomson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Leah S. Torrie
- Drug Discovery Unit (DDU), Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Margus Varjak
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Sainan Wang
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Stuart G. Wilkinson
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Paul G. Wyatt
- Drug Discovery Unit (DDU), Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Eva Zusinaite
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Ali Zaid
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
- School of Medical Sciences, Griffith University, Gold Coast, Queensland, Australia
| | - Sam J. Wilson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Suresh Mahalingam
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
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858
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Ribeiro IRS, da Silva RF, Silveira CP, Galdino FE, Cardoso MB. Nano-targeting lessons from the SARS-CoV-2. NANO TODAY 2021; 36:101012. [PMID: 33139972 PMCID: PMC7584425 DOI: 10.1016/j.nantod.2020.101012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/03/2020] [Accepted: 10/14/2020] [Indexed: 05/20/2023]
Abstract
The lack of targeting efficacy has frequently led functionalized nanoparticles to accumulate in unwanted cells and tissues while boosting toxicity-related effects. Conversely, viruses are natural nanoparticles that precisely and responsively interact with the biological machinery through an effective-driven fashion. This interaction is enhanced by a meticulous spatial arrangement which results in a quasi-crystalline distribution of proteins on the viruses' surface. Amidst the COVID-19 pandemic, we propose to look at the SARS-CoV-2 nanoscale viral scaffold as an example of a highly-ordered architecture that must inspire and tailor the production of targeted synthetic nanoparticles.
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Affiliation(s)
- I R S Ribeiro
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, Brazil
- Institute of Chemistry (IQ), University of Campinas (UNICAMP), 13083-970, Post Office Box 6154, Campinas, SP, Brazil
| | - R F da Silva
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, Brazil
| | - C P Silveira
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, Brazil
| | - F E Galdino
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, Brazil
- Institute of Chemistry (IQ), University of Campinas (UNICAMP), 13083-970, Post Office Box 6154, Campinas, SP, Brazil
| | - M B Cardoso
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, Brazil
- Institute of Chemistry (IQ), University of Campinas (UNICAMP), 13083-970, Post Office Box 6154, Campinas, SP, Brazil
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859
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Nunes-Santos CJ, Kuehn HS, Rosenzweig SD. N-Glycan Modification in Covid-19 Pathophysiology: In vitro Structural Changes with Limited Functional Effects. J Clin Immunol 2021; 41:335-344. [PMID: 33245474 PMCID: PMC7691692 DOI: 10.1007/s10875-020-00905-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/28/2020] [Indexed: 12/15/2022]
Abstract
In 2014, we reported two siblings with a rare congenital disorder of glycosylation due to mutations in mannosyl-oligosaccharide glucosidase (MOGS). The glycan alteration derived from this disease resulted in an in vitro infection resistance to particular enveloped, N-glycosylation-dependent viruses as influenza and HIV. As part of the global effort to find safe and effective antiviral therapies for Covid-19, we assessed the in vitro activity of the FDA-approved α-glucosidase inhibitor miglustat against SARS-CoV-2. Expression plasmids encoding SARS-CoV-2 spike (S) and human ACE2 glycoproteins (GP) were tested to evaluate N-glycan modifications induced by α-glucosidase inhibition. Immunoprecipitation was used to assess binding between these two GP. Cell-to-cell fusion was assessed by immunofluorescence of cocultures of SARS-CoV-2 S and ACE2-expressing cells. Miglustat effect on immune response was tested by measuring cytokine release from PBMC exposed to purified SARS-CoV-2 S. In our overexpression system, miglustat successfully and specifically modified N-glycans in both SARS-CoV-2 S and its main receptor ACE2. Binding between these two GP was not affected by glycan modifications. A surrogate marker for viral cytopathic effect, measured as receptor-dependent SARS-CoV-2 S-driven cell-to-cell fusion, was not disrupted by miglustat treatment. This observation was further confirmed in MOGS-null transfected cells. Miglustat produced no statistically significant effects on cytokine production following SARS-CoV-2 S glycoprotein stimulation of PBMC. Our work shows that despite clear N-glycan alteration in the presence of miglustat, the functions of the Covid-19-related glycoproteins studied were not affected, making it unlikely that miglustat can change the natural course of the disease.
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Affiliation(s)
- Cristiane J Nunes-Santos
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health (NIH) Clinical Center, 10 Center Dr., Bldg 10, Rm. 2C410F, Bethesda, MD, 20892, USA
| | - Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health (NIH) Clinical Center, 10 Center Dr., Bldg 10, Rm. 2C410F, Bethesda, MD, 20892, USA
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health (NIH) Clinical Center, 10 Center Dr., Bldg 10, Rm. 2C410F, Bethesda, MD, 20892, USA.
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860
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Bhattacharjee S, Bhattacharyya R, Sengupta J. Dynamics and electrostatics define an allosteric druggable site within the receptor-binding domain of SARS-CoV-2 spike protein. FEBS Lett 2021; 595:442-451. [PMID: 33449359 PMCID: PMC8014131 DOI: 10.1002/1873-3468.14038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/11/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023]
Abstract
The pathogenesis of the SARS‐CoV‐2 virus initiates through recognition of the angiotensin‐converting enzyme 2 (ACE2) receptor of the host cells by the receptor‐binding domain (RBD) located at the spikes of the virus. Here, using molecular dynamics simulations, we have demonstrated the allosteric crosstalk within the RBD in the apo‐ and the ACE2 receptor‐bound states, revealing the contribution of the dynamics‐based correlated motions and the electrostatic energy perturbations to this crosstalk. While allostery, based on correlated motions, dominates inherent distal communication in the apo‐RBD, the electrostatic energy perturbations determine favorable pairwise crosstalk within the RBD residues upon binding to ACE2. Interestingly, the allosteric path is composed of residues which are evolutionarily conserved within closely related coronaviruses, pointing toward the biological relevance of the communication and its potential as a target for drug development.
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Affiliation(s)
- Sayan Bhattacharjee
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Rajanya Bhattacharyya
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jayati Sengupta
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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861
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The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. Biochem Biophys Res Commun 2021; 538:104-107. [PMID: 33199022 PMCID: PMC7643658 DOI: 10.1016/j.bbrc.2020.10.109] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022]
Abstract
The development of the SARS-CoV-2 pandemic has prompted an extensive worldwide sequencing effort to characterise the geographical spread and molecular evolution of the virus. A point mutation in the spike protein, D614G, emerged as the virus spread from Asia into Europe and the USA, and has rapidly become the dominant form worldwide. Here we review how the D614G variant was identified and discuss recent evidence about the effect of the mutation on the characteristics of the virus, clinical outcome of infection and host immune response.
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862
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Santopolo S, Riccio A, Santoro MG. The biogenesis of SARS-CoV-2 spike glycoprotein: multiple targets for host-directed antiviral therapy. Biochem Biophys Res Commun 2021; 538:80-87. [PMID: 33303190 PMCID: PMC7698684 DOI: 10.1016/j.bbrc.2020.10.080] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19 (coronavirus disease-19), represents a far more serious threat to public health than SARS and MERS coronaviruses, due to its ability to spread more efficiently than its predecessors. Currently, there is no worldwide-approved effective treatment for COVID-19, urging the scientific community to intense efforts to accelerate the discovery and development of prophylactic and therapeutic solutions against SARS-CoV-2 infection. In particular, effective antiviral drugs are urgently needed. With few exceptions, therapeutic approaches to combat viral infections have traditionally focused on targeting unique viral components or enzymes; however, it has now become evident that this strategy often fails due to the rapid emergence of drug-resistant viruses. Targeting host factors that are essential for the virus life cycle, but are dispensable for the host, has recently received increasing attention. The spike glycoprotein, a component of the viral envelope that decorates the virion surface as a distinctive crown ("corona") and is essential for SARS-CoV-2 entry into host cells, represents a key target for developing therapeutics capable of blocking virus invasion. This review highlights aspects of the SARS-CoV-2 spike biogenesis that may be amenable to host-directed antiviral targeting.
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Affiliation(s)
- Silvia Santopolo
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Anna Riccio
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - M. Gabriella Santoro
- Department of Biology, University of Rome Tor Vergata, Rome, Italy,Institute of Translational Pharmacology, CNR, Rome, Italy,Corresponding author. Department of Biology, University of Rome Tor Vergata, Rome, Italy
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863
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Wong NA, Saier MH. The SARS-Coronavirus Infection Cycle: A Survey of Viral Membrane Proteins, Their Functional Interactions and Pathogenesis. Int J Mol Sci 2021; 22:1308. [PMID: 33525632 PMCID: PMC7865831 DOI: 10.3390/ijms22031308] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a novel epidemic strain of Betacoronavirus that is responsible for the current viral pandemic, coronavirus disease 2019 (COVID-19), a global health crisis. Other epidemic Betacoronaviruses include the 2003 SARS-CoV-1 and the 2009 Middle East Respiratory Syndrome Coronavirus (MERS-CoV), the genomes of which, particularly that of SARS-CoV-1, are similar to that of the 2019 SARS-CoV-2. In this extensive review, we document the most recent information on Coronavirus proteins, with emphasis on the membrane proteins in the Coronaviridae family. We include information on their structures, functions, and participation in pathogenesis. While the shared proteins among the different coronaviruses may vary in structure and function, they all seem to be multifunctional, a common theme interconnecting these viruses. Many transmembrane proteins encoded within the SARS-CoV-2 genome play important roles in the infection cycle while others have functions yet to be understood. We compare the various structural and nonstructural proteins within the Coronaviridae family to elucidate potential overlaps and parallels in function, focusing primarily on the transmembrane proteins and their influences on host membrane arrangements, secretory pathways, cellular growth inhibition, cell death and immune responses during the viral replication cycle. We also offer bioinformatic analyses of potential viroporin activities of the membrane proteins and their sequence similarities to the Envelope (E) protein. In the last major part of the review, we discuss complement, stimulation of inflammation, and immune evasion/suppression that leads to CoV-derived severe disease and mortality. The overall pathogenesis and disease progression of CoVs is put into perspective by indicating several stages in the resulting infection process in which both host and antiviral therapies could be targeted to block the viral cycle. Lastly, we discuss the development of adaptive immunity against various structural proteins, indicating specific vulnerable regions in the proteins. We discuss current CoV vaccine development approaches with purified proteins, attenuated viruses and DNA vaccines.
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Affiliation(s)
- Nicholas A. Wong
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
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864
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Verkhivker GM, Di Paola L. Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches. J Phys Chem B 2021; 125:850-873. [PMID: 33448856 PMCID: PMC7839160 DOI: 10.1021/acs.jpcb.0c10637] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/08/2021] [Indexed: 12/13/2022]
Abstract
The rapidly growing body of structural and biochemical studies of the SARS-CoV-2 spike glycoprotein has revealed a variety of distinct functional states with radically different arrangements of the receptor-binding domain, highlighting a remarkable function-driven conformational plasticity and adaptability of the spike proteins. In this study, we examined molecular mechanisms underlying conformational and dynamic changes in the SARS-CoV-2 spike mutant trimers through the lens of dynamic analysis of allosteric interaction networks and atomistic modeling of signal transmission. Using an integrated approach that combined coarse-grained molecular simulations, protein stability analysis, and perturbation-based modeling of residue interaction networks, we examined how mutations in the regulatory regions of the SARS-CoV-2 spike protein can differentially affect dynamics and allosteric signaling in distinct functional states. The results of this study revealed key functional regions and regulatory centers that govern collective dynamics, allosteric interactions, and control signal transmission in the SARS-CoV-2 spike proteins. We found that the experimentally confirmed regulatory hotspots that dictate dynamic switching between conformational states of the SARS-CoV-2 spike protein correspond to the key hinge sites and global mediating centers of the allosteric interaction networks. The results of this study provide a novel insight into allosteric regulatory mechanisms of SARS-CoV-2 spike proteins showing that mutations at the key regulatory positions can differentially modulate distribution of states and determine topography of signal communication pathways operating through state-specific cascades of control switch points. This analysis provides a plausible strategy for allosteric probing of the conformational equilibrium and therapeutic intervention by targeting specific hotspots of allosteric interactions and communications in the SARS-CoV-2 spike proteins.
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Affiliation(s)
- Gennady M. Verkhivker
- Keck
Center for Science and Engineering, Schmid College of Science and
Technology, Chapman University, One University Drive, Orange, California 92866, United States
- Department
of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
| | - Luisa Di Paola
- Unit
of Chemical-Physics Fundamentals in Chemical Engineering, Department
of Engineering, Università Campus
Bio-Medico di Roma, via
Álvaro del Portillo 21, 00128 Rome, Italy
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865
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Powell A, Zhang K, Sanyal M, Tang S, Weidenbacher PA, Li S, Pham TD, Pak JE, Chiu W, Kim PS. A Single Immunization with Spike-Functionalized Ferritin Vaccines Elicits Neutralizing Antibody Responses against SARS-CoV-2 in Mice. ACS CENTRAL SCIENCE 2021; 7:183-199. [PMID: 33527087 PMCID: PMC7805605 DOI: 10.1021/acscentsci.0c01405] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Indexed: 05/05/2023]
Abstract
The development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SΔC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines, and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SΔC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SΔC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.
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Affiliation(s)
- Abigail
E. Powell
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Kaiming Zhang
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - Mrinmoy Sanyal
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Shaogeng Tang
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Payton A. Weidenbacher
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Shanshan Li
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - Tho D. Pham
- Department
of Pathology, Stanford University, Stanford, California 94305, United States
- Stanford
Blood Center, Palo Alto, California 94304, United States
| | - John E. Pak
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
| | - Wah Chiu
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
- Division
of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Peter S. Kim
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
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866
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Murrell I, Forde D, Zelek W, Tyson L, Chichester L, Palmer N, Jones R, Morgan BP, Moore C. Temporal development and neutralising potential of antibodies against SARS-CoV-2 in hospitalised COVID-19 patients: An observational cohort study. PLoS One 2021; 16:e0245382. [PMID: 33497420 PMCID: PMC7837461 DOI: 10.1371/journal.pone.0245382] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022] Open
Abstract
Antibody responses are important in the control of viral respiratory infection in the human host. What is not clear for SARS-CoV-2 is how rapidly this response occurs, or when antibodies with protective capability evolve. Hence, defining the events of SARS-CoV-2 seroconversion and the time frame for the development of antibodies with protective potential may help to explain the different clinical presentations of COVID-19. Furthermore, accurate descriptions of seroconversion are needed to inform the best use of serological assays for diagnostic testing and serosurveillance studies. Here, we describe the humoral responses in a cohort of hospitalised COVID-19 patients (n = 19) shortly following the onset of symptoms. Commercial and 'in-house' serological assays were used to measure IgG antibodies against different SARS-CoV-2 structural antigens-Spike (S) S1 sub-unit and Nucleocapsid protein (NP)-and to assess the potential for virus neutralisation mediated specifically by inhibition of binding between the viral attachment protein (S protein) and cognate receptor (ACE-2). Antibody response kinetics varied amongst the cohort, with patients seroconverting within 1 week, between 1-2 weeks, or after 2 weeks, following symptom onset. Anti-NP IgG responses were generally detected earlier, but reached maximum levels slower, than anti-S1 IgG responses. The earliest IgG antibodies produced by all patients included those that recognised the S protein receptor-binding domain (RBD) and were capable of inhibiting binding to ACE-2. These data revealed events and patterns of SARS-CoV-2 seroconversion that may be important predictors of the outcome of infection and guide the delivery of clinical services in the COVID-19 response.
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Affiliation(s)
- Isa Murrell
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Donall Forde
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Wioleta Zelek
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Linda Tyson
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Lisa Chichester
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Nicki Palmer
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Rachel Jones
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - B. Paul Morgan
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, Wales, United Kingdom
| | - Catherine Moore
- Wales Specialist Virology Centre, Public Health Wales Microbiology, University Hospital of Wales, Cardiff, Wales, United Kingdom
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867
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Gowthaman R, Guest JD, Yin R, Adolf-Bryfogle J, Schief WR, Pierce BG. CoV3D: a database of high resolution coronavirus protein structures. Nucleic Acids Res 2021; 49:D282-D287. [PMID: 32890396 PMCID: PMC7778948 DOI: 10.1093/nar/gkaa731] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/11/2020] [Accepted: 08/21/2020] [Indexed: 12/19/2022] Open
Abstract
SARS-CoV-2, the etiologic agent of COVID-19, exemplifies the general threat to global health posed by coronaviruses. The urgent need for effective vaccines and therapies is leading to a rapid rise in the number of high resolution structures of SARS-CoV-2 proteins that collectively reveal a map of virus vulnerabilities. To assist structure-based design of vaccines and therapeutics against SARS-CoV-2 and other coronaviruses, we have developed CoV3D, a database and resource for coronavirus protein structures, which is updated on a weekly basis. CoV3D provides users with comprehensive sets of structures of coronavirus proteins and their complexes with antibodies, receptors, and small molecules. Integrated molecular viewers allow users to visualize structures of the spike glycoprotein, which is the major target of neutralizing antibodies and vaccine design efforts, as well as sets of spike-antibody complexes, spike sequence variability, and known polymorphisms. In order to aid structure-based design and analysis of the spike glycoprotein, CoV3D permits visualization and download of spike structures with modeled N-glycosylation at known glycan sites, and contains structure-based classification of spike conformations, generated by unsupervised clustering. CoV3D can serve the research community as a centralized reference and resource for spike and other coronavirus protein structures, and is available at: https://cov3d.ibbr.umd.edu.
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Affiliation(s)
- Ragul Gowthaman
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Johnathan D Guest
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Rui Yin
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Jared Adolf-Bryfogle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Institute for Protein Innovation, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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868
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Repositioning of histamine H 1 receptor antagonist: Doxepin inhibits viropexis of SARS-CoV-2 Spike pseudovirus by blocking ACE2. Eur J Pharmacol 2021; 896:173897. [PMID: 33497607 PMCID: PMC7826143 DOI: 10.1016/j.ejphar.2021.173897] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/10/2021] [Accepted: 01/19/2021] [Indexed: 01/01/2023]
Abstract
The spread of the corona virus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been intensifying in the past year, posing a huge threat to global health. There is an urgent need for effective drugs and vaccines to fight the COVID-19, but their advent may not be quite fast. Drug repurposing is a feasible strategy in the current situation, which could greatly shorten drug development time and help to response quickly to the novel virus outbreak. It has been reported that histamine H1 receptor antagonists have broad-spectrum antiviral effects. Therefore, in this study, we aim to screen potential drugs among histamine H1 receptor antagonists that may inhibit SARS-CoV-2 infection. Based on the model of angiotensin-converting enzyme 2 (ACE2) overexpressing HEK293T cell membrane chromatography (CMC), five FDA-approved histamine H1 receptor antagonists were found to have bioaffinity to ACE2. Then we determined the interaction between these drugs and ACE2 by frontal analysis and surface plasmon resonance (SPR), which consistently demonstrated that these hits bind to ACE2 at micromolar levels of affinity. Through the pseudovirus assay, we finally identified that doxepin could inhibit SARS-CoV-2 spike pseudovirus from entering the ACE2-expressing cell, reducing the infection rate to 25.82%. These preliminary results indicate that the histamine H1 receptor antagonist, doxepin, is a viable drug candidate for clinical trials. Therefore, we hope the work timely provides rational help for developing anti-SARS-CoV-2 drugs to control the rapid spread of SARS-CoV-2.
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869
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Pendu JL, Breiman A, Rocher J, Dion M, Ruvoën-Clouet N. ABO Blood Types and COVID-19: Spurious, Anecdotal, or Truly Important Relationships? A Reasoned Review of Available Data. Viruses 2021; 13:160. [PMID: 33499228 PMCID: PMC7911989 DOI: 10.3390/v13020160] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/19/2021] [Accepted: 01/19/2021] [Indexed: 12/19/2022] Open
Abstract
Since the emergence of COVID-19, many publications have reported associations with ABO blood types. Despite between-study discrepancies, an overall consensus has emerged whereby blood group O appears associated with a lower risk of COVID-19, while non-O blood types appear detrimental. Two major hypotheses may explain these findings: First, natural anti-A and anti-B antibodies could be partially protective against SARS-CoV-2 virions carrying blood group antigens originating from non-O individuals. Second, O individuals are less prone to thrombosis and vascular dysfunction than non-O individuals and therefore could be at a lesser risk in case of severe lung dysfunction. Here, we review the literature on the topic in light of these hypotheses. We find that between-study variation may be explained by differences in study settings and that both mechanisms are likely at play. Moreover, as frequencies of ABO phenotypes are highly variable between populations or geographical areas, the ABO coefficient of variation, rather than the frequency of each individual phenotype is expected to determine impact of the ABO system on virus transmission. Accordingly, the ABO coefficient of variation correlates with COVID-19 prevalence. Overall, despite modest apparent risk differences between ABO subtypes, the ABO blood group system might play a major role in the COVID-19 pandemic when considered at the population level.
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Affiliation(s)
- Jacques Le Pendu
- CRCINA, INSERM, Université de Nantes, F-44000 Nantes, France; (A.B.); (J.R.); (N.R.-C.)
| | - Adrien Breiman
- CRCINA, INSERM, Université de Nantes, F-44000 Nantes, France; (A.B.); (J.R.); (N.R.-C.)
- CHU de Nantes, F-44000 Nantes, France
| | - Jézabel Rocher
- CRCINA, INSERM, Université de Nantes, F-44000 Nantes, France; (A.B.); (J.R.); (N.R.-C.)
| | - Michel Dion
- Microbiotes Hosts Antibiotics and Bacterial Resistances (MiHAR), Université de Nantes, F-44000 Nantes, France;
| | - Nathalie Ruvoën-Clouet
- CRCINA, INSERM, Université de Nantes, F-44000 Nantes, France; (A.B.); (J.R.); (N.R.-C.)
- Oniris, Ecole Nationale Vétérinaire, Agroalimentaire et de l’Alimentation, F-44307 Nantes, France
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870
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Mori T, Jung J, Kobayashi C, Dokainish HM, Re S, Sugita Y. Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein. Biophys J 2021; 120:1060-1071. [PMID: 33484712 PMCID: PMC7825899 DOI: 10.1016/j.bpj.2021.01.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/31/2020] [Accepted: 01/13/2021] [Indexed: 12/23/2022] Open
Abstract
The ongoing COVID-19 pandemic caused by the new coronavirus, SARS-CoV-2, calls for urgent developments of vaccines and antiviral drugs. The spike protein of SARS-CoV-2 (S-protein), which consists of trimeric polypeptide chains with glycosylated residues on the surface, triggers the virus entry into a host cell. Extensive structural and functional studies on this protein have rapidly advanced our understanding of the S-protein structure at atomic resolutions, although most of these structural studies overlook the effect of glycans attached to the S-protein on the conformational stability and functional motions between the inactive down and active up forms. Here, we performed all-atom molecular dynamics simulations of both down and up forms of a fully glycosylated S-protein in solution as well as targeted molecular dynamics simulations between them to elucidate key interdomain interactions for stabilizing each form and inducing the large-scale conformational transitions. The residue-level interaction analysis of the simulation trajectories detects distinct amino acid residues and N-glycans as determinants on conformational stability of each form. During the conformational transitions between them, interdomain interactions mediated by glycosylated residues are switched to play key roles on the stabilization of another form. Electrostatic interactions, as well as hydrogen bonds between the three receptor binding domains, work as driving forces to initiate the conformational transitions toward the active form. This study sheds light on the mechanisms underlying conformational stability and functional motions of the S-protein, which are relevant for vaccine and antiviral drug developments.
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Affiliation(s)
- Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Jaewoon Jung
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan; Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan
| | - Hisham M Dokainish
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Osaka, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan; Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan; Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
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871
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Gadanec LK, McSweeney KR, Qaradakhi T, Ali B, Zulli A, Apostolopoulos V. Can SARS-CoV-2 Virus Use Multiple Receptors to Enter Host Cells? Int J Mol Sci 2021; 22:992. [PMID: 33498183 PMCID: PMC7863934 DOI: 10.3390/ijms22030992] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
The occurrence of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for coronavirus disease 2019 (COVD-19), represents a catastrophic threat to global health. Protruding from the viral surface is a densely glycosylated spike (S) protein, which engages angiotensin-converting enzyme 2 (ACE2) to mediate host cell entry. However, studies have reported viral susceptibility in intra- and extrapulmonary immune and non-immune cells lacking ACE2, suggesting that the S protein may exploit additional receptors for infection. Studies have demonstrated interactions between S protein and innate immune system, including C-lectin type receptors (CLR), toll-like receptors (TLR) and neuropilin-1 (NRP1), and the non-immune receptor glucose regulated protein 78 (GRP78). Recognition of carbohydrate moieties clustered on the surface of the S protein may drive receptor-dependent internalization, accentuate severe immunopathological inflammation, and allow for systemic spread of infection, independent of ACE2. Furthermore, targeting TLRs, CLRs, and other receptors (Ezrin and dipeptidyl peptidase-4) that do not directly engage SARS-CoV-2 S protein, but may contribute to augmented anti-viral immunity and viral clearance, may represent therapeutic targets against COVID-19.
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872
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Stuible M, Gervais C, Lord-Dufour S, Perret S, L'Abbé D, Schrag J, St-Laurent G, Durocher Y. Rapid, high-yield production of full-length SARS-CoV-2 spike ectodomain by transient gene expression in CHO cells. J Biotechnol 2021; 326:21-27. [PMID: 33301853 PMCID: PMC7720734 DOI: 10.1016/j.jbiotec.2020.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/29/2020] [Accepted: 12/06/2020] [Indexed: 01/06/2023]
Abstract
Recombinant forms of the spike protein of SARS-CoV-2 and related viruses have proven difficult to produce with good yields in mammalian cells. Given the panoply of potential COVID-19 diagnostic tools and therapeutic candidates that require purified spike protein and its importance for ongoing SARS-CoV-2 research, we have explored new approaches for spike production and purification. Three transient gene expression methods based on PEI-mediated transfection of CHO or HEK293 cells in suspension culture in chemically-defined media were compared for rapid production of full-length SARS-CoV-2 spike ectodomain. A high-cell-density protocol using DXB11-derived CHOBRI/55E1 cells gave substantially better yields than the other methods. Different forms of the spike ectodomain were expressed, including the wild-type SARS-CoV-2 sequence and a mutated form (to favor expression of the full-length spike ectodomain stabilized in pre-fusion conformation), with and without fusion to putative trimerization domains. An efficient two-step affinity purification method was also developed. Ultimately, we have been able to produce highly homogenous preparations of full-length spike, both monomeric and trimeric, with yields of 100-150 mg/L in the harvested medium. The speed and productivity of this method support further development of CHO-based approaches for recombinant spike protein manufacturing.
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Affiliation(s)
- Matthew Stuible
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Christian Gervais
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Simon Lord-Dufour
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Sylvie Perret
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Denis L'Abbé
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Joseph Schrag
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Gilles St-Laurent
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Yves Durocher
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada.
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873
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Kifer D, Bugada D, Villar-Garcia J, Gudelj I, Menni C, Sudre C, Vučković F, Ugrina I, Lorini LF, Posso M, Bettinelli S, Ughi N, Maloberti A, Epis O, Giannattasio C, Rossetti C, Kalogjera L, Peršec J, Ollivere L, Ollivere BJ, Yan H, Cai T, Aithal GP, Steves CJ, Kantele A, Kajova M, Vapalahti O, Sajantila A, Wojtowicz R, Wierzba W, Krol Z, Zaczynski A, Zycinska K, Postula M, Lukšić I, Čivljak R, Markotić A, Brachmann J, Markl A, Mahnkopf C, Murray B, Ourselin S, Valdes AM, Horcajada JP, Castells X, Pascual J, Allegri M, Primorac D, Spector TD, Barrios C, Lauc G. Effects of Environmental Factors on Severity and Mortality of COVID-19. Front Med (Lausanne) 2021; 7:607786. [PMID: 33553204 PMCID: PMC7855590 DOI: 10.3389/fmed.2020.607786] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Most respiratory viruses show pronounced seasonality, but for SARS-CoV-2, this still needs to be documented. Methods: We examined the disease progression of COVID-19 in 6,914 patients admitted to hospitals in Europe and China. In addition, we evaluated progress of disease symptoms in 37,187 individuals reporting symptoms into the COVID Symptom Study application. Findings: Meta-analysis of the mortality risk in seven European hospitals estimated odds ratios per 1-day increase in the admission date to be 0.981 (0.973-0.988, p < 0.001) and per increase in ambient temperature of 1°C to be 0.854 (0.773-0.944, p = 0.007). Statistically significant decreases of comparable magnitude in median hospital stay, probability of transfer to the intensive care unit, and need for mechanical ventilation were also observed in most, but not all hospitals. The analysis of individually reported symptoms of 37,187 individuals in the UK also showed the decrease in symptom duration and disease severity with time. Interpretation: Severity of COVID-19 in Europe decreased significantly between March and May and the seasonality of COVID-19 is the most likely explanation.
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Affiliation(s)
- Domagoj Kifer
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Dario Bugada
- Emergency and Intensive Care Department, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Judit Villar-Garcia
- Hospital del Mar-Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Ivan Gudelj
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Carole Sudre
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | | | - Ivo Ugrina
- Faculty of Science, University of Split, Split, Croatia
| | - Luca F. Lorini
- Emergency and Intensive Care Department, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Margarita Posso
- Hospital del Mar-Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Silvia Bettinelli
- Emergency and Intensive Care Department, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Nicola Ughi
- Azienda Socio Sanitaria Territoriale Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Alessandro Maloberti
- Azienda Socio Sanitaria Territoriale Grande Ospedale Metropolitano Niguarda, Milan, Italy
- School of Medicine and Surgery, Milano-Bicocca University, Milan, Italy
| | - Oscar Epis
- Azienda Socio Sanitaria Territoriale Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Cristina Giannattasio
- Azienda Socio Sanitaria Territoriale Grande Ospedale Metropolitano Niguarda, Milan, Italy
- School of Medicine and Surgery, Milano-Bicocca University, Milan, Italy
| | - Claudio Rossetti
- Azienda Socio Sanitaria Territoriale Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Livije Kalogjera
- Department of Otolaryngology-Head and Neck Surgery, Zagreb School of Medicine, University Hospital Centre “Sestre milosrdnice”, Zagreb, Croatia
| | - Jasminka Peršec
- Clinical Department of Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava Zagreb, Zagreb, Croatia
- University of Zagreb School of Dental Medicine, Zagreb, Croatia
| | - Luke Ollivere
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust and the University of Nottingham, Nottingham, United Kingdom
| | - Benjamin J. Ollivere
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust and the University of Nottingham, Nottingham, United Kingdom
| | - Huadong Yan
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Department of Infectious Diseases, Hwamei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Ting Cai
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Department of Infectious Diseases, Hwamei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Guruprasad P. Aithal
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust and the University of Nottingham, Nottingham, United Kingdom
| | - Claire J. Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Anu Kantele
- Inflammation Centre, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Mikael Kajova
- Inflammation Centre, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Helsingin ja Uudenmaan Sairaanhoitopiiri Diagnostic Center, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Rafal Wojtowicz
- Central Clinical Hospital of Ministry of the Interior and Administration, Warsaw, Poland
| | - Waldemar Wierzba
- Central Clinical Hospital of Ministry of the Interior and Administration, Warsaw, Poland
| | - Zbigniew Krol
- Central Clinical Hospital of Ministry of the Interior and Administration, Warsaw, Poland
| | - Artur Zaczynski
- Central Clinical Hospital of Ministry of the Interior and Administration, Warsaw, Poland
| | - Katarina Zycinska
- Central Clinical Hospital of Ministry of the Interior and Administration, Warsaw, Poland
- Medical University of Warsaw, Warsaw, Poland
| | - Marek Postula
- Department of Experimental and Clinical Pharmacology, Center for Preclinical Research and Technology CEPT, Medical University of Warsaw, Warsaw, Poland
| | - Ivica Lukšić
- University of Zagreb School of Medicine, University Hospital Dubrava, Zagreb, Croatia
| | - Rok Čivljak
- University Hospital for Infectious Diseases “Fran Mihaljević”, University of Zagreb School of Medicine, Zagreb, Croatia
- University Hospital for Infectious Diseases “Fran Mihaljević”, Catholic University of Croatia, Zagreb, Croatia
- Medical School, University of Rijeka, Rijeka, Croatia
| | - Alemka Markotić
- University Hospital for Infectious Diseases “Fran Mihaljević”, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Johannes Brachmann
- REGIOMED Kliniken, Coburg, Germany
- University of Split School of Medicine, Split, Croatia
| | | | | | - Benjamin Murray
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, United Kingdom
| | - Sebastien Ourselin
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, United Kingdom
| | - Ana M. Valdes
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust and the University of Nottingham, Nottingham, United Kingdom
| | - Juan P. Horcajada
- Hospital del Mar-Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Xavier Castells
- Hospital del Mar-Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Julio Pascual
- Hospital del Mar-Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Massimo Allegri
- Pain Therapy Service Policlinico of Monza Hospital, Monza, Italy
| | - Dragan Primorac
- REGIOMED Kliniken, Coburg, Germany
- University of Split School of Medicine, Split, Croatia
- St. Catharine Hospital, Zagreb, Croatia
- Eberly College of Science, Penn State University, University Park, PA, United States
- University of Osijek School of Medicine, Osijek, Croatia
- Faculty of Dental Medicine and Health, University of Rijeka School of Medicine, University of Rijeka, Rijeka, Croatia
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Clara Barrios
- Hospital del Mar-Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Gordan Lauc
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
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874
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The role of chemical biology in the fight against SARS-CoV-2. Biochem J 2021; 478:157-177. [PMID: 33439990 DOI: 10.1042/bcj20200514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 01/18/2023]
Abstract
Since late 2019, biomedical labs all over the world have been struggling to cope with the 'new normal' and to find ways in which they can contribute to the fight against COVID-19. In this unique situation where a biomedical issue dominates people's lives and the news cycle, chemical biology has a great deal to contribute. This review will describe the importance of science at the chemistry/biology interface to both understand and combat the SARS-CoV-2 pandemic.
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875
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Finkelstein MT, Mermelstein AG, Parker Miller E, Seth PC, Stancofski ESD, Fera D. Structural Analysis of Neutralizing Epitopes of the SARS-CoV-2 Spike to Guide Therapy and Vaccine Design Strategies. Viruses 2021; 13:134. [PMID: 33477902 PMCID: PMC7833398 DOI: 10.3390/v13010134] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/01/2021] [Accepted: 01/14/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus research has gained tremendous attention because of the COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus (nCoV or SARS-CoV-2). In this review, we highlight recent studies that provide atomic-resolution structural details important for the development of monoclonal antibodies (mAbs) that can be used therapeutically and prophylactically and for vaccines against SARS-CoV-2. Structural studies with SARS-CoV-2 neutralizing mAbs have revealed a diverse set of binding modes on the spike's receptor-binding domain and N-terminal domain and highlight alternative targets on the spike. We consider this structural work together with mAb effects in vivo to suggest correlations between structure and clinical applications. We also place mAbs against severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses in the context of the SARS-CoV-2 spike to suggest features that may be desirable to design mAbs or vaccines capable of conferring broad protection.
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Affiliation(s)
| | | | | | | | | | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA; (M.T.F.); (A.G.M.); (E.P.M.); (P.C.S.); (E.-S.D.S.)
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876
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Watanabe Y, Mendonça L, Allen ER, Howe A, Lee M, Allen JD, Chawla H, Pulido D, Donnellan F, Davies H, Ulaszewska M, Belij-Rammerstorfer S, Morris S, Krebs AS, Dejnirattisai W, Mongkolsapaya J, Supasa P, Screaton GR, Green CM, Lambe T, Zhang P, Gilbert SC, Crispin M. Native-like SARS-CoV-2 spike glycoprotein expressed by ChAdOx1 nCoV-19/AZD1222 vaccine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.15.426463. [PMID: 33501433 PMCID: PMC7836103 DOI: 10.1101/2021.01.15.426463] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Vaccine development against the SARS-CoV-2 virus focuses on the principal target of the neutralizing immune response, the spike (S) glycoprotein. Adenovirus-vectored vaccines offer an effective platform for the delivery of viral antigen, but it is important for the generation of neutralizing antibodies that they produce appropriately processed and assembled viral antigen that mimics that observed on the SARS-CoV-2 virus. Here, we describe the structure, conformation and glycosylation of the S protein derived from the adenovirus-vectored ChAdOx1 nCoV-19/AZD1222 vaccine. We demonstrate native-like post-translational processing and assembly, and reveal the expression of S proteins on the surface of cells adopting the trimeric prefusion conformation. The data presented here confirms the use of ChAdOx1 adenovirus vectors as a leading platform technology for SARS-CoV-2 vaccines.
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Affiliation(s)
- Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Luiza Mendonça
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Elizabeth R. Allen
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew Howe
- Electron Bio-imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Mercede Lee
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Himanshi Chawla
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - David Pulido
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Francesca Donnellan
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hannah Davies
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marta Ulaszewska
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sandra Belij-Rammerstorfer
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susan Morris
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna-Sophia Krebs
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Wanwisa Dejnirattisai
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Juthathip Mongkolsapaya
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Chinese Academy of Medical Science(CAMS) Oxford Institute (COI), University of Oxford, Oxford, U.K
| | - Piyada Supasa
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Gavin R. Screaton
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Division of Medical Sciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Catherine M. Green
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Teresa Lambe
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Peijun Zhang
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
- Electron Bio-imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Sarah C. Gilbert
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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877
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Alteri C, Cento V, Piralla A, Costabile V, Tallarita M, Colagrossi L, Renica S, Giardina F, Novazzi F, Gaiarsa S, Matarazzo E, Antonello M, Vismara C, Fumagalli R, Epis OM, Puoti M, Perno CF, Baldanti F. Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy. Nat Commun 2021; 12:434. [PMID: 33469026 PMCID: PMC7815831 DOI: 10.1038/s41467-020-20688-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/10/2020] [Indexed: 12/21/2022] Open
Abstract
From February to April 2020, Lombardy (Italy) reported the highest numbers of SARS-CoV-2 cases worldwide. By analyzing 346 whole SARS-CoV-2 genomes, we demonstrate the presence of seven viral lineages in Lombardy, frequently sustained by local transmission chains and at least two likely to have originated in Italy. Six single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. The seven lineages, and the presence of local transmission clusters within three of them, revealed that sustained community transmission was underway before the first COVID-19 case had been detected in Lombardy. The Lombardy region of Italy was heavily affected early in the SARS-CoV-2 pandemic. Here, the authors use whole genome sequencing and show that there were multiple introductions into the region, with transmission occurring before the first case was detected.
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Affiliation(s)
- Claudia Alteri
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Valeria Cento
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Valentino Costabile
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Monica Tallarita
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Luna Colagrossi
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Renica
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Federica Giardina
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Federica Novazzi
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Stefano Gaiarsa
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elisa Matarazzo
- Residency in Microbiology and Virology, University of Milan, Milan, Italy
| | - Maria Antonello
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Chiara Vismara
- Chemico-clinical and Microbiological Analyses, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Roberto Fumagalli
- Department of Anesthesiology, Critical Care and Pain Medicine, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | - Massimo Puoti
- Infectious Diseases Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Carlo Federico Perno
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
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878
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Zhou Y, Zhang J, Wang D, Wang D, Guan W, Qin J, Xu X, Fang J, Fu B, Zheng X, Wang D, Zhao H, Chen X, Tian Z, Xu X, Wang G, Wei H. Profiling of the immune repertoire in COVID-19 patients with mild, severe, convalescent, or retesting-positive status. J Autoimmun 2021; 118:102596. [PMID: 33540371 PMCID: PMC7837046 DOI: 10.1016/j.jaut.2021.102596] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 01/22/2023]
Abstract
Forty-seven samples of peripheral blood mononuclear cells from four groups of coronavirus disease (COVID)-19 patients (mild, severe, convalescent, retesting-positive) and healthy controls were applied to profile the immune repertoire of COVID-19 patients in acute infection or convalescence by transcriptome sequencing and immune-receptor repertoire (IRR) sequencing. Transcriptome analyses showed that genes within principal component group 1 (PC1) were associated with infection and disease severity whereas genes within PC2 were associated with recovery from COVID-19. A "dual-injury mechanism" of COVID-19 severity was related to an increased number of proinflammatory pathways and activated hypercoagulable pathways. A machine-learning model based on the genes associated with inflammatory and hypercoagulable pathways had the potential to be employed to monitor COVID-19 severity. Signature analyses of B-cell receptors (BCRs) and T-cell receptors (TCRs) revealed the dominant selection of longer V-J pairs (e.g., IGHV3-9-IGHJ6 and IGHV3-23-IGHJ6) and continuous tyrosine motifs in BCRs and lower diversity of TCRs. These findings provide potential predictors for COVID-19 outcomes, and new potential targets for COVID-19 treatment.
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Affiliation(s)
- Yonggang Zhou
- Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China; Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Institute of Immunology, University of Science and Technology of China, Hefei, 230027, China
| | - Jinhe Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Institute of Immunology, University of Science and Technology of China, Hefei, 230027, China
| | - Dongyao Wang
- Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China; Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Institute of Immunology, University of Science and Technology of China, Hefei, 230027, China
| | - Dong Wang
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Institute of Immunology, University of Science and Technology of China, Hefei, 230027, China
| | - Wuxiang Guan
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Jingkun Qin
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Institute of Immunology, University of Science and Technology of China, Hefei, 230027, China
| | - Xiuxiu Xu
- Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China; Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Institute of Immunology, University of Science and Technology of China, Hefei, 230027, China
| | - Jingwen Fang
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang, 311200, China
| | - Binqing Fu
- Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China; Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Institute of Immunology, University of Science and Technology of China, Hefei, 230027, China
| | - Xiaohu Zheng
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Institute of Immunology, University of Science and Technology of China, Hefei, 230027, China
| | - Dongsheng Wang
- Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Hong Zhao
- Department of Infectious Diseases, Peking University First Hospital, Beijing, 100034, China
| | - Xianxiang Chen
- Department of Tuberculosis, Wuhan Pulmonary Hospital, Wuhan, 430030, China
| | - Zhigang Tian
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Institute of Immunology, University of Science and Technology of China, Hefei, 230027, China
| | - Xiaoling Xu
- Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Guiqiang Wang
- Department of Infectious Diseases, Peking University First Hospital, Beijing, 100034, China.
| | - Haiming Wei
- Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China; Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Institute of Immunology, University of Science and Technology of China, Hefei, 230027, China.
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879
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McCallum M, Marco AD, Lempp F, Tortorici MA, Pinto D, Walls AC, Beltramello M, Chen A, Liu Z, Zatta F, Zepeda S, di Iulio J, Bowen JE, Montiel-Ruiz M, Zhou J, Rosen LE, Bianchi S, Guarino B, Fregni CS, Abdelnabi R, Caroline Foo SY, Rothlauf PW, Bloyet LM, Benigni F, Cameroni E, Neyts J, Riva A, Snell G, Telenti A, Whelan SPJ, Virgin HW, Corti D, Pizzuto MS, Veesler D. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.14.426475. [PMID: 33469588 PMCID: PMC7814825 DOI: 10.1101/2021.01.14.426475] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
SARS-CoV-2 entry into host cells is orchestrated by the spike (S) glycoprotein that contains an immunodominant receptor-binding domain (RBD) targeted by the largest fraction of neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge. SARS-CoV-2 variants, including the 501Y.V2 and B.1.1.7 lineages, harbor frequent mutations localized in the NTD supersite suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs to protective immunity.
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880
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Polycarpou A, Grigoriadou S, Klavinskis L, Sacks S. Does the Lectin Complement Pathway Link Kawasaki Disease and SARS-CoV-2? Front Immunol 2021; 11:604512. [PMID: 33584675 PMCID: PMC7874141 DOI: 10.3389/fimmu.2020.604512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/14/2020] [Indexed: 12/18/2022] Open
Affiliation(s)
- Anastasia Polycarpou
- School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Sofia Grigoriadou
- Immunology Department, Royal London Hospital, Barts Health NHS Trust, London, United Kingdom
| | - Linda Klavinskis
- School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Steven Sacks
- School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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881
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Chen H, Raffaele S, Dong S. Silent control: microbial plant pathogens evade host immunity without coding sequence changes. FEMS Microbiol Rev 2021; 45:6095737. [PMID: 33440001 DOI: 10.1093/femsre/fuab002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
Both animals and plants have evolved a robust immune system to surveil and defeat invading pathogenic microbes. Evasion of host immune surveillance is the key for pathogens to initiate successful infection. To evade the host immunity, plant pathogens evolved a variety of strategies such as masking themselves from host immune recognitions, blocking immune signaling transductions, reprogramming immune responses and adapting to immune microenvironmental changes. Gain of new virulence genes, sequence and structural variations enables plant pathogens to evade host immunity through changes in the genetic code. However, recent discoveries demonstrated that variations at the transcriptional, post-transcriptional, post-translational and glycome level enable pathogens to cope with the host immune system without coding sequence changes. The biochemical modification of pathogen associated molecular patterns and silencing of effector genes emerged as potent ways for pathogens to hide from host recognition. Altered processing in mRNA activities provide pathogens with resilience to microenvironment changes. Importantly, these hiding variants are directly or indirectly modulated by catalytic enzymes or enzymatic complexes and cannot be revealed by classical genomics alone. Unveiling these novel host evasion mechanisms in plant pathogens enables us to better understand the nature of plant disease and pinpoints strategies for rational diseases management in global food protection.
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Affiliation(s)
- Han Chen
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Microorganismes, INRAE, CNRS, 24 Chemin de Borde Rouge - Auzeville, CS52627, F31326 Castanet Tolosan Cedex, France
| | - Suomeng Dong
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
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882
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Vallbracht M, Klupp BG, Mettenleiter TC. Influence of N-glycosylation on Expression and Function of Pseudorabies Virus Glycoprotein gB. Pathogens 2021; 10:61. [PMID: 33445487 PMCID: PMC7827564 DOI: 10.3390/pathogens10010061] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 01/13/2023] Open
Abstract
Envelope glycoprotein (g)B is conserved throughout the Herpesviridae and mediates fusion of the viral envelope with cellular membranes for infectious entry and spread. Like all viral envelope fusion proteins, gB is modified by asparagine (N)-linked glycosylation. Glycans can contribute to protein function, intracellular transport, trafficking, structure and immune evasion. gB of the alphaherpesvirus pseudorabies virus (PrV) contains six consensus sites for N-linked glycosylation, but their functional relevance is unknown. Here, we investigated the occupancy and functional relevance of N-glycosylation sites in PrV gB. To this end, all predicted N-glycosylation sites were inactivated either singly or in combination by the introduction of conservative mutations (N➔Q). The resulting proteins were tested for expression, fusion activity in cell-cell fusion assays and complementation of a gB-deficient PrV mutant. Our results indicate that all six sites are indeed modified. However, while glycosylation at most sites was dispensable for gB expression and fusogenicity, inactivation of N154 and N700 affected gB processing by furin cleavage and surface localization. Although all single mutants were functional in cell-cell fusion and viral entry, simultaneous inactivation of all six N-glycosylation sites severely impaired fusion activity and viral entry, suggesting a critical role of N-glycans for maintaining gB structure and function.
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Affiliation(s)
| | | | - Thomas C. Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (M.V.); (B.G.K.)
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883
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Shagufta, Ahmad I. The race to treat COVID-19: Potential therapeutic agents for the prevention and treatment of SARS-CoV-2. Eur J Med Chem 2021; 213:113157. [PMID: 33486200 PMCID: PMC7802596 DOI: 10.1016/j.ejmech.2021.113157] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/10/2020] [Accepted: 01/02/2021] [Indexed: 12/13/2022]
Abstract
The unforeseen emergence of coronavirus disease 2019 (COVID-19), a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the Wuhan province of China in December 2019, subsequently its abrupt spread across the world has severely affected human life. In a short span of time, COVID-19 has sacked more than one million human lives and marked as a severe global pandemic, which is drastically accountable for the adverse effect directly to the human society, particularly the health care system and the economy. The unavailability of approved and effective drugs or vaccines against COVID-19 further created conditions more adverse and terrifying. To win the war against this pandemic within time there is a desperate need for the most adequate therapeutic treatment, which can be achieved by the collaborative research work among scientists worldwide. In continuation of our efforts to support the scientific community, a review has been presented which discusses the structure and the activity of numerous molecules exhibiting promising SARS-CoV-2 and other CoVs inhibition activities. Furthermore, this review offers an overview of the structure, a plausible mechanism of action of SARS-CoV-2, and crucial structural features substantial to inhibit the primary virus-based and host-based targets involved in SARS-CoV-2 treatment. We anticipate optimistically that this perspective will provide the reader and researcher’s better understanding regarding COVID-19 and pave the path in the direction of COVID-19 drug discovery and development paradigm.
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Affiliation(s)
- Shagufta
- Department of Mathematics and Natural Sciences, School of Arts and Sciences, American University of Ras Al Khaimah, Ras Al Khaimah, United Arab Emirates.
| | - Irshad Ahmad
- Department of Mathematics and Natural Sciences, School of Arts and Sciences, American University of Ras Al Khaimah, Ras Al Khaimah, United Arab Emirates
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884
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Affiliation(s)
- Tobias
P. Wörner
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Tatiana M. Shamorkina
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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885
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Mészáros B, Sámano-Sánchez H, Alvarado-Valverde J, Čalyševa J, Martínez-Pérez E, Alves R, Shields DC, Kumar M, Rippmann F, Chemes LB, Gibson TJ. Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications. Sci Signal 2021; 14:eabd0334. [PMID: 33436497 PMCID: PMC7928535 DOI: 10.1126/scisignal.abd0334] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022]
Abstract
The first reported receptor for SARS-CoV-2 on host cells was the angiotensin-converting enzyme 2 (ACE2). However, the viral spike protein also has an RGD motif, suggesting that cell surface integrins may be co-receptors. We examined the sequences of ACE2 and integrins with the Eukaryotic Linear Motif (ELM) resource and identified candidate short linear motifs (SLiMs) in their short, unstructured, cytosolic tails with potential roles in endocytosis, membrane dynamics, autophagy, cytoskeleton, and cell signaling. These SLiM candidates are highly conserved in vertebrates and may interact with the μ2 subunit of the endocytosis-associated AP2 adaptor complex, as well as with various protein domains (namely, I-BAR, LC3, PDZ, PTB, and SH2) found in human signaling and regulatory proteins. Several motifs overlap in the tail sequences, suggesting that they may act as molecular switches, such as in response to tyrosine phosphorylation status. Candidate LC3-interacting region (LIR) motifs are present in the tails of integrin β3 and ACE2, suggesting that these proteins could directly recruit autophagy components. Our findings identify several molecular links and testable hypotheses that could uncover mechanisms of SARS-CoV-2 attachment, entry, and replication against which it may be possible to develop host-directed therapies that dampen viral infection and disease progression. Several of these SLiMs have now been validated to mediate the predicted peptide interactions.
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Affiliation(s)
- Bálint Mészáros
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
| | - Hugo Sámano-Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Jesús Alvarado-Valverde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Jelena Čalyševa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Elizabeth Martínez-Pérez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Laboratorio de bioinformática estructural, Fundación Instituto Leloir, C1405BWE Buenos Aires, Argentina
| | - Renato Alves
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Denis C Shields
- School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
| | - Friedrich Rippmann
- Computational Chemistry & Biology, Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Lucía B Chemes
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde", IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de San Martín, CP1650 San Martín, Buenos Aires, Argentina.
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
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886
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Herrera N, Morano NC, Celikgil A, Georgiev GI, Malonis RJ, Lee JH, Tong K, Vergnolle O, Massimi AB, Yen LY, Noble AJ, Kopylov M, Bonanno JB, Garrett-Thomson SC, Hayes DB, Bortz RH, Wirchnianski AS, Florez C, Laudermilch E, Haslwanter D, Fels JM, Dieterle ME, Jangra RK, Barnhill J, Mengotto A, Kimmel D, Daily JP, Pirofski LA, Chandran K, Brenowitz M, Garforth SJ, Eng ET, Lai JR, Almo SC. Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis. ACS OMEGA 2021; 6:85-102. [PMID: 33458462 PMCID: PMC7771249 DOI: 10.1021/acsomega.0c03512] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/03/2020] [Indexed: 05/22/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a global health crisis caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and there is a critical need to produce large quantities of high-quality SARS-CoV-2 Spike (S) protein for use in both clinical and basic science settings. To address this need, we have evaluated the expression and purification of two previously reported S protein constructs in Expi293F and ExpiCHO-S cells, two different cell lines selected for increased protein expression. We show that ExpiCHO-S cells produce enhanced yields of both SARS-CoV-2 S proteins. Biochemical, biophysical, and structural (cryo-EM) characterizations of the SARS-CoV-2 S proteins produced in both cell lines demonstrate that the reported purification strategy yields high-quality S protein (nonaggregated, uniform material with appropriate biochemical and biophysical properties), and analysis of 20 deposited S protein cryo-EM structures reveals conformation plasticity in the region composed of amino acids 614-642 and 828-854. Importantly, we show that multiple preparations of these two recombinant S proteins from either cell line exhibit identical behavior in two different serology assays. We also evaluate the specificity of S protein-mediated host cell binding by examining interactions with proposed binding partners in the human secretome and report no novel binding partners and notably fail to validate the Spike:CD147 interaction. In addition, the antigenicity of these proteins is demonstrated by standard ELISAs and in a flexible protein microarray format. Collectively, we establish an array of metrics for ensuring the production of high-quality S protein to support clinical, biological, biochemical, structural, and mechanistic studies to combat the global pandemic caused by SARS-CoV-2.
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Affiliation(s)
- Natalia
G. Herrera
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Nicholas C. Morano
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Alev Celikgil
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - George I. Georgiev
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Ryan J. Malonis
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - James H. Lee
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Karen Tong
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Olivia Vergnolle
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Aldo B. Massimi
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Laura Y. Yen
- National
Resource for Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave., New York, New York 10027, United States
| | - Alex J. Noble
- National
Resource for Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave., New York, New York 10027, United States
| | - Mykhailo Kopylov
- National
Resource for Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave., New York, New York 10027, United States
| | - Jeffrey B. Bonanno
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Sarah C. Garrett-Thomson
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - David B. Hayes
- International
Solidarity of Scientists LLC, 9 Chuck Wagon Lane, Danbury, Connecticut 06810, United States
| | - Robert H. Bortz
- Department
of Microbiology and Immunology, Albert Einstein
College of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Ariel S. Wirchnianski
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
- Department
of Microbiology and Immunology, Albert Einstein
College of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Catalina Florez
- Department
of Microbiology and Immunology, Albert Einstein
College of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
- Department
of Chemistry and Life Science, United States
Military Academy at West Point, 646 Swift Road, West Point, New York 10996, United States
| | - Ethan Laudermilch
- Department
of Microbiology and Immunology, Albert Einstein
College of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Denise Haslwanter
- Department
of Microbiology and Immunology, Albert Einstein
College of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - J. Maximilian Fels
- Department
of Microbiology and Immunology, Albert Einstein
College of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - M. Eugenia Dieterle
- Department
of Microbiology and Immunology, Albert Einstein
College of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Rohit K. Jangra
- Department
of Microbiology and Immunology, Albert Einstein
College of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Jason Barnhill
- Department
of Chemistry and Life Science, United States
Military Academy at West Point, 646 Swift Road, West Point, New York 10996, United States
| | - Amanda Mengotto
- Division
of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, New York, New York 10461, United States
| | - Duncan Kimmel
- Division
of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, New York, New York 10461, United States
| | - Johanna P. Daily
- Department
of Microbiology and Immunology, Albert Einstein
College of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
- Division
of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, New York, New York 10461, United States
| | - Liise-anne Pirofski
- Department
of Microbiology and Immunology, Albert Einstein
College of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
- Division
of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, New York, New York 10461, United States
| | - Kartik Chandran
- Department
of Microbiology and Immunology, Albert Einstein
College of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Michael Brenowitz
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Scott J. Garforth
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Edward T. Eng
- National
Resource for Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave., New York, New York 10027, United States
| | - Jonathan R. Lai
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
| | - Steven C. Almo
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Ave., Bronx, New York 10461, United
States
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887
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Huang K, Lin M, Kuo T, Chen C, Lin C, Chou Y, Chao T, Pang Y, Kao H, Huang R, Lin S, Chang S, Yang P. Humanized COVID-19 decoy antibody effectively blocks viral entry and prevents SARS-CoV-2 infection. EMBO Mol Med 2021; 13:e12828. [PMID: 33159417 PMCID: PMC7799362 DOI: 10.15252/emmm.202012828] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 12/17/2022] Open
Abstract
To circumvent the devastating pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, a humanized decoy antibody (ACE2-Fc fusion protein) was designed to target the interaction between viral spike protein and its cellular receptor, angiotensin-converting enzyme 2 (ACE2). First, we demonstrated that ACE2-Fc could specifically abrogate virus replication by blocking the entry of SARS-CoV-2 spike-expressing pseudotyped virus into both ACE2-expressing lung cells and lung organoids. The impairment of viral entry was not affected by virus variants, since efficient inhibition was also observed in six SARS-CoV-2 clinical strains, including the D614G variants which have been shown to exhibit increased infectivity. The preservation of peptidase activity also enables ACE2-Fc to reduce the angiotensin II-mediated cytokine cascade. Furthermore, this Fc domain of ACE2-Fc was shown to activate NK cell degranulation after co-incubation with Spike-expressing H1975 cells. These promising characteristics potentiate the therapeutic prospects of ACE2-Fc as an effective treatment for COVID-19.
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Affiliation(s)
- Kuo‐Yen Huang
- Institute of Biomedical SciencesAcademia SinicaTaipeiTaiwan
| | - Ming‐Shiu Lin
- Institute of Biomedical SciencesAcademia SinicaTaipeiTaiwan
| | - Ting‐Chun Kuo
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Ci‐Ling Chen
- Institute of Biomedical SciencesAcademia SinicaTaipeiTaiwan
| | - Chung‐Chih Lin
- Institute of Biomedical SciencesAcademia SinicaTaipeiTaiwan
| | - Yu‐Chi Chou
- Biomedical Translation Research Center (BioTReC)Academia SinicaTaipeiTaiwan
| | - Tai‐Ling Chao
- Department of Clinical Laboratory Sciences and Medical BiotechnologyNational Taiwan University College of MedicineTaipeiTaiwan
| | - Yu‐Hao Pang
- Department of Clinical Laboratory Sciences and Medical BiotechnologyNational Taiwan University College of MedicineTaipeiTaiwan
| | - Han‐Chieh Kao
- Department of Clinical Laboratory Sciences and Medical BiotechnologyNational Taiwan University College of MedicineTaipeiTaiwan
| | - Rih‐Sheng Huang
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
| | - Steven Lin
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
- Institute of Biochemical SciencesNational Taiwan UniversityTaipeiTaiwan
| | - Sui‐Yuan Chang
- Department of Clinical Laboratory Sciences and Medical BiotechnologyNational Taiwan University College of MedicineTaipeiTaiwan
- Department of Laboratory MedicineNational Taiwan University HospitalTaipeiTaiwan
| | - Pan‐Chyr Yang
- Institute of Biomedical SciencesAcademia SinicaTaipeiTaiwan
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
- Genomics Research CenterAcademia SinicaTaipeiTaiwan
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888
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Oommen A, Cunningham S, Joshi L. Transcriptomic Analysis of Respiratory Tissue and Cell Line Models to Examine Glycosylation Machinery during SARS-CoV-2 Infection. Viruses 2021; 13:v13010082. [PMID: 33435561 PMCID: PMC7827443 DOI: 10.3390/v13010082] [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] [Received: 11/20/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Glycosylation, being the most abundant post-translational modification, plays a profound role affecting expression, localization and function of proteins and macromolecules in immune response to infection. Presented are the findings of a transcriptomic analysis performed using high-throughput functional genomics data from public repository to examine the altered transcription of the human glycosylation machinery in response to SARS-CoV-2 stimulus and infection. In addition to the conventional in silico functional enrichment analysis methods we also present results from the manual analysis of biomedical literature databases to bring about the biological significance of glycans and glycan-binding proteins in modulating the host immune response during SARS-CoV-2 infection. Our analysis revealed key immunomodulatory lectins, proteoglycans and glycan epitopes implicated in exerting both negative and positive downstream inflammatory signaling pathways, in addition to its vital role as adhesion receptors for SARS-CoV-2 pathogen. A hypothetical correlation of the differentially expressed human glycogenes with the altered host inflammatory response and the cytokine storm-generated in response to SARS-CoV-2 pathogen is proposed. These markers can provide novel insights into the diverse roles and functioning of glycosylation pathways modulated by SARS-CoV-2, provide avenues of stratification, treatment, and targeted approaches for COVID-19 immunity and other viral infectious agents.
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Affiliation(s)
- Anup Oommen
- Advanced Glycoscience Research Cluster (AGRC), National University of Ireland Galway, H91 TK33 Galway, Ireland; (A.O.); (S.C.)
- Centre for Research in Medical Devices (CURAM), National University of Ireland Galway, H91 TK33 Galway, Ireland
| | - Stephen Cunningham
- Advanced Glycoscience Research Cluster (AGRC), National University of Ireland Galway, H91 TK33 Galway, Ireland; (A.O.); (S.C.)
- Centre for Research in Medical Devices (CURAM), National University of Ireland Galway, H91 TK33 Galway, Ireland
| | - Lokesh Joshi
- Advanced Glycoscience Research Cluster (AGRC), National University of Ireland Galway, H91 TK33 Galway, Ireland; (A.O.); (S.C.)
- Centre for Research in Medical Devices (CURAM), National University of Ireland Galway, H91 TK33 Galway, Ireland
- Correspondence:
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889
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Su H, Zhou F, Huang Z, Ma X, Natarajan K, Zhang M, Huang Y, Su H. Molecular Insights into Small-Molecule Drug Discovery for SARS-CoV-2. Angew Chem Int Ed Engl 2021; 60:9789-9802. [PMID: 32729180 DOI: 10.1002/anie.202008835] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/28/2020] [Indexed: 01/03/2023]
Abstract
The mainstream approach to antiviral drugs against COVID-19 is to focus on key stages of the SARS-CoV-2 life cycle. The vast majority of candidates under investigation are repurposed from agents of other indications. Understanding protein-inhibitor interactions at the molecular scale will provide crucial insights for drug discovery to stop this pandemic. In this article, we summarize and analyze the most recent structural data on several viral targets in the presence of promising inhibitors for COVID-19 in the context of the perspective of modes of action (MOA) to unravel insightful mechanistic features with atomistic resolution. The targets include spike glycoprotein and various host proteases mediating the entry of the virus into the cells, viral chymotrypsin- and papain-like proteases, and RNA-dependent RNA polymerase. The main purpose of this review is to present detailed MOA analysis to inspire fresh ideas for both de novo drug design and optimization of known scaffolds to combat COVID-19.
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Affiliation(s)
- Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine, 4339 Huai-shang Road, Bengbu, Anhui, 233080, P. R. China
| | - Feng Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Ziru Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xiaohua Ma
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Minchuan Zhang
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, Singapore
| | - Yong Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
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890
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Su H, Zhou F, Huang Z, Ma X, Natarajan K, Zhang M, Huang Y, Su H. Molecular Insights into Small‐Molecule Drug Discovery for SARS‐CoV‐2. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202008835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine 4339 Huai-shang Road Bengbu Anhui 233080 P. R. China
| | - Feng Zhou
- Department of Chemistry The Hong Kong University of Science and Technology Clear Water Bay Hong Kong China
| | - Ziru Huang
- Department of Chemistry The Hong Kong University of Science and Technology Clear Water Bay Hong Kong China
| | - Xiaohua Ma
- Department of Chemistry The Hong Kong University of Science and Technology Clear Water Bay Hong Kong China
| | | | - Minchuan Zhang
- Lee Kong Chian School of Medicine Nanyang Technological University 11 Mandalay Road Singapore Singapore
| | - Yong Huang
- Department of Chemistry The Hong Kong University of Science and Technology Clear Water Bay Hong Kong China
| | - Haibin Su
- Department of Chemistry The Hong Kong University of Science and Technology Clear Water Bay Hong Kong China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) The Hong Kong University of Science and Technology Clear Water Bay Hong Kong China
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891
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Carter OWL, Xu Y, Sadler PJ. Minerals in biology and medicine. RSC Adv 2021; 11:1939-1951. [PMID: 35424161 PMCID: PMC8693805 DOI: 10.1039/d0ra09992a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/21/2020] [Indexed: 01/08/2023] Open
Abstract
Natural minerals ('stone drugs') have been used in traditional Chinese medicines for over 2000 years, but there is potential for modern-day use of inorganic minerals to combat viral infections, antimicrobial resistance, and for other areas in need of new therapies and diagnostic aids. Metal and mineral surfaces on scales from milli-to nanometres, either natural or synthetic, are patterned or can be modified with hydrophilic/hydrophobic and ionic/covalent target-recognition sites. They introduce new strategies for medical applications. Such surfaces have novel properties compared to single metal centres. Moreover, 3D mineral particles (including hybrid organo-minerals) can have reactive cavities, and some minerals have dynamic movement of metal ions, anions, and other molecules within their structures. Minerals have a unique ability to interact with viruses, microbes and macro-biomolecules through multipoint ionic and/or non-covalent contacts, with potential for novel applications in therapy and biotechnology. Investigations of mineral deposits in biology, with their often inherent heterogeneity and tendency to become chemically-modified on isolation, are highly challenging, but new methods for their study, including in intact tissues, hold promise for future advances.
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Affiliation(s)
- Oliver W L Carter
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
- MAS CDT, Senate House, University of Warwick Coventry CV4 7AL UK
| | - Yingjian Xu
- GoldenKeys High-Tech Materials Co., Ltd, Building B, Innovation & Entrepreneurship Park Guian New Area Guizhou Province 550025 China
| | - Peter J Sadler
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
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892
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Hackett WE, Zaia J. Calculating Glycoprotein Similarities From Mass Spectrometric Data. Mol Cell Proteomics 2021; 20:100028. [PMID: 32883803 PMCID: PMC8724611 DOI: 10.1074/mcp.r120.002223] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/24/2020] [Accepted: 09/03/2020] [Indexed: 12/23/2022] Open
Abstract
Complex protein glycosylation occurs through biosynthetic steps in the secretory pathway that create macro- and microheterogeneity of structure and function. Required for all life forms, glycosylation diversifies and adapts protein interactions with binding partners that underpin interactions at cell surfaces and pericellular and extracellular environments. Because these biological effects arise from heterogeneity of structure and function, it is necessary to measure their changes as part of the quest to understand nature. Quite often, however, the assumption behind proteomics that posttranslational modifications are discrete additions that can be modeled using the genome as a template does not apply to protein glycosylation. Rather, it is necessary to quantify the glycosylation distribution at each glycosite and to aggregate this information into a population of mature glycoproteins that exist in a given biological system. To date, mass spectrometric methods for assigning singly glycosylated peptides are well-established. But it is necessary to quantify glycosylation heterogeneity accurately in order to gauge the alterations that occur during biological processes. The task is to quantify the glycosylated peptide forms as accurately as possible and then apply appropriate bioinformatics algorithms to the calculation of micro- and macro-similarities. In this review, we summarize current approaches for protein quantification as they apply to this glycoprotein similarity problem.
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Affiliation(s)
- William E Hackett
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Joseph Zaia
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University, Boston, Massachusetts, USA.
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893
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Wilson IA, Stanfield RL. 50 Years of structural immunology. J Biol Chem 2021; 296:100745. [PMID: 33957119 PMCID: PMC8163984 DOI: 10.1016/j.jbc.2021.100745] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
Fifty years ago, the first landmark structures of antibodies heralded the dawn of structural immunology. Momentum then started to build toward understanding how antibodies could recognize the vast universe of potential antigens and how antibody-combining sites could be tailored to engage antigens with high specificity and affinity through recombination of germline genes (V, D, J) and somatic mutation. Equivalent groundbreaking structures in the cellular immune system appeared some 15 to 20 years later and illustrated how processed protein antigens in the form of peptides are presented by MHC molecules to T cell receptors. Structures of antigen receptors in the innate immune system then explained their inherent specificity for particular microbial antigens including lipids, carbohydrates, nucleic acids, small molecules, and specific proteins. These two sides of the immune system act immediately (innate) to particular microbial antigens or evolve (adaptive) to attain high specificity and affinity to a much wider range of antigens. We also include examples of other key receptors in the immune system (cytokine receptors) that regulate immunity and inflammation. Furthermore, these antigen receptors use a limited set of protein folds to accomplish their various immunological roles. The other main players are the antigens themselves. We focus on surface glycoproteins in enveloped viruses including SARS-CoV-2 that enable entry and egress into host cells and are targets for the antibody response. This review covers what we have learned over the past half century about the structural basis of the immune response to microbial pathogens and how that information can be utilized to design vaccines and therapeutics.
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MESH Headings
- Adaptive Immunity
- Allergy and Immunology/history
- Animals
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibody Specificity
- Antigen Presentation
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- COVID-19/immunology
- COVID-19/virology
- Crystallography/history
- Crystallography/methods
- History, 20th Century
- History, 21st Century
- Humans
- Immunity, Innate
- Protein Folding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Cytokine/chemistry
- Receptors, Cytokine/genetics
- Receptors, Cytokine/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- V(D)J Recombination
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Affiliation(s)
- Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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894
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Fadda E. Understanding the Structure and Function of Viral Glycosylation by Molecular Simulations: State-of-the-Art and Recent Case Studies. COMPREHENSIVE GLYCOSCIENCE 2021. [PMCID: PMC7834635 DOI: 10.1016/b978-0-12-819475-1.00056-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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895
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Xu C, Wang Y, Liu C, Zhang C, Han W, Hong X, Wang Y, Hong Q, Wang S, Zhao Q, Wang Y, Yang Y, Chen K, Zheng W, Kong L, Wang F, Zuo Q, Huang Z, Cong Y. Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM. SCIENCE ADVANCES 2021; 7:eabe5575. [PMID: 33277323 PMCID: PMC7775788 DOI: 10.1126/sciadv.abe5575] [Citation(s) in RCA: 271] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/04/2020] [Indexed: 05/21/2023]
Abstract
The recent outbreaks of SARS-CoV-2 pose a global health emergency. The SARS-CoV-2 trimeric spike (S) glycoprotein interacts with the human ACE2 receptor to mediate viral entry into host cells. We report the cryo-EM structures of a tightly closed SARS-CoV-2 S trimer with packed fusion peptide and an ACE2-bound S trimer at 2.7- and 3.8-Å resolution, respectively. Accompanying ACE2 binding to the up receptor-binding domain (RBD), the associated ACE2-RBD exhibits continuous swing motions. Notably, the SARS-CoV-2 S trimer appears much more sensitive to the ACE2 receptor than the SARS-CoV S trimer regarding receptor-triggered transformation from the closed prefusion state to the fusion-prone open state, potentially contributing to the superior infectivity of SARS-CoV-2. We defined the RBD T470-T478 loop and Y505 as viral determinants for specific recognition of SARS-CoV-2 RBD by ACE2. Our findings depict the mechanism of ACE2-induced S trimer conformational transitions from the ground prefusion state toward the postfusion state, facilitating development of anti-SARS-CoV-2 vaccines and therapeutics.
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Affiliation(s)
- Cong Xu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanxing Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Caixuan Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenyu Han
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Hong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qin Hong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shutian Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiaoyu Zhao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yalei Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Yang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Kaijian Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zheng
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangliang Kong
- The National Facility for Protein Science in Shanghai (NFPS), Shanghai 201210, China
| | - Fangfang Wang
- The National Facility for Protein Science in Shanghai (NFPS), Shanghai 201210, China
| | - Qinyu Zuo
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhong Huang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yao Cong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201210, China
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896
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Margolin E, Allen JD, Verbeek M, van Diepen M, Ximba P, Chapman R, Meyers A, Williamson AL, Crispin M, Rybicki E. Site-Specific Glycosylation of Recombinant Viral Glycoproteins Produced in Nicotiana benthamiana. FRONTIERS IN PLANT SCIENCE 2021; 12:709344. [PMID: 34367227 PMCID: PMC8341435 DOI: 10.3389/fpls.2021.709344] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/24/2021] [Indexed: 05/03/2023]
Abstract
There is an urgent need to establish large scale biopharmaceutical manufacturing capacity in Africa where the infrastructure for biologics production is severely limited. Molecular farming, whereby pharmaceuticals are produced in plants, offers a cheaper alternative to mainstream expression platforms, and is amenable to rapid large-scale production. However, there are several differences along the plant protein secretory pathway compared to mammalian systems, which constrain the production of complex pharmaceuticals. Viral envelope glycoproteins are important targets for immunization, yet in some cases they accumulate poorly in plants and may not be properly processed. Whilst the co-expression of human chaperones and furin proteases has shown promise, it is presently unclear how plant-specific differences in glycosylation impact the production of these proteins. In many cases it may be necessary to reproduce features of their native glycosylation to produce immunologically relevant vaccines, given that glycosylation is central to the folding and immunogenicity of these antigens. Building on previous work, we transiently expressed model glycoproteins from HIV and Marburg virus in Nicotiana benthamiana and mammalian cells. The proteins were purified and their site-specific glycosylation was determined by mass-spectrometry. Both glycoproteins yielded increased amounts of protein aggregates when produced in plants compared to the equivalent mammalian cell-derived proteins. The glycosylation profiles of the plant-produced glycoproteins were distinct from the mammalian cell produced proteins: they displayed lower levels of glycan occupancy, reduced complex glycans and large amounts of paucimannosidic structures. The elucidation of the site-specific glycosylation of viral glycoproteins produced in N. benthamiana is an important step toward producing heterologous viral glycoproteins in plants with authentic human-like glycosylation.
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Affiliation(s)
- Emmanuel Margolin
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
- *Correspondence: Emmanuel Margolin,
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Matthew Verbeek
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Michiel van Diepen
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Phindile Ximba
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Rosamund Chapman
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ann Meyers
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Anna-Lise Williamson
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
- Max Crispin,
| | - Edward Rybicki
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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897
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Segreto R, Deigin Y, McCairn K, Sousa A, Sirotkin D, Sirotkin K, Couey JJ, Jones A, Zhang D. Should we discount the laboratory origin of COVID-19? ENVIRONMENTAL CHEMISTRY LETTERS 2021; 19:2743-2757. [PMID: 33786037 PMCID: PMC7993900 DOI: 10.1007/s10311-021-01211-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Rossana Segreto
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | | | | | - Alejandro Sousa
- Regional Hospital of Monforte, Lugo, Spain
- University of Santiago de Compostela, Santiago, Spain
| | | | | | | | - Adrian Jones
- Independent Bioinformatics Researcher, Melbourne, Australia
| | - Daoyu Zhang
- Independent Genetics Researcher, Sydney, Australia
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898
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Grenga L, Armengaud J. Proteomics in the COVID-19 Battlefield: First Semester Check-Up. Proteomics 2021; 21:e2000198. [PMID: 33236484 PMCID: PMC7744874 DOI: 10.1002/pmic.202000198] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/09/2020] [Indexed: 12/11/2022]
Abstract
Proteomics offers a wide collection of methodologies to study biological systems at the finest granularity. Faced with COVID-19, the most worrying pandemic in a century, proteomics researchers have made significant progress in understanding how the causative virus hijacks the host's cellular machinery and multiplies exponentially, how the disease can be diagnosed, and how it develops, as well as its severity predicted. Numerous cellular targets of potential interest for the development of new antiviral drugs have been documented. Here, the most striking results obtained in the proteomics field over this first semester of the pandemic are presented. The molecular machinery of SARS-CoV-2 is much more complex than initially believed, as many post-translational modifications can occur, leading to a myriad of proteoforms and a broad heterogeneity of viral particles. The interplay of protein-protein interactions, protein abundances, and post-translational modifications has yet to be fully documented to provide a full picture of this intriguing but lethal biological threat. Proteomics has the potential to provide rapid detection of the SARS-CoV-2 virus by mass spectrometry proteotyping, and to further increase the knowledge of severe respiratory syndrome COVID-19 and its long-term health consequences.
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Affiliation(s)
- Lucia Grenga
- Université Paris‐SaclayCEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPIBagnols‐sur‐CezeF‐30200France
| | - Jean Armengaud
- Université Paris‐SaclayCEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPIBagnols‐sur‐CezeF‐30200France
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899
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Bajardi F, Altucci L, Benedetti R, Capozziello S, Sorbo MRD, Franci G, Altucci C. DNA Mutations via Chern-Simons Currents. EUROPEAN PHYSICAL JOURNAL PLUS 2021; 136:1080. [PMID: 34725629 PMCID: PMC8551353 DOI: 10.1140/epjp/s13360-021-01960-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/13/2021] [Indexed: 05/04/2023]
Abstract
We test the validity of a possible schematization of DNA structure and dynamics based on the Chern-Simons theory, that is a topological field theory mostly considered in the context of effective gravity theories. By means of the expectation value of the Wilson Loop, derived from this analogue gravity approach, we find the point-like curvature of genomic strings in KRAS human gene and COVID-19 sequences, correlating this curvature with the genetic mutations. The point-like curvature profile, obtained by means of the Chern-Simons currents, can be used to infer the position of the given mutations within the genetic string. Generally, mutations take place in the highest Chern-Simons current gradient locations and subsequent mutated sequences appear to have a smoother curvature than the initial ones, in agreement with a free energy minimization argument.
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Affiliation(s)
- Francesco Bajardi
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli“Federico II”, Compl. Univ. di Monte S. Angelo, Edificio G, Via Cinthia, 80126 Napoli, Italy
- INFN Sezione di Napoli, Compl. Univ. di Monte S. Angelo, Edificio G, Via Cinthia, 80126 Napoli, Italy
| | - Lucia Altucci
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
- Biogem “Istituto di Biologia molecolare e genetica”, 83031 Ariano Irpino, Italy
| | - Rosaria Benedetti
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - Salvatore Capozziello
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli“Federico II”, Compl. Univ. di Monte S. Angelo, Edificio G, Via Cinthia, 80126 Napoli, Italy
- INFN Sezione di Napoli, Compl. Univ. di Monte S. Angelo, Edificio G, Via Cinthia, 80126 Napoli, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Maria Rosaria Del Sorbo
- Istituto Statale d’Istruzione Superiore “Leonardo da Vinci”, via F. Turati Poggiomarino, Naples, Italy
- Dipartimento di Ingegneria Industriale, Università degli Studi di Napoli“Federico II”, Via Claudio n.21, 80125 Napoli, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, SA Italy
- Sezione Microbiologia Clinica, A.O.U. S. Giovanni di Dio e Ruggi D’Aragona, Largo Città di Ippocrate, 84131 Salerno, Italy
| | - Carlo Altucci
- INFN Sezione di Napoli, Compl. Univ. di Monte S. Angelo, Edificio G, Via Cinthia, 80126 Napoli, Italy
- Dipartimento di Scienze Biomediche Avanzate, Università degli Studi di Napoli “Federico II”, via Pansini 5, Napoli, Italy
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900
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Zhang XL, Qu H. The Role of Glycosylation in Infectious Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1325:219-237. [PMID: 34495538 DOI: 10.1007/978-3-030-70115-4_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glycosylation plays an important role in infectious diseases. Many important interactions between pathogens and hosts involve their carbohydrate structures (glycans). Glycan interactions can mediate adhesion, recognition, invasion, and immune evasion of pathogens. To date, changes in many protein N/O-linked glycosylation have been identified as biomarkers for the development of infectious diseases and cancers. In this review, we will discuss the principal findings and the roles of glycosylation of both pathogens and host cells in the context of human important infectious diseases. Understanding the role and mechanism of glycan-lectin interaction between pathogens and hosts may create a new paradigm for discovering novel glycan-based therapies that can lead to eradication or functional cure of pathogens infection.
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Affiliation(s)
- Xiao-Lian Zhang
- State Key Laboratory of Virology, Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.
| | - Haoran Qu
- State Key Laboratory of Virology, Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China
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