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Han Y, Yuan Z, Yi Z. Identification of a membrane-associated element (MAE) in the C-terminal region of SARS-CoV-2 nsp6 that is essential for viral replication. J Virol 2024; 98:e0034924. [PMID: 38639488 DOI: 10.1128/jvi.00349-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 03/29/2024] [Indexed: 04/20/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the novel coronavirus severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), has rapidly spread worldwide since its emergence in late 2019. Its ongoing evolution poses challenges for antiviral drug development. Coronavirus nsp6, a multiple-spanning transmembrane protein, participates in the biogenesis of the viral replication complex, which accommodates the viral replication-transcription complex. The roles of its structural domains in viral replication are not well studied. Herein, we predicted the structure of the SARS-CoV-2 nsp6 protein using AlphaFold2 and identified a highly folded C-terminal region (nsp6C) downstream of the transmembrane helices. The enhanced green fluorescent protein (EGFP)-fused nsp6C was found to cluster in the cytoplasm and associate with membranes. Functional mapping identified a minimal membrane-associated element (MAE) as the region from amino acids 237 to 276 (LGV-KLL), which is mainly composed of the α-helix H1 and the α-helix H2; the latter exhibits characteristics of an amphipathic helix (AH). Mutagenesis studies and membrane flotation experiments demonstrate that AH-like H2 is required for MAE-mediated membrane association. This MAE was functionally conserved across MERS-CoV, HCoV-OC43, HCoV-229E, HCoV-HKU1, and HCoV-NL63, all capable of mediating membrane association. In a SARS-CoV-2 replicon system, mutagenesis studies of H2 and replacements of H1 and H2 with their homologous counterparts demonstrated requirements of residues on both sides of the H2 and properly paired H1-H2 for MAE-mediated membrane association and viral replication. Notably, mutations I266A and K274A significantly attenuated viral replication without dramatically affecting membrane association, suggesting a dual role of the MAE in viral replication: mediating membrane association as well as participating in protein-protein interactions.IMPORTANCESevere acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) assembles a double-membrane vesicle (DMV) by the viral non-structural proteins for viral replication. Understanding the mechanisms of the DMV assembly is of paramount importance for antiviral development. Nsp6, a multiple-spanning transmembrane protein, plays an important role in the DMV biogenesis. Herein, we predicted the nsp6 structure of SARS-CoV-2 and other human coronaviruses using AlphaFold2 and identified a putative membrane-associated element (MAE) in the highly conserved C-terminal regions of nsp6. Experimentally, we verified a functionally conserved minimal MAE composed of two α-helices, the H1, and the amphipathic helix-like H2. Mutagenesis studies confirmed the requirement of H2 for MAE-mediated membrane association and viral replication and demonstrated a dual role of the MAE in viral replication, by mediating membrane association and participating in residue-specific interactions. This functionally conserved MAE may serve as a novel anti-viral target.
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Affiliation(s)
- Yuying Han
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Zhigang Yi
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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Yang R, Han P, Han P, Li D, Zhao R, Niu S, Liu K, Li S, Tian WX, Gao GF. Molecular basis of hippopotamus ACE2 binding to SARS-CoV-2. J Virol 2024; 98:e0045124. [PMID: 38591877 DOI: 10.1128/jvi.00451-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a wide range of hosts, including hippopotami, which are semi-aquatic mammals and phylogenetically closely related to Cetacea. In this study, we characterized the binding properties of hippopotamus angiotensin-converting enzyme 2 (hiACE2) to the spike (S) protein receptor binding domains (RBDs) of the SARS-CoV-2 prototype (PT) and variants of concern (VOCs). Furthermore, the cryo-electron microscopy (cryo-EM) structure of the SARS-CoV-2 PT S protein complexed with hiACE2 was resolved. Structural and mutational analyses revealed that L30 and F83, which are specific to hiACE2, played a crucial role in the hiACE2/SARS-CoV-2 RBD interaction. In addition, comparative and structural analysis of ACE2 orthologs suggested that the cetaceans may have the potential to be infected by SARS-CoV-2. These results provide crucial molecular insights into the susceptibility of hippopotami to SARS-CoV-2 and suggest the potential risk of SARS-CoV-2 VOCs spillover and the necessity for surveillance. IMPORTANCE The hippopotami are the first semi-aquatic artiodactyl mammals wherein SARS-CoV-2 infection has been reported. Exploration of the invasion mechanism of SARS-CoV-2 will provide important information for the surveillance of SARS-CoV-2 in hippopotami, as well as other semi-aquatic mammals and cetaceans. Here, we found that hippopotamus ACE2 (hiACE2) could efficiently bind to the RBDs of the SARS-CoV-2 prototype (PT) and variants of concern (VOCs) and facilitate the transduction of SARS-CoV-2 PT and VOCs pseudoviruses into hiACE2-expressing cells. The cryo-EM structure of the SARS-CoV-2 PT S protein complexed with hiACE2 elucidated a few critical residues in the RBD/hiACE2 interface, especially L30 and F83 of hiACE2 which are unique to hiACE2 and contributed to the decreased binding affinity to PT RBD compared to human ACE2. Our work provides insight into cross-species transmission and highlights the necessity for monitoring host jumps and spillover events on SARS-CoV-2 in semi-aquatic/aquatic mammals.
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Affiliation(s)
- Ruirui Yang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Pu Han
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Pengcheng Han
- School of Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Dedong Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Runchu Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Sheng Niu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Shihua Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wen-Xia Tian
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - George Fu Gao
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
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Scheim DE, Parry PI, Rabbolini DJ, Aldous C, Yagisawa M, Clancy R, Borody TJ, Hoy WE. Back to the Basics of SARS-CoV-2 Biochemistry: Microvascular Occlusive Glycan Bindings Govern Its Morbidities and Inform Therapeutic Responses. Viruses 2024; 16:647. [PMID: 38675987 PMCID: PMC11054389 DOI: 10.3390/v16040647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Consistent with the biochemistry of coronaviruses as well established over decades, SARS-CoV-2 makes its initial attachment to host cells through the binding of its spike protein (SP) to sialylated glycans (containing the monosaccharide sialic acid) on the cell surface. The virus can then slide over and enter via ACE2. SARS-CoV-2 SP attaches particularly tightly to the trillions of red blood cells (RBCs), platelets and endothelial cells in the human body, each cell very densely coated with sialic acid surface molecules but having no ACE2 or minimal ACE2. These interlaced attachments trigger the blood cell aggregation, microvascular occlusion and vascular damage that underlie the hypoxia, blood clotting and related morbidities of severe COVID-19. Notably, the two human betacoronaviruses that express a sialic acid-cleaving enzyme are benign, while the other three-SARS, SARS-CoV-2 and MERS-are virulent. RBC aggregation experimentally induced in several animal species using an injected polysaccharide caused most of the same morbidities of severe COVID-19. This glycan biochemistry is key to disentangling controversies that have arisen over the efficacy of certain generic COVID-19 treatment agents and the safety of SP-based COVID-19 vaccines. More broadly, disregard for the active physiological role of RBCs yields unreliable or erroneous reporting of pharmacokinetic parameters as routinely obtained for most drugs and other bioactive agents using detection in plasma, with whole-blood levels being up to 30-fold higher. Appreciation of the active role of RBCs can elucidate the microvascular underpinnings of other health conditions, including cardiovascular disease, and therapeutic opportunities to address them.
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Affiliation(s)
- David E. Scheim
- US Public Health Service, Commissioned Corps, Inactive Reserve, Blacksburg, VA 24060, USA
| | - Peter I. Parry
- Children’s Health Research Clinical Unit, Faculty of Medicine, The University of Queensland, South Brisbane, QLD 4101, Australia;
- Department of Psychiatry, Flinders University, Bedford Park, SA 5042, Australia
| | - David J. Rabbolini
- Kolling Institute, Faculty of Medicine and Health, The University of Sydney, St Leonards, NSW 2064, Australia
| | - Colleen Aldous
- College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa;
| | - Morimasa Yagisawa
- Satoshi Omura Memorial Research Institute, Kitasato University, Tokyo 108-8641, Japan
- Louis Pasteur Center for Medical Research, Kyoto 606-8225, Japan
| | - Robert Clancy
- Emeritus Professor, School of Medicine and Public Health, University of Newcastle, Newcastle, NE1 7RU, Australia
| | | | - Wendy E. Hoy
- Emeritus Professor of Medicine, University of Queensland, Herston, QLD 4029, Australia
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Dolliver SM, Galbraith C, Khaperskyy DA. Human Betacoronavirus OC43 Interferes with the Integrated Stress Response Pathway in Infected Cells. Viruses 2024; 16:212. [PMID: 38399988 PMCID: PMC10893100 DOI: 10.3390/v16020212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/20/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Viruses evolve many strategies to ensure the efficient synthesis of their proteins. One such strategy is the inhibition of the integrated stress response-the mechanism through which infected cells arrest translation through the phosphorylation of the alpha subunit of the eukaryotic translation initiation factor 2 (eIF2α). We have recently shown that the human common cold betacoronavirus OC43 actively inhibits eIF2α phosphorylation in response to sodium arsenite, a potent inducer of oxidative stress. In this work, we examined the modulation of integrated stress responses by OC43 and demonstrated that the negative feedback regulator of eIF2α phosphorylation GADD34 is strongly induced in infected cells. However, the upregulation of GADD34 expression induced by OC43 was independent from the activation of the integrated stress response and was not required for the inhibition of eIF2α phosphorylation in virus-infected cells. Our work reveals a complex interplay between the common cold coronavirus and the integrated stress response, in which efficient viral protein synthesis is ensured by the inhibition of eIF2α phosphorylation but the GADD34 negative feedback loop is disrupted.
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Affiliation(s)
| | | | - Denys A. Khaperskyy
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
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Saunders N, Fernandez I, Planchais C, Michel V, Rajah MM, Baquero Salazar E, Postal J, Porrot F, Guivel-Benhassine F, Blanc C, Chauveau-Le Friec G, Martin A, Grzelak L, Oktavia RM, Meola A, Ahouzi O, Hoover-Watson H, Prot M, Delaune D, Cornelissen M, Deijs M, Meriaux V, Mouquet H, Simon-Lorière E, van der Hoek L, Lafaye P, Rey F, Buchrieser J, Schwartz O. TMPRSS2 is a functional receptor for human coronavirus HKU1. Nature 2023; 624:207-214. [PMID: 37879362 DOI: 10.1038/s41586-023-06761-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023]
Abstract
Four endemic seasonal human coronaviruses causing common colds circulate worldwide: HKU1, 229E, NL63 and OC43 (ref. 1). After binding to cellular receptors, coronavirus spike proteins are primed for fusion by transmembrane serine protease 2 (TMPRSS2) or endosomal cathepsins2-9. NL63 uses angiotensin-converting enzyme 2 as a receptor10, whereas 229E uses human aminopeptidase-N11. HKU1 and OC43 spikes bind cells through 9-O-acetylated sialic acid, but their protein receptors remain unknown12. Here we show that TMPRSS2 is a functional receptor for HKU1. TMPRSS2 triggers HKU1 spike-mediated cell-cell fusion and pseudovirus infection. Catalytically inactive TMPRSS2 mutants do not cleave HKU1 spike but allow pseudovirus infection. Furthermore, TMPRSS2 binds with high affinity to the HKU1 receptor binding domain (Kd 334 and 137 nM for HKU1A and HKU1B genotypes) but not to SARS-CoV-2. Conserved amino acids in the HKU1 receptor binding domain are essential for binding to TMPRSS2 and pseudovirus infection. Newly designed anti-TMPRSS2 nanobodies potently inhibit HKU1 spike attachment to TMPRSS2, fusion and pseudovirus infection. The nanobodies also reduce infection of primary human bronchial cells by an authentic HKU1 virus. Our findings illustrate the various evolution strategies of coronaviruses, which use TMPRSS2 to either directly bind to target cells or prime their spike for membrane fusion and entry.
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Affiliation(s)
- Nell Saunders
- Virus & Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | - Ignacio Fernandez
- Structural Virology Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | - Cyril Planchais
- Humoral Immunology Unit, Institut Pasteur, Université de Paris Cité, INSERM U1222, Paris, France
| | - Vincent Michel
- Pathogenesis of Vascular Infections Unit, Institut Pasteur, INSERM, Paris, France
| | - Maaran Michael Rajah
- Virus & Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | - Eduard Baquero Salazar
- Nanoimaging core, Institut Pasteur, Université de Paris Cité, INSERM U1222, Paris, France
| | - Jeanne Postal
- Virus & Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | - Francoise Porrot
- Virus & Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | | | - Catherine Blanc
- Pasteur-TheraVectys Joint Lab, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Gaëlle Chauveau-Le Friec
- Antibody Engineering Platform, C2RT, Institut Pasteur, Université de Paris Cité, CNRS UMR 3528, Paris, France
| | - Augustin Martin
- Virus & Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | - Ludivine Grzelak
- Virus & Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | - Rischa Maya Oktavia
- Structural Virology Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | - Annalisa Meola
- Structural Virology Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | - Olivia Ahouzi
- Structural Virology Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | - Hunter Hoover-Watson
- Virus & Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | - Matthieu Prot
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France
| | - Deborah Delaune
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France
- Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | - Marion Cornelissen
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Molecular Diagnostic Unit, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Martin Deijs
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Laboratory of Experimental Virology, University of Amsterdam, Amsterdam, The Netherlands
| | - Véronique Meriaux
- Antibody Engineering Platform, C2RT, Institut Pasteur, Université de Paris Cité, CNRS UMR 3528, Paris, France
| | - Hugo Mouquet
- Humoral Immunology Unit, Institut Pasteur, Université de Paris Cité, INSERM U1222, Paris, France
| | - Etienne Simon-Lorière
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France
- National Reference Center for viruses of respiratory infections, Institut Pasteur, Paris, France
| | - Lia van der Hoek
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Laboratory of Experimental Virology, University of Amsterdam, Amsterdam, The Netherlands
| | - Pierre Lafaye
- Antibody Engineering Platform, C2RT, Institut Pasteur, Université de Paris Cité, CNRS UMR 3528, Paris, France
| | - Felix Rey
- Structural Virology Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | - Julian Buchrieser
- Virus & Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France.
| | - Olivier Schwartz
- Virus & Immunity Unit, Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Paris, France.
- Vaccine Research Institute, Creteil, France.
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Hu Y, Liu K, Han P, Xu Z, Zheng A, Pan X, Jia Y, Su C, Tang L, Wu L, Bai B, Zhao X, Tian D, Chen Z, Qi J, Wang Q, Gao GF. Host range and structural analysis of bat-origin RshSTT182/200 coronavirus binding to human ACE2 and its animal orthologs. EMBO J 2023; 42:e111737. [PMID: 36519268 PMCID: PMC9877840 DOI: 10.15252/embj.2022111737] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/07/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
Bat-origin RshSTT182 and RshSTT200 coronaviruses (CoV) from Rhinolophus shameli in Southeast Asia (Cambodia) share 92.6% whole-genome identity with SARS-CoV-2 and show identical receptor-binding domains (RBDs). In this study, we determined the structure of the RshSTT182/200 receptor binding domain (RBD) in complex with human angiotensin-converting enzyme 2 (hACE2) and identified the key residues that influence receptor binding. The binding of the RshSTT182/200 RBD to ACE2 orthologs from 39 animal species, including 18 bat species, was used to evaluate its host range. The RshSTT182/200 RBD broadly recognized 21 of 39 ACE2 orthologs, although its binding affinities for the orthologs were weaker than those of the RBD of SARS-CoV-2. Furthermore, RshSTT182 pseudovirus could utilize human, fox, and Rhinolophus affinis ACE2 receptors for cell entry. Moreover, we found that SARS-CoV-2 induces cross-neutralizing antibodies against RshSTT182 pseudovirus. Taken together, these findings indicate that RshSTT182/200 can potentially infect susceptible animals, but requires further evolution to obtain strong interspecies transmission abilities like SARS-CoV-2.
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Affiliation(s)
- Yu Hu
- School of Life Sciences, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Pu Han
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Zepeng Xu
- Faculty of Health SciencesUniversity of MacauMacau SARChina
| | - Anqi Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoqian Pan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yunfei Jia
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Veterinary MedicineShanxi Agricultural UniversityJinzhongChina
| | - Chao Su
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- Department of Biomedical SciencesCity University of Hong KongHong Kong SARChina
| | - Lingfeng Tang
- Faculty of Health SciencesUniversity of MacauMacau SARChina
| | - Lili Wu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Bin Bai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Di Tian
- Center of Infectious Disease, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Zhihai Chen
- Center of Infectious Disease, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qihui Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - George F Gao
- School of Life Sciences, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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Abstract
In 2019, a new pandemic virus belonging to the betacoronavirus family emerged, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This new coronavirus appeared in Wuhan, China, and is responsible for severe respiratory pneumonia in humans, namely, coronavirus disease 2019 (COVID-19). Having infected almost 200 million people worldwide and caused more than 4.1 million deaths as of today, this new disease has raised a significant number of questions about its molecular mechanism of replication and, in particular, how infectious viral particles are produced. Although viral entry is well characterized, the full assembly steps of SARS-CoV-2 have still not been fully described. Coronaviruses, including SARS-CoV-2, have four main structural proteins, namely, the spike glycoprotein (S), the membrane glycoprotein (M), the envelope protein (E), and the nucleocapsid protein (N). All these proteins have key roles in the process of coronavirus assembly and budding. In this review, we gathered the current knowledge about betacoronavirus structural proteins involved in viral particle assembly, membrane curvature and scission, and then egress in order to suggest and question a coherent model for SARS-CoV-2 particle production and release.
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Affiliation(s)
- David Bracquemond
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS UMR9004, Montpellier, France
| | - Delphine Muriaux
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS UMR9004, Montpellier, France
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Lapp SA, Edara VV, Lu A, Lai L, Hussaini L, Chahroudi A, Anderson LJ, Suthar MS, Anderson EJ, Rostad CA. Original antigenic sin responses to Betacoronavirus spike proteins are observed in a mouse model, but are not apparent in children following SARS-CoV-2 infection. PLoS One 2021; 16:e0256482. [PMID: 34449792 PMCID: PMC8396729 DOI: 10.1371/journal.pone.0256482] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/06/2021] [Indexed: 11/19/2022] Open
Abstract
Background The effects of pre-existing endemic human coronavirus (HCoV) immunity on SARS-CoV-2 serologic and clinical responses are incompletely understood. Objectives We sought to determine the effects of prior exposure to HCoV Betacoronavirus HKU1 spike protein on serologic responses to SARS-CoV-2 spike protein after intramuscular administration in mice. We also sought to understand the baseline seroprevalence of HKU1 spike antibodies in healthy children and to measure their correlation with SARS-CoV-2 binding and neutralizing antibodies in children hospitalized with acute coronavirus disease 2019 (COVID-19) or multisystem inflammatory syndrome (MIS-C). Methods Groups of 5 mice were injected intramuscularly with two doses of alum-adjuvanted HKU1 spike followed by SARS-CoV-2 spike; or the reciprocal regimen of SARS-Cov-2 spike followed by HKU1 spike. Sera collected 21 days following each injection was analyzed for IgG antibodies to HKU1 spike, SARS-CoV-2 spike, and SARS-CoV-2 neutralization. Sera from children hospitalized with acute COVID-19, MIS-C or healthy controls (n = 14 per group) were analyzed for these same antibodies. Results Mice primed with SARS-CoV-2 spike and boosted with HKU1 spike developed high titers of SARS-CoV-2 binding and neutralizing antibodies; however, mice primed with HKU1 spike and boosted with SARS-CoV-2 spike were unable to mount neutralizing antibodies to SARS-CoV-2. HKU1 spike antibodies were detected in all children with acute COVID-19, MIS-C, and healthy controls. Although children with MIS-C had significantly higher HKU1 spike titers than healthy children (GMT 37239 vs. 7551, P = 0.012), these titers correlated positively with both SARS-CoV-2 binding (r = 0.7577, P<0.001) and neutralizing (r = 0.6201, P = 0.001) antibodies. Conclusions Prior murine exposure to HKU1 spike protein completely impeded the development of neutralizing antibodies to SARS-CoV-2, consistent with original antigenic sin. In contrast, the presence of HKU1 spike IgG antibodies in children with acute COVID-19 or MIS-C was not associated with diminished neutralizing antibody responses to SARS-CoV-2.
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Affiliation(s)
- Stacey A. Lapp
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States of America
- Center for Childhood Infections and Vaccines, Children’s Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, United States of America
| | - Venkata Viswanadh Edara
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States of America
- Center for Childhood Infections and Vaccines, Children’s Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, United States of America
- Yerkes Primate Center, Emory University, Atlanta, GA, United States of America
| | - Austin Lu
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States of America
- Center for Childhood Infections and Vaccines, Children’s Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, United States of America
| | - Lilin Lai
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States of America
- Center for Childhood Infections and Vaccines, Children’s Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, United States of America
- Yerkes Primate Center, Emory University, Atlanta, GA, United States of America
| | - Laila Hussaini
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States of America
- Center for Childhood Infections and Vaccines, Children’s Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, United States of America
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States of America
- Center for Childhood Infections and Vaccines, Children’s Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, United States of America
| | - Larry J. Anderson
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States of America
- Center for Childhood Infections and Vaccines, Children’s Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, United States of America
| | - Mehul S. Suthar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States of America
- Center for Childhood Infections and Vaccines, Children’s Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, United States of America
- Yerkes Primate Center, Emory University, Atlanta, GA, United States of America
| | - Evan J. Anderson
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States of America
- Center for Childhood Infections and Vaccines, Children’s Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, United States of America
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Christina A. Rostad
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States of America
- Center for Childhood Infections and Vaccines, Children’s Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, United States of America
- * E-mail:
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9
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Adams LE, Dinnon KH, Hou YJ, Sheahan TP, Heise MT, Baric RS. Critical ACE2 Determinants of SARS-CoV-2 and Group 2B Coronavirus Infection and Replication. mBio 2021; 12:e03149-20. [PMID: 33727353 PMCID: PMC8092278 DOI: 10.1128/mbio.03149-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
The angiotensin-converting enzyme 2 (ACE2) receptor is a major severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) host range determinant, and understanding SARS-CoV-2-ACE2 interactions will provide important insights into COVID-19 pathogenesis and animal model development. SARS-CoV-2 cannot infect mice due to incompatibility between its receptor binding domain and the murine ACE2 receptor. Through molecular modeling and empirical in vitro validation, we identified 5 key amino acid differences between murine and human ACE2 that mediate SARS-CoV-2 infection, generating a chimeric humanized murine ACE2. Additionally, we examined the ability of the humanized murine ACE2 receptor to permit infection by an additional preemergent group 2B coronavirus, WIV-1, providing evidence for the potential pan-virus capabilities of this chimeric receptor. Finally, we predicted the ability of these determinants to inform host range identification of preemergent coronaviruses by evaluating hot spot contacts between SARS-CoV-2 and additional potential host receptors. Our results identify residue determinants that mediate coronavirus receptor usage and host range for application in SARS-CoV-2 and emerging coronavirus animal model development.IMPORTANCE SARS-CoV-2 (the causative agent of COVID-19) is a major public health threat and one of two related coronaviruses that have caused epidemics in modern history. A method of screening potential infectible hosts for preemergent and future emergent coronaviruses would aid in mounting rapid response and intervention strategies during future emergence events. Here, we evaluated determinants of SARS-CoV-2 receptor interactions, identifying key changes that enable or prevent infection. The analysis detailed in this study will aid in the development of model systems to screen emergent coronaviruses as well as treatments to counteract infections.
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Affiliation(s)
- Lily E Adams
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kenneth H Dinnon
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark T Heise
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ralph S Baric
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill, North Carolina, USA
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10
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Devarakonda CKV, Meredith E, Ghosh M, Shapiro LH. Coronavirus Receptors as Immune Modulators. J Immunol 2021; 206:923-929. [PMID: 33380494 PMCID: PMC7889699 DOI: 10.4049/jimmunol.2001062] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022]
Abstract
The Coronaviridae family includes the seven known human coronaviruses (CoV) that cause mild to moderate respiratory infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1) as well as severe illness and death (MERS-CoV, SARS-CoV, SARS-CoV-2). Severe infections induce hyperinflammatory responses that are often intensified by host adaptive immune pathways to profoundly advance disease severity. Proinflammatory responses are triggered by CoV entry mediated by host cell surface receptors. Interestingly, five of the seven strains use three cell surface metallopeptidases (CD13, CD26, and ACE2) as receptors, whereas the others employ O-acetylated-sialic acid (a key feature of metallopeptidases) for entry. Why CoV evolved to use peptidases as their receptors is unknown, but the peptidase activities of the receptors are dispensable, suggesting the virus uses/benefits from other functions of these molecules. Indeed, these receptors participate in the immune modulatory pathways that contribute to the pathological hyperinflammatory response. This review will focus on the role of CoV receptors in modulating immune responses.
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Affiliation(s)
| | - Emily Meredith
- Center for Vascular Biology, University of Connecticut School of Medicine, Farmington, CT 06030
| | - Mallika Ghosh
- Center for Vascular Biology, University of Connecticut School of Medicine, Farmington, CT 06030
| | - Linda H Shapiro
- Center for Vascular Biology, University of Connecticut School of Medicine, Farmington, CT 06030
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11
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Krichel B, Bylapudi G, Schmidt C, Blanchet C, Schubert R, Brings L, Koehler M, Zenobi R, Svergun D, Lorenzen K, Madhugiri R, Ziebuhr J, Uetrecht C. Hallmarks of Alpha- and Betacoronavirus non-structural protein 7+8 complexes. Sci Adv 2021; 7:7/10/eabf1004. [PMID: 33658206 PMCID: PMC7929516 DOI: 10.1126/sciadv.abf1004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/19/2021] [Indexed: 05/02/2023]
Abstract
Coronaviruses infect many different species including humans. The last two decades have seen three zoonotic coronaviruses, with SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) causing a pandemic in 2020. Coronaviral non-structural proteins (nsps) form the replication-transcription complex (RTC). Nsp7 and nsp8 interact with and regulate the RNA-dependent RNA-polymerase and other enzymes in the RTC. However, the structural plasticity of nsp7+8 complexes has been under debate. Here, we present the framework of nsp7+8 complex stoichiometry and topology based on native mass spectrometry and complementary biophysical techniques of nsp7+8 complexes from seven coronaviruses in the genera Alpha- and Betacoronavirus including SARS-CoV-2. Their complexes cluster into three groups, which systematically form either heterotrimers or heterotetramers or both, exhibiting distinct topologies. Moreover, even at high protein concentrations, SARS-CoV-2 nsp7+8 consists primarily of heterotetramers. From these results, the different assembly paths can be pinpointed to specific residues and an assembly model proposed.
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Affiliation(s)
- Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Ganesh Bylapudi
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | | | | | | | | | - Martin Koehler
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zürich, Switzerland
| | - Dmitri Svergun
- EMBL Hamburg c/o DESY, Notkestraße 85, 22607 Hamburg, Germany
| | | | - Ramakanth Madhugiri
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.
- European XFEL GmbH, Schenefeld, Germany
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12
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Martínez YA, Guo X, Portales-Pérez DP, Rivera G, Castañeda-Delgado JE, García-Pérez CA, Enciso-Moreno JA, Lara-Ramírez EE. The analysis on the human protein domain targets and host-like interacting motifs for the MERS-CoV and SARS-CoV/CoV-2 infers the molecular mimicry of coronavirus. PLoS One 2021; 16:e0246901. [PMID: 33596252 PMCID: PMC7888644 DOI: 10.1371/journal.pone.0246901] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/28/2021] [Indexed: 12/14/2022] Open
Abstract
The MERS-CoV, SARS-CoV, and SARS-CoV-2 are highly pathogenic viruses that can cause severe pneumonic diseases in humans. Unfortunately, there is a non-available effective treatment to combat these viruses. Domain-motif interactions (DMIs) are an essential means by which viruses mimic and hijack the biological processes of host cells. To disentangle how viruses achieve this process can help to develop new rational therapies. Data mining was performed to obtain DMIs stored as regular expressions (regexp) in 3DID and ELM databases. The mined regexp information was mapped on the coronaviruses' proteomes. Most motifs on viral protein that could interact with human proteins are shared across the coronavirus species, indicating that molecular mimicry is a common strategy for coronavirus infection. Enrichment ontology analysis for protein domains showed a shared biological process and molecular function terms related to carbon source utilization and potassium channel regulation. Some of the mapped motifs were nested on B, and T cell epitopes, suggesting that it could be as an alternative way for reverse vaccinology. The information obtained in this study could be used for further theoretic and experimental explorations on coronavirus infection mechanism and development of medicines for treatment.
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Affiliation(s)
- Yamelie A. Martínez
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
- Laboratorio de Inmunología y Biología Celular y Molecular, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Xianwu Guo
- Laboratorio de Biotecnología Genómica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, México
| | - Diana P. Portales-Pérez
- Laboratorio de Inmunología y Biología Celular y Molecular, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, México
| | - Julio E. Castañeda-Delgado
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
- Cátedras-CONACYT, Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | - Carlos A. García-Pérez
- Information and Communication Technology Department (ICT), Complex Systems, Helmholtz Zentrum München, Neuherberg, Germany
| | - José A. Enciso-Moreno
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | - Edgar E. Lara-Ramírez
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
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13
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Israelow B, Song E, Mao T, Lu P, Meir A, Liu F, Alfajaro MM, Wei J, Dong H, Homer RJ, Ring A, Wilen CB, Iwasaki A. Mouse model of SARS-CoV-2 reveals inflammatory role of type I interferon signaling. J Exp Med 2020; 217:e20201241. [PMID: 32750141 PMCID: PMC7401025 DOI: 10.1084/jem.20201241] [Citation(s) in RCA: 307] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/15/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-Cov-2) has caused over 13,000,000 cases of coronavirus disease (COVID-19) with a significant fatality rate. Laboratory mice have been the stalwart of therapeutic and vaccine development; however, they do not support infection by SARS-CoV-2 due to the virus's inability to use the mouse orthologue of its human entry receptor angiotensin-converting enzyme 2 (hACE2). While hACE2 transgenic mice support infection and pathogenesis, these mice are currently limited in availability and are restricted to a single genetic background. Here we report the development of a mouse model of SARS-CoV-2 based on adeno-associated virus (AAV)-mediated expression of hACE2. These mice support viral replication and exhibit pathological findings found in COVID-19 patients. Moreover, we show that type I interferons do not control SARS-CoV-2 replication in vivo but are significant drivers of pathological responses. Thus, the AAV-hACE2 mouse model enables rapid deployment for in-depth analysis following robust SARS-CoV-2 infection with authentic patient-derived virus in mice of diverse genetic backgrounds.
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Affiliation(s)
- Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Peiwen Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Amit Meir
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT
| | - Feimei Liu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Mia Madel Alfajaro
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT
| | - Jin Wei
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT
| | - Huiping Dong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Robert J. Homer
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | - Aaron Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Craig B. Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
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14
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Rathnasinghe R, Strohmeier S, Amanat F, Gillespie VL, Krammer F, García-Sastre A, Coughlan L, Schotsaert M, Uccellini MB. Comparison of transgenic and adenovirus hACE2 mouse models for SARS-CoV-2 infection. Emerg Microbes Infect 2020; 9:2433-2445. [PMID: 33073694 PMCID: PMC7655046 DOI: 10.1080/22221751.2020.1838955] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 02/08/2023]
Abstract
Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) is currently causing a worldwide pandemic with high morbidity and mortality. Development of animal models that recapitulate important aspects of coronavirus disease 2019 (COVID-19) is critical for the evaluation of vaccines and antivirals, and understanding disease pathogenesis. SARS-CoV-2 has been shown to use the same entry receptor as SARS-CoV-1, human angiotensin-converting enzyme 2 (hACE2) [1-3]. Due to amino acid differences between murine and hACE2, inbred mouse strains fail to support high titer viral replication of SARS-CoV-2 virus. Therefore, a number of transgenic and knock-in mouse models, as well as viral vector-mediated hACE2 delivery systems have been developed. Here we compared the K18-hACE2 transgenic model to adenovirus-mediated delivery of hACE2 to the mouse lung. We show that K18-hACE2 mice replicate virus to high titers in the nasal turbinates, lung and brain, with high lethality, and cytokine/chemokine production. In contrast, adenovirus-mediated delivery results in viral replication to lower titers limited to the nasal turbinates and lung, and no clinical signs of infection. The K18-hACE2 model provides a stringent model for testing vaccines and antivirals, whereas the adenovirus delivery system has the flexibility to be used across multiple genetic backgrounds and modified mouse strains.
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Affiliation(s)
- Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Virginia L. Gillespie
- The Center for Comparative Medicine and Surgery (CCMS) Comparative Pathology Laboratory, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, The Tisch Cancer Institute, New York, NY, USA
| | - Lynda Coughlan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology and Immunology and Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, NY, USA
| | - Melissa B. Uccellini
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, NY, USA
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15
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Kosmeri C, Koumpis E, Tsabouri S, Siomou E, Makis A. Hematological manifestations of SARS-CoV-2 in children. Pediatr Blood Cancer 2020; 67:e28745. [PMID: 33009893 PMCID: PMC7646039 DOI: 10.1002/pbc.28745] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/11/2020] [Accepted: 09/18/2020] [Indexed: 12/18/2022]
Abstract
Infection from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), though mainly a respiratory disease, can impair many systems, including causing hematological complications. Lymphopenia and hypercoagulability have been reported in adults with coronavirus disease 2019 (COVID-19) and are considered markers of poor prognosis. This review summarizes the hematological findings in children with SARS-CoV-2 infection. The majority of infected children had a normal leukocyte count, while the most common white blood cell abnormality was leukopenia. Lymphopenia, which may be a marker of severe disease, was rarer in children than in adults, possibly due to their immature immune system or due to the less severe manifestation of COVID-19 in this age group. Age may have an impact, and in neonates and infants the most common abnormality was lymphocytosis. Abnormalities of red blood cells and platelets were uncommon. Anemia and hypercoagulability were reported mainly in children presenting the novel multisystem inflammatory syndrome (MIS) associated with SARS-CoV-2.
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Affiliation(s)
- Chrysoula Kosmeri
- Department of Pediatrics, Faculty of MedicineUniversity of IoanninaIoanninaGreece
| | - Epameinondas Koumpis
- Department of Internal Medicine, Faculty of MedicineUniversity of IoanninaIoanninaGreece
| | - Sophia Tsabouri
- Department of Pediatrics, Faculty of MedicineUniversity of IoanninaIoanninaGreece
| | - Ekaterini Siomou
- Department of Pediatrics, Faculty of MedicineUniversity of IoanninaIoanninaGreece
| | - Alexandros Makis
- Department of Pediatrics, Faculty of MedicineUniversity of IoanninaIoanninaGreece
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16
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Kneller DW, Galanie S, Phillips G, O'Neill HM, Coates L, Kovalevsky A. Malleability of the SARS-CoV-2 3CL M pro Active-Site Cavity Facilitates Binding of Clinical Antivirals. Structure 2020; 28:1313-1320.e3. [PMID: 33152262 PMCID: PMC7584437 DOI: 10.1016/j.str.2020.10.007] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/12/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 requires rapid development of specific therapeutics and vaccines. The main protease of SARS-CoV-2, 3CL Mpro, is an established drug target for the design of inhibitors to stop the virus replication. Repurposing existing clinical drugs can offer a faster route to treatments. Here, we report on the binding mode and inhibition properties of several inhibitors using room temperature X-ray crystallography and in vitro enzyme kinetics. The enzyme active-site cavity reveals a high degree of malleability, allowing aldehyde leupeptin and hepatitis C clinical protease inhibitors (telaprevir, narlaprevir, and boceprevir) to bind and inhibit SARS-CoV-2 3CL Mpro. Narlaprevir, boceprevir, and telaprevir are low-micromolar inhibitors, whereas the binding affinity of leupeptin is substantially weaker. Repurposing hepatitis C clinical drugs as COVID-19 treatments may be a useful option to pursue. The observed malleability of the enzyme active-site cavity should be considered for the successful design of specific protease inhibitors.
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Affiliation(s)
- Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA; National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA; Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA; National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Hugh M O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA; National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA; Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA; National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA.
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17
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Payandeh Z, Rahbar MR, Jahangiri A, Hashemi ZS, Zakeri A, Jafarisani M, Rasaee MJ, Khalili S. Design of an engineered ACE2 as a novel therapeutics against COVID-19. J Theor Biol 2020; 505:110425. [PMID: 32735992 PMCID: PMC7387268 DOI: 10.1016/j.jtbi.2020.110425] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/05/2020] [Accepted: 07/27/2020] [Indexed: 01/02/2023]
Abstract
The interaction between the angiotensin-converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of the spike protein from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a pivotal role in virus entry into the host cells. Since recombinant ACE2 protein has been suggested as an anti-SARS-CoV-2 therapeutic agent, this study was conducted to design an ACE2 protein with more desirable properties. In this regard, the amino acids with central roles in enzymatic activity of the ACE2 were substituted. Moreover, saturation mutagenesis at the interaction interface between the ACE2 and RBD was performed to increase their interaction affinity. The best mutations to increase the structural and thermal stability of the ACE2 were also selected based on B factors and mutation effects. The obtained resulted revealed that the Arg273Gln and Thr445Gly mutation have drastically reduced the binding affinity of the angiotensin-II into the active site of ACE2. The Thr27Arg mutation was determined to be the most potent mutation to increase the binding affinity. The Asp427Arg mutation was done to decrease the flexibility of the region with high B factor. The Pro451Met mutation along with the Gly448Trp mutation was predicted to increase the thermodynamic stability and thermostability of the ACE2. The designed therapeutic ACE2 would have no enzymatic activity while it could bear stronger interaction with Spike glycoprotein of the SARS-CoV-2. Moreover, decreased in vivo enzymatic degradation would be anticipated due to increased thermostability. This engineered ACE2 could be exploited as a novel therapeutic agent against COVID-19 after necessary evaluations.
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Affiliation(s)
- Zahra Payandeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Zahra Sadat Hashemi
- ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Alireza Zakeri
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Moslem Jafarisani
- Clinical Biochemistry, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Mohammad Javad Rasaee
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran.
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18
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Yan L, Zhang Y, Ge J, Zheng L, Gao Y, Wang T, Jia Z, Wang H, Huang Y, Li M, Wang Q, Rao Z, Lou Z. Architecture of a SARS-CoV-2 mini replication and transcription complex. Nat Commun 2020; 11:5874. [PMID: 33208736 PMCID: PMC7675986 DOI: 10.1038/s41467-020-19770-1] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/28/2020] [Indexed: 12/13/2022] Open
Abstract
Non-structural proteins (nsp) constitute the SARS-CoV-2 replication and transcription complex (RTC) to play a pivotal role in the virus life cycle. Here we determine the atomic structure of a SARS-CoV-2 mini RTC, assembled by viral RNA-dependent RNA polymerase (RdRp, nsp12) with a template-primer RNA, nsp7 and nsp8, and two helicase molecules (nsp13-1 and nsp13-2), by cryo-electron microscopy. Two groups of mini RTCs with different conformations of nsp13-1 are identified. In both of them, nsp13-1 stabilizes overall architecture of the mini RTC by contacting with nsp13-2, which anchors the 5'-extension of RNA template, as well as interacting with nsp7-nsp8-nsp12-RNA. Orientation shifts of nsp13-1 results in its variable interactions with other components in two forms of mini RTC. The mutations on nsp13-1:nsp12 and nsp13-1:nsp13-2 interfaces prohibit the enhancement of helicase activity achieved by mini RTCs. These results provide an insight into how helicase couples with polymerase to facilitate its function in virus replication and transcription.
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Affiliation(s)
- Liming Yan
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
| | - Ying Zhang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Ji Ge
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Litao Zheng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yan Gao
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Tao Wang
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
| | - Zhihui Jia
- Research Centre of Microbiome, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Haofeng Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yucen Huang
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
| | - Mingyu Li
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
| | - Quan Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zihe Rao
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China.
- School of Life Sciences, Tsinghua University, Beijing, China.
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Zhiyong Lou
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China.
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19
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Abstract
This Article summarizes the likely benefits of central nervous system oxidative preconditioning in the reduction of COVID-19 based on its putative pathogenesis. The current COVID-19 outbreak caused a pandemic with millions of infected patients and death cases worldwide. The clinical features of severe acute respiratory syndrome coronavirus (SARS-CoV) was initially linked with respiratory disorders, but recent studies have reported alterations of neurological and cerebrovascular functions in COVID-19 patients. The main viral infection features are related to cell death, inflammation, and cytokine generation, which can be associated with the dysregulation of redox systems or oxidative stress. However, until now, there is no available and effective therapeutic approach. Thus, it is necessary to search for care and adequate protection against the disease, especially for susceptible and vulnerable groups. Preconditioning, a well-known antioxidative stress and anti-inflammatory approach, is protective against many neurological age-related disorders. COVID-19 severity and morbidity have been observed in elderly patients. The aim of the present study is to elucidate the possible protective role of oxidative preconditioning in aged patients at high risk of developing severe COVID-19 complications.
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Affiliation(s)
- Rachid Akki
- Department
of Plant Protection, National School of
Agriculture-Meknes/ENA, BP S/40, Meknès 50001, Morocco
| | - Nada Fath
- Compared
Anatomy Unit, School of Veterinary Medicine, Hassan II Institute of Agronomy and Veterinary Medicine, Rabat 10000, Morocco
- Physiology
and Pathophysiology Laboratory, Department of Biology, Faculty of
Sciences, Mohamed V University, Rabat BP 8007.NU, Morocco
| | - Hicham Mohti
- Management
and Valorization of Natural Resources, Faculty of Sciences, Moulay Ismail University of Meknes, Meknes BP 11201, Morocco
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20
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Jin W, Zhang W, Mitra D, McCandless MG, Sharma P, Tandon R, Zhang F, Linhardt RJ. The structure-activity relationship of the interactions of SARS-CoV-2 spike glycoproteins with glucuronomannan and sulfated galactofucan from Saccharina japonica. Int J Biol Macromol 2020; 163:1649-1658. [PMID: 32979436 PMCID: PMC7513770 DOI: 10.1016/j.ijbiomac.2020.09.184] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/08/2020] [Accepted: 09/21/2020] [Indexed: 11/21/2022]
Abstract
The SARS-CoV-2 spike glycoproteins (SGPs) and human angiotensin converting enzyme 2 (ACE2) are the two key targets for the prevention and treatment of COVID-19. Host cell surface heparan sulfate (HS) is believed to interact with SARS-CoV-2 SGPs to facilitate host cell entry. In the current study, a series of polysaccharides from Saccharina japonica were prepared to investigate the structure-activity relationship on the binding abilities of polysaccharides (oligosaccharides) to pseudotype particles, including SARS-CoV-2 SGPs, and ACE2 using surface plasmon resonance. Sulfated galactofucan (SJ-D-S-H) and glucuronomannan (Gn) displayed strongly inhibited interaction between SARS-CoV-2 SGPs and heparin while showing negligible inhibition of the interaction between SARS-CoV-2 SGPs and ACE2. The IC50 values of SJ-D-S-H and Gn in blocking heparin SGP binding were 27 and 231 nM, respectively. NMR analysis showed that the structure of SJ-D-S-H featured with a backbone of 1, 3-linked α-L-Fucp residues sulfated at C4 and C2/C4 and 1, 3-linked α-L-Fucp residues sulfated at C4 and branched with 1, 6-linked β-D-galacto-biose; Gn had a backbone of alternating 1, 4-linked β-D-GlcAp residues and 1, 2-linked α-D-Manp residues. The sulfated galactofucan and glucuronomannan showed strong binding ability to SARS-CoV-2 SGPs, suggesting that these polysaccharides might be good candidates for preventing and/or treating SARS-CoV-2.
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Affiliation(s)
- Weihua Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China; Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Wenjing Zhang
- Department of Endocrinology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Dipanwita Mitra
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Martin G McCandless
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Poonam Sharma
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Ritesh Tandon
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Robert J Linhardt
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Departments of Biological Science, Chemistry and Chemical Biology and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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21
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Lin MH, Chang SC, Chiu YC, Jiang BC, Wu TH, Hsu CH. Structural, Biophysical, and Biochemical Elucidation of the SARS-CoV-2 Nonstructural Protein 3 Macro Domain. ACS Infect Dis 2020; 6:2970-2978. [PMID: 32946224 PMCID: PMC7537548 DOI: 10.1021/acsinfecdis.0c00441] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Indexed: 12/16/2022]
Abstract
The pandemic outbreak of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has threatened the global public health and economy since late December 2019. SARS-CoV-2 encodes the conserved macro domain within nonstructural protein 3, which may reverse cellular ADP-ribosylation and potentially cut the signal of a viral infection in the cell. Herein, we report that the SARS-CoV-2 macro domain was examined as a poly-ADP-ribose (ADPR) binding module and possessed mono-ADPR cleavage enzyme activity. After confirming the ADPR binding ability via a biophysical approach, the X-ray crystal structure of the SARS-CoV-2 macro domain was determined and structurally compared with those of other viruses. This study provides structural, biophysical, and biochemical bases to further evaluate the role of the SARS-CoV-2 macro domain in the host response via ADP-ribose binding but also as a potential target for drug design against COVID-19.
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Affiliation(s)
- Meng-Hsuan Lin
- Genome and Systems Biology Degree
Program, National Taiwan University and Academia
Sinica, Taipei 10617,
Taiwan
| | - San-Chi Chang
- Department of Agricultural Chemistry,
National Taiwan University, Taipei
10617, Taiwan
| | - Yi-Chih Chiu
- Genome and Systems Biology Degree
Program, National Taiwan University and Academia
Sinica, Taipei 10617,
Taiwan
| | - Bo-Chen Jiang
- Department of Agricultural Chemistry,
National Taiwan University, Taipei
10617, Taiwan
| | - Tsung-Han Wu
- Genome and Systems Biology Degree
Program, National Taiwan University and Academia
Sinica, Taipei 10617,
Taiwan
| | - Chun-Hua Hsu
- Genome and Systems Biology Degree
Program, National Taiwan University and Academia
Sinica, Taipei 10617,
Taiwan
- Department of Agricultural Chemistry,
National Taiwan University, Taipei
10617, Taiwan
- Institute of Biochemical Sciences,
National Taiwan University, Taipei
10617, Taiwan
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22
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Rydyznski Moderbacher C, Ramirez SI, Dan JM, Grifoni A, Hastie KM, Weiskopf D, Belanger S, Abbott RK, Kim C, Choi J, Kato Y, Crotty EG, Kim C, Rawlings SA, Mateus J, Tse LPV, Frazier A, Baric R, Peters B, Greenbaum J, Ollmann Saphire E, Smith DM, Sette A, Crotty S. Antigen-Specific Adaptive Immunity to SARS-CoV-2 in Acute COVID-19 and Associations with Age and Disease Severity. Cell 2020; 183:996-1012.e19. [PMID: 33010815 PMCID: PMC7494270 DOI: 10.1016/j.cell.2020.09.038] [Citation(s) in RCA: 1239] [Impact Index Per Article: 309.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/21/2020] [Accepted: 09/11/2020] [Indexed: 12/29/2022]
Abstract
Limited knowledge is available on the relationship between antigen-specific immune responses and COVID-19 disease severity. We completed a combined examination of all three branches of adaptive immunity at the level of SARS-CoV-2-specific CD4+ and CD8+ T cell and neutralizing antibody responses in acute and convalescent subjects. SARS-CoV-2-specific CD4+ and CD8+ T cells were each associated with milder disease. Coordinated SARS-CoV-2-specific adaptive immune responses were associated with milder disease, suggesting roles for both CD4+ and CD8+ T cells in protective immunity in COVID-19. Notably, coordination of SARS-CoV-2 antigen-specific responses was disrupted in individuals ≥ 65 years old. Scarcity of naive T cells was also associated with aging and poor disease outcomes. A parsimonious explanation is that coordinated CD4+ T cell, CD8+ T cell, and antibody responses are protective, but uncoordinated responses frequently fail to control disease, with a connection between aging and impaired adaptive immune responses to SARS-CoV-2.
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Affiliation(s)
- Carolyn Rydyznski Moderbacher
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Sydney I Ramirez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Kathryn M Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Simon Belanger
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Robert K Abbott
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Christina Kim
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jinyong Choi
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Yu Kato
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Eleanor G Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Cheryl Kim
- Flow Cytometry Core Facility, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Stephen A Rawlings
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Jose Mateus
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Long Ping Victor Tse
- Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Ralph Baric
- Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jason Greenbaum
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Davey M Smith
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
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23
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Kreye J, Reincke SM, Kornau HC, Sánchez-Sendin E, Corman VM, Liu H, Yuan M, Wu NC, Zhu X, Lee CCD, Trimpert J, Höltje M, Dietert K, Stöffler L, von Wardenburg N, van Hoof S, Homeyer MA, Hoffmann J, Abdelgawad A, Gruber AD, Bertzbach LD, Vladimirova D, Li LY, Barthel PC, Skriner K, Hocke AC, Hippenstiel S, Witzenrath M, Suttorp N, Kurth F, Franke C, Endres M, Schmitz D, Jeworowski LM, Richter A, Schmidt ML, Schwarz T, Müller MA, Drosten C, Wendisch D, Sander LE, Osterrieder N, Wilson IA, Prüss H. A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model. Cell 2020; 183:1058-1069.e19. [PMID: 33058755 PMCID: PMC7510528 DOI: 10.1016/j.cell.2020.09.049] [Citation(s) in RCA: 240] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 12/15/2022]
Abstract
The emergence of SARS-CoV-2 led to pandemic spread of coronavirus disease 2019 (COVID-19), manifesting with respiratory symptoms and multi-organ dysfunction. Detailed characterization of virus-neutralizing antibodies and target epitopes is needed to understand COVID-19 pathophysiology and guide immunization strategies. Among 598 human monoclonal antibodies (mAbs) from 10 COVID-19 patients, we identified 40 strongly neutralizing mAbs. The most potent mAb, CV07-209, neutralized authentic SARS-CoV-2 with an IC50 value of 3.1 ng/mL. Crystal structures of two mAbs in complex with the SARS-CoV-2 receptor-binding domain at 2.55 and 2.70 Å revealed a direct block of ACE2 attachment. Interestingly, some of the near-germline SARS-CoV-2-neutralizing mAbs reacted with mammalian self-antigens. Prophylactic and therapeutic application of CV07-209 protected hamsters from SARS-CoV-2 infection, weight loss, and lung pathology. Our results show that non-self-reactive virus-neutralizing mAbs elicited during SARS-CoV-2 infection are a promising therapeutic strategy.
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MESH Headings
- Angiotensin-Converting Enzyme 2
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Antibodies, Viral/therapeutic use
- Antigen-Antibody Reactions
- Betacoronavirus/immunology
- Betacoronavirus/metabolism
- Betacoronavirus/pathogenicity
- Binding Sites
- COVID-19
- Coronavirus Infections/drug therapy
- Coronavirus Infections/pathology
- Coronavirus Infections/virology
- Cricetinae
- Crystallography, X-Ray
- Disease Models, Animal
- Humans
- Kinetics
- Lung/immunology
- Lung/metabolism
- Lung/pathology
- Mice
- Mice, Inbred C57BL
- Molecular Dynamics Simulation
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/drug therapy
- Pneumonia, Viral/pathology
- Pneumonia, Viral/virology
- Protein Binding
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Jakob Kreye
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany.
| | - S Momsen Reincke
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Hans-Christian Kornau
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Elisa Sánchez-Sendin
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Victor Max Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jakob Trimpert
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Markus Höltje
- Institute of Integrative Neuroanatomy Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Kristina Dietert
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany; Veterinary Centre for Resistance Research, Freie Universität Berlin, 14163 Berlin, Germany
| | - Laura Stöffler
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Niels von Wardenburg
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Scott van Hoof
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Marie A Homeyer
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Julius Hoffmann
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Azza Abdelgawad
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Achim D Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Luca D Bertzbach
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Daria Vladimirova
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Lucie Y Li
- Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Institute of Integrative Neuroanatomy Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Paula Charlotte Barthel
- Institute of Integrative Neuroanatomy Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Karl Skriner
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Andreas C Hocke
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Stefan Hippenstiel
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine and I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20359 Hamburg, Germany
| | - Christiana Franke
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Matthias Endres
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Center for Stroke Research Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Excellence Cluster NeuroCure Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10785 Berlin, Germany
| | - Dietmar Schmitz
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Lara Maria Jeworowski
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Anja Richter
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Marie Luisa Schmidt
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Tatjana Schwarz
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Marcel Alexander Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Daniel Wendisch
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Leif E Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Nikolaus Osterrieder
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany.
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24
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Peters MH, Bastidas O, Kokron DS, Henze CE. Static all-atom energetic mappings of the SARS-Cov-2 spike protein and dynamic stability analysis of "Up" versus "Down" protomer states. PLoS One 2020; 15:e0241168. [PMID: 33170884 PMCID: PMC7654774 DOI: 10.1371/journal.pone.0241168] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/10/2020] [Indexed: 11/23/2022] Open
Abstract
The SARS-CoV-2 virion responsible for the current world-wide pandemic COVID-19 has a characteristic Spike protein (S) on its surface that embellishes both a prefusion state and fusion state. The prefusion Spike protein (S) is a large trimeric protein where each protomer may be in a so-called Up state or Down state, depending on the configuration of its receptor binding domain (RBD) within its distal, prefusion S1 domain. The Up state is believed to allow binding of the virion to ACE-2 receptors on human epithelial cells, whereas the Down state is believed to be relatively inactive or reduced in its binding behavior. We have performed detailed all-atom, dominant energy landscape mappings for noncovalent interactions (charge, partial charge, and van der Waals) of the SARS-CoV-2 Spike protein in its static prefusion state based on two recent and independent experimental structure publications. We included both interchain interactions and intrachain (domain) interactions in our mappings in order to determine any telling differences (different so-called “glue” points) between residues in the Up and Down state protomers. The S2 proximal, fusion domain demonstrated no appreciable energetic differences between Up and Down protomers, including interchain as well as each protomer’s intrachain, S1-S2 interactions. However, the S1 domain interactions across neighboring protomers, which include the RBD-NTD cross chain interactions, showed significant energetic differences between Up-Down and Down-Down neighboring protomers. This included, for example, a key RBD residue ARG357 in the Up-Down interaction and a three residue sequence ALA520-PRO521-ALA522, associated with a turn structure in the RBD of the Up state protomer, acting as a stabilizing interaction with the NTD of its neighbor protomer. Additionally, our intra chain dominant energy mappings within each protomer, identified a significant “glue” point or possible “latch” for the Down state protomer between the S1 subdomain, SD1, and the RBD domain of the same protomer that was completely missing in the Up state protomer analysis. Ironically, this dominant energetic interaction in the Down state protomer involved the backbone atoms of the same three residue sequence ALA520-PRO521-ALA522 of the RBD with the amino acid R-group of GLN564 in the SD1 domain. Thus, this same three residue sequence acts as a stabilizer of the RBD in the Up conformation through its interactions with its neighboring NTD chain and a kind of latch in the Down state conformation through its interactions with its own SD1 domain. The dominant interaction energy residues identified here are also conserved across reported variations of SARS-CoV-2, as well as the closely related virions SARS-Cov and the bat corona virus RatG13. We conducted preliminary molecular dynamics simulations across 0.1 μ seconds to see if this latch provided structural stability and indeed found that a single point mutation (Q564G) resulted in the latch releasing transforming the protomer from the Down to the Up state conformation. Full trimeric Spike protein studies of the same mutation across all protomers, however, did not exhibit latch release demonstrating the critical importance of interchain interactions across the S1 domain, including RBD-NTD neighboring chain interactions. Therapies aimed at disrupting these noncovalent interactions could be a viable route for the physico-chemical mitigation of this deadly virion.
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Affiliation(s)
- Michael H. Peters
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
| | - Oscar Bastidas
- College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Daniel S. Kokron
- NASA Ames Research Center, Moffett Field, California, United Sates of America
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25
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Barros R, Junior FLCC, Pereira WS, Oliveira NMN, Ramos RM. Interaction of Drug Candidates with Various SARS-CoV-2 Receptors: An in Silico Study to Combat COVID-19. J Proteome Res 2020; 19:4567-4575. [PMID: 32786890 PMCID: PMC7640951 DOI: 10.1021/acs.jproteome.0c00327] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Indexed: 12/22/2022]
Abstract
The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world, and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions are accelerating the discovery of vaccines and therapies for COVID-19. In this work, molecular docking was used to study (in silico) the interaction of 24 ligands, divided into four groups, with four SARS-CoV-2 receptors, Nsp9 replicase, main protease (Mpro), NSP15 endoribonuclease, and spike protein (S-protein) interacting with human ACE2. The results showed that the antimalarial drug Metaquine and anti-HIV antiretroviral Saquinavir interacted with all the studied receptors, indicating that they are potential candidates for multitarget drugs for COVID-19.
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Affiliation(s)
- Romulo
O. Barros
- Research
Laboratory in Information Systems, Department of Information, Environment,
Health and Food Production, Federal Institute
of Piaui, LaPeSI/IFPI, Teresina, Piaui, 64019-368, Brazil
| | - Fabio L. C. C. Junior
- Research
Laboratory in Information Systems, Department of Information, Environment,
Health and Food Production, Federal Institute
of Piaui, LaPeSI/IFPI, Teresina, Piaui, 64019-368, Brazil
| | - Wildrimak S. Pereira
- Research
Laboratory in Information Systems, Department of Information, Environment,
Health and Food Production, Federal Institute
of Piaui, LaPeSI/IFPI, Teresina, Piaui, 64019-368, Brazil
| | - Neiva M. N. Oliveira
- Research
Laboratory in Information Systems, Department of Information, Environment,
Health and Food Production, Federal Institute
of Piaui, LaPeSI/IFPI, Teresina, Piaui, 64019-368, Brazil
| | - Ricardo M. Ramos
- Research
Laboratory in Information Systems, Department of Information, Environment,
Health and Food Production, Federal Institute
of Piaui, LaPeSI/IFPI, Teresina, Piaui, 64019-368, Brazil
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26
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Achutha AS, Pushpa VL, Suchitra S. Theoretical Insights into the Anti-SARS-CoV-2 Activity of Chloroquine and Its Analogs and In Silico Screening of Main Protease Inhibitors. J Proteome Res 2020; 19:4706-4717. [PMID: 32960061 PMCID: PMC7640984 DOI: 10.1021/acs.jproteome.0c00683] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Indexed: 12/24/2022]
Abstract
Corona virus disease (COVID-19) is a dangerous disease rapidly spreading all over the world today. Currently there are no treatment options for it. Drug repurposing studies explored the potency of antimalarial drugs, chloroquine and hydroxychloroquine, against SARS-CoV-2 virus. These drugs can inhibit the viral protease, called chymotrypsin-like cysteine protease, also known as Main protease (3CLpro); hence, we studied the binding efficiencies of 4-aminoquinoline and 8-aminoquinoline analogs of chloroquine. Six compounds furnished better binding energies than chloroquine and hydroxychloroquine. The interactions with the active site residues especially with Cys145 and His41, which are involved in catalytic diad for proteolysis, make these compounds potent main protease inhibitors. A regression model correlating binding energy and the molecular descriptors for chloroquine analogs was generated with R2 = 0.9039 and Q2 = 0.8848. This model was used to screen new analogs of primaquine and molecules from the Asinex compound library. The docking and regression analysis showed these analogs to be more potent inhibitors of 3CLpro than hydroxychloroquine and primaquine. The molecular dynamic simulations of the hits were carried out to determine the binding stabilities. Finally, we propose four compounds that show drug likeness toward SARS-CoV-2 that can be further validated through in vitro and in vivo studies.
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Affiliation(s)
- A. S. Achutha
- PG
and Research Department of Chemistry, Sree
Narayana College, Kollam, Kerala 691001, India
| | - V. L. Pushpa
- PG
and Research Department of Chemistry, Sree
Narayana College, Kollam, Kerala 691001, India
| | - Surendran Suchitra
- PG
and Research Department of Chemistry, Sree
Narayana College, Kollam, Kerala 691001, India
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27
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Goh GKM, Dunker AK, Foster JA, Uversky VN. A Novel Strategy for the Development of Vaccines for SARS-CoV-2 (COVID-19) and Other Viruses Using AI and Viral Shell Disorder. J Proteome Res 2020; 19:4355-4363. [PMID: 33006287 PMCID: PMC7640981 DOI: 10.1021/acs.jproteome.0c00672] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Indexed: 12/29/2022]
Abstract
A model that predicts levels of coronavirus (CoV) respiratory and fecal-oral transmission potentials based on the shell disorder has been built using neural network (artificial intelligence, AI) analysis of the percentage of disorder (PID) in the nucleocapsid, N, and membrane, M, proteins of the inner and outer viral shells, respectively. Using primarily the PID of N, SARS-CoV-2 is grouped as having intermediate levels of both respiratory and fecal-oral transmission potentials. Related studies, using similar methodologies, have found strong positive correlations between virulence and inner shell disorder among numerous viruses, including Nipah, Ebola, and Dengue viruses. There is some evidence that this is also true for SARS-CoV-2 and SARS-CoV, which have N PIDs of 48% and 50%, and case-fatality rates of 0.5-5% and 10.9%, respectively. The underlying relationship between virulence and respiratory potentials has to do with the viral loads of vital organs and body fluids, respectively. Viruses can spread by respiratory means only if the viral loads in saliva and mucus exceed certain minima. Similarly, a patient is likelier to die when the viral load overwhelms vital organs. Greater disorder in inner shell proteins has been known to play important roles in the rapid replication of viruses by enhancing the efficiency pertaining to protein-protein/DNA/RNA/lipid bindings. This paper suggests a novel strategy in attenuating viruses involving comparison of disorder patterns of inner shells (N) of related viruses to identify residues and regions that could be ideal for mutation. The M protein of SARS-CoV-2 has one of the lowest M PID values (6%) in its family, and therefore, this virus has one of the hardest outer shells, which makes it resistant to antimicrobial enzymes in body fluid. While this is likely responsible for its greater contagiousness, the risks of creating an attenuated virus with a more disordered M are discussed.
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Affiliation(s)
| | - A. Keith Dunker
- Center
for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - James A. Foster
- Department
of Biological Sciences, University of Idaho, Moscow, Idaho 83844, United States
- Institute
for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho 83844, United States
| | - Vladimir N. Uversky
- Department
of Molecular Medicine, USF Health Byrd Alzheimer’s Research
Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33620, United States
- Laboratory
of New Methods in Biology, Institute for Biological Instrumentation
of the Russian Academy of Sciences, Federal
Research Center “Pushchino Scientific Center for Biological
Research of the Russian Academy of Sciences”, Pushchino, Moscow region 142290, Russia
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28
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Zhao Z, Bourne PE. Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery. J Proteome Res 2020; 19:4698-4705. [PMID: 32946692 PMCID: PMC7640976 DOI: 10.1021/acs.jproteome.0c00623] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Indexed: 01/18/2023]
Abstract
The coronavirus disease of 2019 (COVID-19) pandemic speaks to the need for drugs that not only are effective but also remain effective given the mutation rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To this end, we describe structural binding-site insights for facilitating COVID-19 drug design when targeting RNA-dependent RNA polymerase (RDRP), a common conserved component of RNA viruses. We combined an RDRP structure data set, including 384 RDRP PDB structures and all corresponding RDRP-ligand interaction fingerprints, thereby revealing the structural characteristics of the active sites for application to RDRP-targeted drug discovery. Specifically, we revealed the intrinsic ligand-binding modes and associated RDRP structural characteristics. Four types of binding modes with corresponding binding pockets were determined, suggesting two major subpockets available for drug discovery. We screened a drug data set of 7894 compounds against these binding pockets and presented the top-10 small molecules as a starting point in further exploring the prevention of virus replication. In summary, the binding characteristics determined here help rationalize RDRP-targeted drug discovery and provide insights into the specific binding mechanisms important for containing the SARS-CoV-2 virus.
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Affiliation(s)
- Zheng Zhao
- School
of Data Science, University of Virginia, Charlottesville, Virginia 22904, United States of America
- Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States of America
| | - Philip E. Bourne
- School
of Data Science, University of Virginia, Charlottesville, Virginia 22904, United States of America
- Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States of America
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29
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Nadeau R, Shahryari Fard S, Scheer A, Hashimoto-Roth E, Nygard D, Abramchuk I, Chung YE, Bennett SAL, Lavallée-Adam M. Computational Identification of Human Biological Processes and Protein Sequence Motifs Putatively Targeted by SARS-CoV-2 Proteins Using Protein-Protein Interaction Networks. J Proteome Res 2020; 19:4553-4566. [PMID: 33103435 PMCID: PMC7640966 DOI: 10.1021/acs.jproteome.0c00422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Indexed: 12/13/2022]
Abstract
While the COVID-19 pandemic is causing important loss of life, knowledge of the effects of the causative SARS-CoV-2 virus on human cells is currently limited. Investigating protein-protein interactions (PPIs) between viral and host proteins can provide a better understanding of the mechanisms exploited by the virus and enable the identification of potential drug targets. We therefore performed an in-depth computational analysis of the interactome of SARS-CoV-2 and human proteins in infected HEK 293 cells published by Gordon et al. (Nature2020, 583, 459-468) to reveal processes that are potentially affected by the virus and putative protein binding sites. Specifically, we performed a set of network-based functional and sequence motif enrichment analyses on SARS-CoV-2-interacting human proteins and on PPI networks generated by supplementing viral-host PPIs with known interactions. Using a novel implementation of our GoNet algorithm, we identified 329 Gene Ontology terms for which the SARS-CoV-2-interacting human proteins are significantly clustered in PPI networks. Furthermore, we present a novel protein sequence motif discovery approach, LESMoN-Pro, that identified 9 amino acid motifs for which the associated proteins are clustered in PPI networks. Together, these results provide insights into the processes and sequence motifs that are putatively implicated in SARS-CoV-2 infection and could lead to potential therapeutic targets.
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Affiliation(s)
- Rachel Nadeau
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Soroush Shahryari Fard
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Amit Scheer
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Emily Hashimoto-Roth
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Dallas Nygard
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Iryna Abramchuk
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Yun-En Chung
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Steffany A. L. Bennett
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- uOttawa Brain and Mind Research Institute, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- uOttawa Brain and Mind Research Institute, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
- Department of Chemistry and Biomolecular Sciences, Centre
for Catalysis and Research Innovation, University
of Ottawa, 150 Louis-Pasteur Pvt, Ottawa, Ontario K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
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30
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Abstract
The development of computational strategies for the quantitative characterization of the functional mechanisms of SARS-CoV-2 spike proteins is of paramount importance in efforts to accelerate the discovery of novel therapeutic agents and vaccines combating the COVID-19 pandemic. Structural and biophysical studies have recently characterized the conformational landscapes of the SARS-CoV-2 spike glycoproteins in the prefusion form, revealing a spectrum of stable and more dynamic states. By employing molecular simulations and network modeling approaches, this study systematically examined functional dynamics and identified the regulatory centers of allosteric interactions for distinct functional states of the wild-type and mutant variants of the SARS-CoV-2 prefusion spike trimer. This study presents evidence that the SARS-CoV-2 spike protein can function as an allosteric regulatory engine that fluctuates between dynamically distinct functional states. Perturbation-based modeling of the interaction networks revealed a key role of the cross-talk between the effector hotspots in the receptor binding domain and the fusion peptide proximal region of the SARS-CoV-2 spike protein. The results have shown that the allosteric hotspots of the interaction networks in the SARS-CoV-2 spike protein can control the dynamic switching between functional conformational states that are associated with virus entry to the host receptor. This study offers a useful and novel perspective on the underlying mechanisms of the SARS-CoV-2 spike protein through the lens of allosteric signaling as a regulatory apparatus of virus transmission that could open up opportunities for targeted allosteric drug discovery against SARS-CoV-2 proteins and contribute to the rapid response to the current and potential future pandemic scenarios.
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Affiliation(s)
- Gennady M. Verkhivker
- Graduate
Program in Computational and Data Sciences, 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
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31
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Gusarov S, Stoyanov SR. COSMO-RS-Based Descriptors for the Machine Learning-Enabled Screening of Nucleotide Analogue Drugs against SARS-CoV-2. J Phys Chem Lett 2020; 11:9408-9414. [PMID: 33104327 PMCID: PMC7605243 DOI: 10.1021/acs.jpclett.0c02836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/15/2020] [Indexed: 05/11/2023]
Abstract
Chemical similarity-based approaches employed to repurpose or develop new treatments for emerging diseases, such as COVID-19, correlates molecular structure-based descriptors of drugs with those of a physiological counterpart or clinical phenotype. We propose novel descriptors based on a COSMO-RS (short for conductor-like screening model for real solvents) σ-profiles for enhanced drug screening enabled by machine learning (ML). The descriptors' performance is hereby illustrated for nucleotide analogue drugs that inhibit the ribonucleic acid-dependent ribonucleic acid polymerase, key to viral transcription and genome replication. The COSMO-RS-based descriptors account for both chemical reactivity and structure, and are more effective for ML-based screening than fingerprints based on molecular structure and simple physical/chemical properties. The descriptors are evaluated using principal component analysis, an unsupervised ML technique. Our results correlate with the active monophosphate forms of the leading drug remdesivir and the prospective drug EIDD-2801 with nucleotides, followed by other promising drugs, and are superior to those from molecular structure-based descriptors and molecular docking. The COSMO-RS-based descriptors could help accelerate drug discovery for the treatment of emerging diseases.
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Affiliation(s)
- Sergey Gusarov
- National
Research Council, Nanotechnology Research Centre, 11421 Saskatchewan Drive NW, Edmonton, Alberta T6G 2M9, Canada
| | - Stanislav R. Stoyanov
- Natural
Resources Canada, CanmetENERGY Devon, 1 Oil Patch Drive, Devon, Alberta T9G 1A8, Canada
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32
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García-Iriepa C, Hognon C, Francés-Monerris A, Iriepa I, Miclot T, Barone G, Monari A, Marazzi M. Thermodynamics of the Interaction between the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus-2 and the Receptor of Human Angiotensin-Converting Enzyme 2. Effects of Possible Ligands. J Phys Chem Lett 2020; 11:9272-9281. [PMID: 33085491 PMCID: PMC7586454 DOI: 10.1021/acs.jpclett.0c02203] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/12/2020] [Indexed: 05/08/2023]
Abstract
Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 1000000 deaths all over the world and still lacks a medical treatment despite the attention of the whole scientific community. Human angiotensin-converting enzyme 2 (ACE2) was recently recognized as the transmembrane protein that serves as the point of entry of SARS-CoV-2 into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the protein complex. Moreover, the free energy of binding between ACE2 and the active receptor binding domain of the SARS-CoV-2 spike protein is evaluated quantitatively, providing for the first time the thermodynamics of virus-receptor recognition. Furthermore, the action of different ACE2 ligands is also examined in particular in their capacity to disrupt SARS-CoV-2 recognition, also providing via a free energy profile the quantification of the ligand-induced decreased affinity. These results improve our knowledge on molecular grounds of the SARS-CoV-2 infection and allow us to suggest rationales that could be useful for the subsequent wise molecular design for the treatment of COVID-19 cases.
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Affiliation(s)
- Cristina García-Iriepa
- Department of Analytical Chemistry,
Physical Chemistry and Chemical Engineering, Universidad
de Alcalá, Ctra. Madrid-Barcelona, Km
33,600, 28871 Alcalá de Henares, Madrid,
Spain
- Chemical Research Institute
“Andrés M. del Río” (IQAR),
Universidad de Alcalá, 28871
Alcalá de Henares, Madrid, Spain
| | - Cécilia Hognon
- Université de
Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy,
France
| | - Antonio Francés-Monerris
- Université de
Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy,
France
- Departament de Química
Física, Universitat de
València, 46100 Burjassot,
Spain
| | - Isabel Iriepa
- Chemical Research Institute
“Andrés M. del Río” (IQAR),
Universidad de Alcalá, 28871
Alcalá de Henares, Madrid, Spain
- Department of Organic and Inorganic
Chemistry, Universidad de Alcalá,
Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares,
Madrid, Spain
| | - Tom Miclot
- Université de
Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy,
France
- Department of Biological, Chemical and
Pharmaceutical Sciences and Technologies,
Università degli Studi di
Palermo, Viale delle Scienze, 90128 Palermo,
Italy
| | - Giampaolo Barone
- Department of Biological, Chemical and
Pharmaceutical Sciences and Technologies,
Università degli Studi di
Palermo, Viale delle Scienze, 90128 Palermo,
Italy
| | - Antonio Monari
- Université de
Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy,
France
| | - Marco Marazzi
- Department of Analytical Chemistry,
Physical Chemistry and Chemical Engineering, Universidad
de Alcalá, Ctra. Madrid-Barcelona, Km
33,600, 28871 Alcalá de Henares, Madrid,
Spain
- Chemical Research Institute
“Andrés M. del Río” (IQAR),
Universidad de Alcalá, 28871
Alcalá de Henares, Madrid, Spain
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33
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Verkhivker G. Coevolution, Dynamics and Allostery Conspire in Shaping Cooperative Binding and Signal Transmission of the SARS-CoV-2 Spike Protein with Human Angiotensin-Converting Enzyme 2. Int J Mol Sci 2020; 21:ijms21218268. [PMID: 33158276 PMCID: PMC7672574 DOI: 10.3390/ijms21218268] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023] Open
Abstract
Binding to the host receptor is a critical initial step for the coronavirus SARS-CoV-2 spike protein to enter into target cells and trigger virus transmission. A detailed dynamic and energetic view of the binding mechanisms underlying virus entry is not fully understood and the consensus around the molecular origins behind binding preferences of SARS-CoV-2 for binding with the angiotensin-converting enzyme 2 (ACE2) host receptor is yet to be established. In this work, we performed a comprehensive computational investigation in which sequence analysis and modeling of coevolutionary networks are combined with atomistic molecular simulations and comparative binding free energy analysis of the SARS-CoV and SARS-CoV-2 spike protein receptor binding domains with the ACE2 host receptor. Different from other computational studies, we systematically examine the molecular and energetic determinants of the binding mechanisms between SARS-CoV-2 and ACE2 proteins through the lens of coevolution, conformational dynamics, and allosteric interactions that conspire to drive binding interactions and signal transmission. Conformational dynamics analysis revealed the important differences in mobility of the binding interfaces for the SARS-CoV-2 spike protein that are not confined to several binding hotspots, but instead are broadly distributed across many interface residues. Through coevolutionary network analysis and dynamics-based alanine scanning, we established linkages between the binding energy hotspots and potential regulators and carriers of signal communication in the virus-host receptor complexes. The results of this study detailed a binding mechanism in which the energetics of the SARS-CoV-2 association with ACE2 may be determined by cumulative changes of a number of residues distributed across the entire binding interface. The central findings of this study are consistent with structural and biochemical data and highlight drug discovery challenges of inhibiting large and adaptive protein-protein interfaces responsible for virus entry and infection transmission.
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Affiliation(s)
- Gennady Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; ; Tel.: +1-714-516-4586
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
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34
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Klein SL, Pekosz A, Park HS, Ursin RL, Shapiro JR, Benner SE, Littlefield K, Kumar S, Naik HM, Betenbaugh MJ, Shrestha R, Wu AA, Hughes RM, Burgess I, Caturegli P, Laeyendecker O, Quinn TC, Sullivan D, Shoham S, Redd AD, Bloch EM, Casadevall A, Tobian AA. Sex, age, and hospitalization drive antibody responses in a COVID-19 convalescent plasma donor population. J Clin Invest 2020; 130:6141-6150. [PMID: 32764200 PMCID: PMC7598041 DOI: 10.1172/jci142004] [Citation(s) in RCA: 337] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023] Open
Abstract
Convalescent plasma is a leading treatment for coronavirus disease 2019 (COVID-19), but there is a paucity of data identifying its therapeutic efficacy. Among 126 potential convalescent plasma donors, the humoral immune response was evaluated using a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus neutralization assay with Vero-E6-TMPRSS2 cells; a commercial IgG and IgA ELISA to detect the spike (S) protein S1 domain (EUROIMMUN); IgA, IgG, and IgM indirect ELISAs to detect the full-length S protein or S receptor-binding domain (S-RBD); and an IgG avidity assay. We used multiple linear regression and predictive models to assess the correlations between antibody responses and demographic and clinical characteristics. IgG titers were greater than either IgM or IgA titers for S1, full-length S, and S-RBD in the overall population. Of the 126 plasma samples, 101 (80%) had detectable neutralizing antibody (nAb) titers. Using nAb titers as the reference, the IgG ELISAs confirmed 95%-98% of the nAb-positive samples, but 20%-32% of the nAb-negative samples were still IgG ELISA positive. Male sex, older age, and hospitalization for COVID-19 were associated with increased antibody responses across the serological assays. There was substantial heterogeneity in the antibody response among potential convalescent plasma donors, but sex, age, and hospitalization emerged as factors that can be used to identify individuals with a high likelihood of having strong antiviral antibody responses.
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Affiliation(s)
- Sabra L. Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology
- Department of Biochemistry and Molecular Biology
- Department of International Health, and
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Han-Sol Park
- W. Harry Feinstone Department of Molecular Microbiology and Immunology
| | | | | | - Sarah E. Benner
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | | | - Swetha Kumar
- Advanced Mammalian Biomanufacturing Innovation Center, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Harnish Mukesh Naik
- Advanced Mammalian Biomanufacturing Innovation Center, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Michael J. Betenbaugh
- Advanced Mammalian Biomanufacturing Innovation Center, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ruchee Shrestha
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Annie A. Wu
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Robert M. Hughes
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Imani Burgess
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Patricio Caturegli
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Oliver Laeyendecker
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Thomas C. Quinn
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - David Sullivan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology
| | - Shmuel Shoham
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Andrew D. Redd
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Evan M. Bloch
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Arturo Casadevall
- W. Harry Feinstone Department of Molecular Microbiology and Immunology
| | - Aaron A.R. Tobian
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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35
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Skendros P, Mitsios A, Chrysanthopoulou A, Mastellos DC, Metallidis S, Rafailidis P, Ntinopoulou M, Sertaridou E, Tsironidou V, Tsigalou C, Tektonidou M, Konstantinidis T, Papagoras C, Mitroulis I, Germanidis G, Lambris JD, Ritis K. Complement and tissue factor-enriched neutrophil extracellular traps are key drivers in COVID-19 immunothrombosis. J Clin Invest 2020; 130:6151-6157. [PMID: 32759504 PMCID: PMC7598040 DOI: 10.1172/jci141374] [Citation(s) in RCA: 499] [Impact Index Per Article: 124.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022] Open
Abstract
Emerging data indicate that complement and neutrophils contribute to the maladaptive immune response that fuels hyperinflammation and thrombotic microangiopathy, thereby increasing coronavirus 2019 (COVID-19) mortality. Here, we investigated how complement interacts with the platelet/neutrophil extracellular traps (NETs)/thrombin axis, using COVID-19 specimens, cell-based inhibition studies, and NET/human aortic endothelial cell (HAEC) cocultures. Increased plasma levels of NETs, tissue factor (TF) activity, and sC5b-9 were detected in patients. Neutrophils of patients yielded high TF expression and released NETs carrying active TF. Treatment of control neutrophils with COVID-19 platelet-rich plasma generated TF-bearing NETs that induced thrombotic activity of HAECs. Thrombin or NETosis inhibition or C5aR1 blockade attenuated platelet-mediated NET-driven thrombogenicity. COVID-19 serum induced complement activation in vitro, consistent with high complement activity in clinical samples. Complement C3 inhibition with compstatin Cp40 disrupted TF expression in neutrophils. In conclusion, we provide a mechanistic basis for a pivotal role of complement and NETs in COVID-19 immunothrombosis. This study supports strategies against severe acute respiratory syndrome coronavirus 2 that exploit complement or NETosis inhibition.
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Affiliation(s)
- Panagiotis Skendros
- First Department of Internal Medicine, University Hospital of Alexandroupolis, and
- Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Alexandros Mitsios
- Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Akrivi Chrysanthopoulou
- Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Simeon Metallidis
- First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Petros Rafailidis
- Second Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Ntinopoulou
- Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eleni Sertaridou
- Intensive Care Unit, University Hospital of Alexandroupolis, Alexandroupolis, Greece
| | - Victoria Tsironidou
- Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christina Tsigalou
- Laboratory of Microbiology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Tektonidou
- First Department of Propaedeutic Internal Medicine, National and Kapodistrian University of Athens, Greece
| | - Theocharis Konstantinidis
- Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Charalampos Papagoras
- First Department of Internal Medicine, University Hospital of Alexandroupolis, and
- Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis Mitroulis
- First Department of Internal Medicine, University Hospital of Alexandroupolis, and
- Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Georgios Germanidis
- First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - John D. Lambris
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Konstantinos Ritis
- First Department of Internal Medicine, University Hospital of Alexandroupolis, and
- Laboratory of Molecular Hematology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
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36
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Rikhtegaran Tehrani Z, Saadat S, Saleh E, Ouyang X, Constantine N, DeVico AL, Harris AD, Lewis GK, Kottilil S, Sajadi MM. Performance of nucleocapsid and spike-based SARS-CoV-2 serologic assays. PLoS One 2020; 15:e0237828. [PMID: 33137138 PMCID: PMC7605638 DOI: 10.1371/journal.pone.0237828] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/15/2020] [Indexed: 01/14/2023] Open
Abstract
There is an urgent need for an accurate antibody test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We have developed 3 ELISA methods, trimer spike IgA, trimer spike IgG, and nucleocapsid IgG, for detecting anti-SARS-CoV-2 antibodies. We evaluated their performance along with four commercial ELISAs, EDI™ Novel Coronavirus COVID-19 ELISA IgG and IgM, Euroimmun Anti-SARS-CoV-2 ELISA IgG and IgA, and one lateral flow assay, DPP® COVID-19 IgM/IgG System (Chembio). Both sensitivity and specificity were evaluated and the probable causes of false-positive reactions were determined. The assays were evaluated using 300 pre-epidemic samples and 100 PCR-confirmed COVID-19 samples. The sensitivities and specificities of the assays were as follows: 90%/100% (in-house trimer spike IgA), 90%/99.3% (in-house trimer spike IgG), 89%/98.3% (in-house nucleocapsid IgG), 73.7%/100% (EDI nucleocapsid IgM), 84.5%/95.1% (EDI nucleocapsid IgG), 95%/93.7% (Euroimmun S1 IgA), 82.8%/99.7% (Euroimmun S1 IgG), 82.0%/91.7% (Chembio nucleocapsid IgM), 92%/93.3% (Chembio nucleocapsid IgG). The presumed causes of false positive results from pre-epidemic samples in commercial and in-house assays were mixed. In some cases, assays lacked reproducibility. In other cases, reactivity was abrogated by competitive inhibition (spiking the sample with the same antigen that was used for coating ELISAs prior to performing the assay), suggesting positive reaction could be attributed to the presence of antibodies against these antigens. In other cases, reactivity was consistently detected but not abrogated by the spiking, suggesting positive reaction was not attributed to the presence of antibodies against these antigens. Overall, there was wide variability in assay performance using our samples, with in-house tests exhibiting the highest combined sensitivity and specificity. The causes of "false positivity" in pre-epidemic samples may be due to plasma antibodies apparently reacting with the corresponding antigen, or spurious reactivity may be directed against non-specific components in the assay system. Identification of these targets will be essential to improving assay performance.
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Affiliation(s)
- Zahra Rikhtegaran Tehrani
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland, Baltimore, Maryland, United States of America
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Saman Saadat
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland, Baltimore, Maryland, United States of America
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Ebtehal Saleh
- Division of Epidemiology & Prevention, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Xin Ouyang
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland, Baltimore, Maryland, United States of America
| | - Niel Constantine
- Division of Epidemiology & Prevention, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Anthony L. DeVico
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Anthony D. Harris
- Department of Epidemiology and Public Health, University of Maryland School of Medicine Baltimore, Maryland, United States of America
| | - George K. Lewis
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Shyam Kottilil
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland, Baltimore, Maryland, United States of America
| | - Mohammad M. Sajadi
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland, Baltimore, Maryland, United States of America
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, Baltimore VA Medical Center, Baltimore, Maryland, United States of America
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37
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Barh D, Tiwari S, Weener ME, Azevedo V, Góes-Neto A, Gromiha MM, Ghosh P. Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19. Comput Biol Med 2020; 126:104051. [PMID: 33131530 PMCID: PMC7547373 DOI: 10.1016/j.compbiomed.2020.104051] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 has ushered a global pandemic with no effective drug being available at present. Although several FDA-approved drugs are currently under clinical trials for drug repositioning, there is an on-going global effort for new drug identification. In this paper, using multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis, we present the biological events associated with SARS-CoV-2 infection and identify several candidate drugs against this viral disease. We found that: (i) Interactome-based infection pathways differ from the other three omics-based profiles. (ii) Viral process, mRNA splicing, cytokine and interferon signaling, and ubiquitin mediated proteolysis are important pathways in SARS-CoV-2 infection. (iii) SARS-CoV-2 infection also shares pathways with Influenza A, Epstein-Barr virus, HTLV-I, Measles, and Hepatitis virus. (iv) Further, bacterial, parasitic, and protozoan infection pathways such as Tuberculosis, Malaria, and Leishmaniasis are also shared by this virus. (v) A total of 50 candidate drugs, including the prophylaxis agents and pathway specific inhibitors are identified against COVID-19. (vi) Betamethasone, Estrogen, Simvastatin, Hydrocortisone, Tositumomab, Cyclosporin A etc. are among the important drugs. (vii) Ozone, Nitric oxide, plasma components, and photosensitizer drugs are also identified as possible therapeutic candidates. (viii) Curcumin, Retinoic acids, Vitamin D, Arsenic, Copper, and Zinc may be the candidate prophylaxis agents. Nearly 70% of our identified agents are previously suggested to have anti-COVID-19 effects or under clinical trials. Among our identified drugs, the ones that are not yet tested, need validation with caution while an appropriate drug combination from these candidate drugs along with a SARS-CoV-2 specific antiviral agent is needed for effective COVID-19 management.
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Affiliation(s)
- Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India.
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marianna E Weener
- Clinical Research Center, Oftalmic, CRO, 119334, Bardina Str.22/4, Moscow, Russia
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aristóteles Góes-Neto
- Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IIT-M), Chennai, 600036, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
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Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 originated from Wuhan, China, in December 2019 and rapidly spread to other areas worldwide. Since then, coronavirus disease 2019 (COVID-19) has reached pandemic proportions with >570 000 deaths globally by mid-July 2020. The magnitude of the outbreak and the potentially severe clinical course of COVID-19 has led to a burst of scientific research on this novel coronavirus and its host receptor ACE (angiotensin-converting enzyme)-2. ACE2 is a homolog of the ACE that acts on several substrates in the renin-Ang (angiotensin) system. With unprecedented speed, scientific research has solved the structure of SARS-CoV-2 and imaged its binding with the ACE2 receptor. In SARS-CoV-2 infection, the viral S (spike) protein receptor-binding domain binds to ACE2 to enter the host cell. ACE2 expression in the lungs is relatively low, but it is present in type II pneumocytes-a cell type also endowed with TMPRSS2 (transmembrane protease serine 2). This protease is critical for priming the SARS-CoV-2 S protein to complex with ACE2 and enter the cells. Herein, we review the current understanding of the interaction of SARS-CoV-2 with ACE2 as it has rapidly unfolded over the last months. While it should not be assumed that we have a complete picture of SARS-CoV-2 mechanism of infection and its interaction with ACE2, much has been learned with clear therapeutic implications. Potential therapies aimed at intercepting SARS-CoV-2 from reaching the full-length membrane-bound ACE2 receptor using soluble ACE2 protein and other potential approaches are briefly discussed as well.
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Affiliation(s)
- Anne M. Davidson
- From the Division of Nephrology and Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Jan Wysocki
- From the Division of Nephrology and Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Daniel Batlle
- From the Division of Nephrology and Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
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39
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Boni MF, Lemey P, Jiang X, Lam TTY, Perry BW, Castoe TA, Rambaut A, Robertson DL. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol 2020; 5:1408-1417. [PMID: 32724171 DOI: 10.1101/2020.03.30.015008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/10/2020] [Indexed: 05/22/2023]
Abstract
There are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination and its time of divergence from animal viruses. We find that the sarbecoviruses-the viral subgenus containing SARS-CoV and SARS-CoV-2-undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor-binding motif, important for specificity to human ACE2 receptors, appears to be an ancestral trait shared with bat viruses and not one acquired recently via recombination. To employ phylogenetic dating methods, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were shown to be consistent for these three approaches and for two different prior specifications of evolutionary rates based on HCoV-OC43 and MERS-CoV. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% highest posterior density (HPD): 1879-1999), 1969 (95% HPD: 1930-2000) and 1982 (95% HPD: 1948-2009), indicating that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades.
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Affiliation(s)
- Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA.
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Leuven, Belgium.
| | - Xiaowei Jiang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Blair W Perry
- Department of Biology, University of Texas Arlington, Arlington, TX, USA
| | - Todd A Castoe
- Department of Biology, University of Texas Arlington, Arlington, TX, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
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40
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Dores-Silva PR, Cauvi DM, Coto ALS, Kiraly VTR, Borges JC, De Maio A. Interaction of HSPA5 (Grp78, BIP) with negatively charged phospholipid membranes via oligomerization involving the N-terminal end domain. Cell Stress Chaperones 2020; 25:979-991. [PMID: 32725381 PMCID: PMC7385938 DOI: 10.1007/s12192-020-01134-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/25/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023] Open
Abstract
Heat shock proteins (HSPs) are ubiquitous polypeptides expressed in all living organisms that participate in several basic cellular processes, including protein folding, from which their denomination as molecular chaperones originated. There are several HSPs, including HSPA5, also known as 78-kDa glucose-regulated protein (GRP78) or binding immunoglobulin protein (BIP) that is an ER resident involved in the folding of polypeptides during their translocation into this compartment prior to the transition to the Golgi network. HSPA5 is detected on the surface of cells or secreted into the extracellular environment. Surface HSPA5 has been proposed to have various roles, such as receptor-mediated signal transduction, a co-receptor for soluble ligands, as well as a participant in tumor survival, proliferation, and resistance. Recently, surface HSPA5 has been reported to be a potential receptor of some viruses, including the novel SARS-CoV-2. In spite of these observations, the association of HSPA5 within the plasma membrane is still unclear. To gain information about this process, we studied the interaction of HSPA5 with liposomes made of different phospholipids. We found that HSPA5 has a high affinity for negatively charged phospholipids, such as palmitoyl-oleoyl phosphoserine (POPS) and cardiolipin (CL). The N-terminal and C-terminal domains of HSPA5 were independently capable of interacting with negatively charged phospholipids, but to a lesser extent than the full-length protein, suggesting that both domains are required for the maximum insertion into membranes. Interestingly, we found that the interaction of HSPA5 with negatively charged liposomes promotes an oligomerization process via intermolecular disulfide bonds in which the N-terminus end of the protein plays a critical role.
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Affiliation(s)
- Paulo Roberto Dores-Silva
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- São Carlos Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - David M Cauvi
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Amanda L S Coto
- São Carlos Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Vanessa T R Kiraly
- São Carlos Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Júlio C Borges
- São Carlos Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Antonio De Maio
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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41
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Tung HYL, Limtung P. Mutations in the phosphorylation sites of SARS-CoV-2 encoded nucleocapsid protein and structure model of sequestration by protein 14-3-3. Biochem Biophys Res Commun 2020; 532:134-138. [PMID: 32829876 PMCID: PMC7428706 DOI: 10.1016/j.bbrc.2020.08.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/11/2020] [Indexed: 02/09/2023]
Abstract
SARS-CoV-2 is the etiologic agent of COVID-19. There is currently no effective means of preventing infections by SARS-CoV-2, except through restriction of population movement and contact. An understanding of the origin, evolution and biochemistry (molecular biology) of SARS-CoV-2 is a prerequisite to its control. Mutations in the phosphorylation sites of SARS-CoV-2 encoded nucleocapsid protein isolated from various populations and locations, are described. Mutations occurred in the phosphorylation sites, all located within a stretch which forms a phosphorylation dependent interaction site, including C-TAK1 phosphorylation sites for 14-3-3. The consequences of these mutations are discussed and a structure-based model for the role of protein 14-3-3 in the sequestration and inhibition of SARS-CoV-2 nucleocapsid protein's function is presented. It is proposed that the phosphorylation of SARS-CoV-2 nucleocapsid protein and its sequestration by Protein 14-3-3 is a cellular response mechanism for the control and inhibition of the replication, transcription and packaging of the SARS-CoV-2 genome.
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Affiliation(s)
- H Y Lim Tung
- Peptide and Protein Chemistry Research Laboratory, Nacbraht Biomedical Research Institute, 3164 21st Street Suite 122, Astoria (NYC), NY, 11106, USA.
| | - Pierre Limtung
- Peptide and Protein Chemistry Research Laboratory, Nacbraht Biomedical Research Institute, 3164 21st Street Suite 122, Astoria (NYC), NY, 11106, USA
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42
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Achar A, Ghosh C. COVID-19-Associated Neurological Disorders: The Potential Route of CNS Invasion and Blood-Brain Relevance. Cells 2020; 9:cells9112360. [PMID: 33120941 PMCID: PMC7692725 DOI: 10.3390/cells9112360] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 12/22/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel human coronavirus that has sparked a global pandemic of the coronavirus disease of 2019 (COVID-19). The virus invades human cells through the angiotensin-converting enzyme 2 (ACE2) receptor-driven pathway, primarily targeting the human respiratory tract. However, emerging reports of neurological manifestations demonstrate the neuroinvasive potential of SARS-CoV-2. This review highlights the possible routes by which SARS-CoV-2 may invade the central nervous system (CNS) and provides insight into recent case reports of COVID-19-associated neurological disorders, namely ischaemic stroke, encephalitis, encephalopathy, epilepsy, neurodegenerative diseases, and inflammatory-mediated neurological disorders. We hypothesize that SARS-CoV-2 neuroinvasion, neuroinflammation, and blood-brain barrier (BBB) dysfunction may be implicated in the development of the observed disorders; however, further research is critical to understand the detailed mechanisms and pathway of infectivity behind CNS pathogenesis.
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Affiliation(s)
- Aneesha Achar
- Cerebrovascular Research, Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - Chaitali Ghosh
- Cerebrovascular Research, Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
- Department of Biomedical Engineering and Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA
- Correspondence: ; Tel.: +1-216-445-0559
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43
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Zhang B, Chao CW, Tsybovsky Y, Abiona OM, Hutchinson GB, Moliva JI, Olia AS, Pegu A, Phung E, Stewart-Jones GBE, Verardi R, Wang L, Wang S, Werner A, Yang ES, Yap C, Zhou T, Mascola JR, Sullivan NJ, Graham BS, Corbett KS, Kwong PD. A platform incorporating trimeric antigens into self-assembling nanoparticles reveals SARS-CoV-2-spike nanoparticles to elicit substantially higher neutralizing responses than spike alone. Sci Rep 2020; 10:18149. [PMID: 33097791 PMCID: PMC7584627 DOI: 10.1038/s41598-020-74949-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/25/2020] [Indexed: 12/12/2022] Open
Abstract
Antigens displayed on self-assembling nanoparticles can stimulate strong immune responses and have been playing an increasingly prominent role in structure-based vaccines. However, the development of such immunogens is often complicated by inefficiencies in their production. To alleviate this issue, we developed a plug-and-play platform using the spontaneous isopeptide-bond formation of the SpyTag:SpyCatcher system to display trimeric antigens on self-assembling nanoparticles, including the 60-subunit Aquifex aeolicus lumazine synthase (LuS) and the 24-subunit Helicobacter pylori ferritin. LuS and ferritin coupled to SpyTag expressed well in a mammalian expression system when an N-linked glycan was added to the nanoparticle surface. The respiratory syncytial virus fusion (F) glycoprotein trimer-stabilized in the prefusion conformation and fused with SpyCatcher-could be efficiently conjugated to LuS-SpyTag or ferritin-SpyTag, enabling multivalent display of F trimers with prefusion antigenicity. Similarly, F-glycoprotein trimers from human parainfluenza virus-type 3 and spike-glycoprotein trimers from SARS-CoV-2 could be displayed on LuS nanoparticles with decent yield and antigenicity. Notably, murine vaccination with 0.08 µg of SARS-CoV-2 spike-LuS nanoparticle elicited similar neutralizing responses as 2.0 µg of spike, which was ~ 25-fold higher on a weight-per-weight basis. The versatile platform described here thus allows for multivalent plug-and-play presentation on self-assembling nanoparticles of trimeric viral antigens, with SARS-CoV-2 spike-LuS nanoparticles inducing particularly potent neutralizing responses.
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Affiliation(s)
- Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cara W Chao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Olubukola M Abiona
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Geoffrey B Hutchinson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Juan I Moliva
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emily Phung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Institute for Biomedical Sciences, George Washington University, Washington, DC, USA
| | - Guillaume B E Stewart-Jones
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anne Werner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christina Yap
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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44
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Dong J, Huang B, Wang B, Titong A, Gallolu Kankanamalage S, Jia Z, Wright M, Parthasarathy P, Liu Y. Development of humanized tri-specific nanobodies with potent neutralization for SARS-CoV-2. Sci Rep 2020; 10:17806. [PMID: 33082473 PMCID: PMC7576208 DOI: 10.1038/s41598-020-74761-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/06/2020] [Indexed: 11/09/2022] Open
Abstract
SARS-CoV-2 is a newly emergent coronavirus, which has adversely impacted human health and has led to the COVID-19 pandemic. There is an unmet need to develop therapies against SARS-CoV-2 due to its severity and lack of treatment options. A promising approach to combat COVID-19 is through the neutralization of SARS-CoV-2 by therapeutic antibodies. Previously, we described a strategy to rapidly identify and generate llama nanobodies (VHH) from naïve and synthetic humanized VHH phage libraries that specifically bind the S1 SARS-CoV-2 spike protein, and block the interaction with the human ACE2 receptor. In this study we used computer-aided design to construct multi-specific VHH antibodies fused to human IgG1 Fc domains based on the epitope predictions for leading VHHs. The resulting tri-specific VHH-Fc antibodies show more potent S1 binding, S1/ACE2 blocking, and SARS-CoV-2 pseudovirus neutralization than the bi-specific VHH-Fcs or combination of individual monoclonal VHH-Fcs. Furthermore, protein stability analysis of the VHH-Fcs shows favorable developability features, which enable them to be quickly and successfully developed into therapeutics against COVID-19.
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Affiliation(s)
| | | | - Bo Wang
- Ab Studio Inc., Hayward, CA, USA
| | | | | | | | | | | | - Yue Liu
- Ab Studio Inc., Hayward, CA, USA
- Ab Therapeutics Inc., Hayward, CA, USA
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45
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Cazares LH, Chaerkady R, Samuel Weng SH, Boo CC, Cimbro R, Hsu HE, Rajan S, Dall’Acqua W, Clarke L, Ren K, McTamney P, Kallewaard-LeLay N, Ghaedi M, Ikeda Y, Hess S. Development of a Parallel Reaction Monitoring Mass Spectrometry Assay for the Detection of SARS-CoV-2 Spike Glycoprotein and Nucleoprotein. Anal Chem 2020; 92:13813-13821. [PMID: 32966064 PMCID: PMC7537550 DOI: 10.1021/acs.analchem.0c02288] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/23/2020] [Indexed: 12/25/2022]
Abstract
There is an urgent need for robust and high-throughput methods for SARS-CoV-2 detection in suspected patient samples to facilitate disease management, surveillance, and control. Although nucleic acid detection methods such as reverse transcription polymerase chain reaction (RT-PCR) are the gold standard, during the current pandemic, the deployment of RT-PCR tests has been extremely slow, and key reagents such as PCR primers and RNA extraction kits are at critical shortages. Rapid point-of-care viral antigen detection methods have been previously employed for the diagnosis of respiratory viruses such as influenza and respiratory syncytial viruses. Therefore, the direct detection of SARS-CoV-2 viral antigens in patient samples could also be used for diagnosis of active infection, and alternative methodologies for specific and sensitive viral protein detection should be explored. Targeted mass spectrometry techniques have enabled the identification and quantitation of a defined subset of proteins/peptides at single amino acid resolution with attomole level sensitivity and high reproducibility. Herein, we report a targeted mass spectrometry assay for the detection of SARS-CoV-2 spike protein and nucleoprotein in a relevant biological matrix. Recombinant full-length spike protein and nucleoprotein were digested and proteotypic peptides were selected for parallel reaction monitoring (PRM) quantitation using a high-resolution Orbitrap instrument. A spectral library, which contained seven proteotypic peptides (four from spike protein and three from nucleoprotein) and the top three to four transitions, was generated and evaluated. From the original spectral library, we selected two best performing peptides for the final PRM assay. The assay was evaluated using mock test samples containing inactivated SARS-CoV-2 virions, added to in vitro derived mucus. The PRM assay provided a limit of detection of ∼200 attomoles and a limit of quantitation of ∼ 390 attomoles. Extrapolating from the test samples, the projected titer of virus particles necessary for the detection of SARS-CoV-2 spike and nucleoprotein detection was approximately 2 × 105 viral particles/mL, making it an attractive alternative to RT-PCR assays. Potentially, mass spectrometry-based methods for viral antigen detection may deliver higher throughput and could serve as a complementary diagnostic tool to RT-PCR. Furthermore, this assay could be used to evaluate the presence of SARS-CoV-2 in archived or recently collected biological fluids, in vitro-derived research materials, and wastewater samples.
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Affiliation(s)
- Lisa H. Cazares
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Raghothama Chaerkady
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Shao Huan Samuel Weng
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Chelsea C. Boo
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Raffaello Cimbro
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Hsiang-En Hsu
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Sarav Rajan
- Biological Therapeutics 1, Antibody
Discovery and Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - William Dall’Acqua
- Biological Therapeutics 1, Antibody
Discovery and Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Lori Clarke
- Cell Therapeutics, Antibody Discovery
and Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Kuishu Ren
- Discovery Anti Infection, Microbial
Sciences, R&D AstraZeneca, Gaithersburg
20878, Maryland, United States
| | - Patrick McTamney
- Discovery Anti Infection, Microbial
Sciences, R&D AstraZeneca, Gaithersburg
20878, Maryland, United States
| | - Nicole Kallewaard-LeLay
- Discovery Anti Infection, Microbial
Sciences, R&D AstraZeneca, Gaithersburg
20878, Maryland, United States
| | - Mahboobe Ghaedi
- Respiratory and Immunology,
R&D AstraZeneca, Gaithersburg
20878, Maryland, United States
| | - Yasuhiro Ikeda
- Cell Therapeutics, Antibody Discovery
and Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Sonja Hess
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
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46
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Rattanapisit K, Shanmugaraj B, Manopwisedjaroen S, Purwono PB, Siriwattananon K, Khorattanakulchai N, Hanittinan O, Boonyayothin W, Thitithanyanont A, Smith DR, Phoolcharoen W. Rapid production of SARS-CoV-2 receptor binding domain (RBD) and spike specific monoclonal antibody CR3022 in Nicotiana benthamiana. Sci Rep 2020. [PMID: 33077899 DOI: 10.21203/rs.3.rs-27160/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the ongoing global outbreak of coronavirus disease (COVID-19) which is a significant threat to global public health. The rapid spread of COVID-19 necessitates the development of cost-effective technology platforms for the production of vaccines, drugs, and protein reagents for appropriate disease diagnosis and treatment. In this study, we explored the possibility of producing the receptor binding domain (RBD) of SARS-CoV-2 and an anti-SARS-CoV monoclonal antibody (mAb) CR3022 in Nicotiana benthamiana. Both RBD and mAb CR3022 were transiently produced with the highest expression level of 8 μg/g and 130 μg/g leaf fresh weight respectively at 3 days post-infiltration. The plant-produced RBD exhibited specific binding to the SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2). Furthermore, the plant-produced mAb CR3022 binds to SARS-CoV-2, but fails to neutralize the virus in vitro. This is the first report showing the production of anti-SARS-CoV-2 RBD and mAb CR3022 in plants. Overall these findings provide a proof-of-concept for using plants as an expression system for the production of SARS-CoV-2 antigens and antibodies or similar other diagnostic reagents against SARS-CoV-2 rapidly, especially during epidemic or pandemic situation.
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MESH Headings
- Angiotensin-Converting Enzyme 2
- Animals
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Betacoronavirus/metabolism
- COVID-19
- Chlorocebus aethiops
- Coronavirus Infections/pathology
- Coronavirus Infections/virology
- Humans
- Neutralization Tests
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/metabolism
- Plant Leaves/metabolism
- Pneumonia, Viral/pathology
- Pneumonia, Viral/virology
- Protein Binding
- Protein Domains/immunology
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/immunology
- Recombinant Proteins/isolation & purification
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Tobacco/metabolism
- Vero Cells
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Affiliation(s)
- Kaewta Rattanapisit
- Research Unit for Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Balamurugan Shanmugaraj
- Research Unit for Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | | | - Priyo Budi Purwono
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Department of Microbiology, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Konlavat Siriwattananon
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Narach Khorattanakulchai
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Oranicha Hanittinan
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Wanuttha Boonyayothin
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | | | - Duncan R Smith
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Waranyoo Phoolcharoen
- Research Unit for Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand.
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand.
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47
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Rattanapisit K, Shanmugaraj B, Manopwisedjaroen S, Purwono PB, Siriwattananon K, Khorattanakulchai N, Hanittinan O, Boonyayothin W, Thitithanyanont A, Smith DR, Phoolcharoen W. Rapid production of SARS-CoV-2 receptor binding domain (RBD) and spike specific monoclonal antibody CR3022 in Nicotiana benthamiana. Sci Rep 2020; 10:17698. [PMID: 33077899 PMCID: PMC7573609 DOI: 10.1038/s41598-020-74904-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 10/06/2020] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the ongoing global outbreak of coronavirus disease (COVID-19) which is a significant threat to global public health. The rapid spread of COVID-19 necessitates the development of cost-effective technology platforms for the production of vaccines, drugs, and protein reagents for appropriate disease diagnosis and treatment. In this study, we explored the possibility of producing the receptor binding domain (RBD) of SARS-CoV-2 and an anti-SARS-CoV monoclonal antibody (mAb) CR3022 in Nicotiana benthamiana. Both RBD and mAb CR3022 were transiently produced with the highest expression level of 8 μg/g and 130 μg/g leaf fresh weight respectively at 3 days post-infiltration. The plant-produced RBD exhibited specific binding to the SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2). Furthermore, the plant-produced mAb CR3022 binds to SARS-CoV-2, but fails to neutralize the virus in vitro. This is the first report showing the production of anti-SARS-CoV-2 RBD and mAb CR3022 in plants. Overall these findings provide a proof-of-concept for using plants as an expression system for the production of SARS-CoV-2 antigens and antibodies or similar other diagnostic reagents against SARS-CoV-2 rapidly, especially during epidemic or pandemic situation.
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MESH Headings
- Angiotensin-Converting Enzyme 2
- Animals
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Betacoronavirus/metabolism
- COVID-19
- Chlorocebus aethiops
- Coronavirus Infections/pathology
- Coronavirus Infections/virology
- Humans
- Neutralization Tests
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/metabolism
- Plant Leaves/metabolism
- Pneumonia, Viral/pathology
- Pneumonia, Viral/virology
- Protein Binding
- Protein Domains/immunology
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/immunology
- Recombinant Proteins/isolation & purification
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Nicotiana/metabolism
- Vero Cells
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Affiliation(s)
- Kaewta Rattanapisit
- Research Unit for Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Balamurugan Shanmugaraj
- Research Unit for Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | | | - Priyo Budi Purwono
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Department of Microbiology, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Konlavat Siriwattananon
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Narach Khorattanakulchai
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Oranicha Hanittinan
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Wanuttha Boonyayothin
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | | | - Duncan R Smith
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Waranyoo Phoolcharoen
- Research Unit for Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand.
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand.
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48
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Vadlamani BS, Uppal T, Verma SC, Misra M. Functionalized TiO 2 Nanotube-Based Electrochemical Biosensor for Rapid Detection of SARS-CoV-2. Sensors (Basel) 2020; 20:s20205871. [PMID: 33080785 DOI: 10.1101/2020.09.07.20190173] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 05/24/2023]
Abstract
The COronaVIrus Disease (COVID-19) is a newly emerging viral disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rapid increase in the number of COVID-19 cases worldwide led the WHO to declare a pandemic within a few months after the first case of infection. Due to the lack of a prophylactic measure to control the virus infection and spread, early diagnosis and quarantining of infected as well as the asymptomatic individuals are necessary for the containment of this pandemic. However, the current methods for SARS-CoV-2 diagnosis are expensive and time consuming, although some promising and inexpensive technologies are becoming available for emergency use. In this work, we report the synthesis of a cheap, yet highly sensitive, cobalt-functionalized TiO2 nanotubes (Co-TNTs)-based electrochemical sensor for rapid detection of SARS-CoV-2 through sensing the spike (receptor binding domain (RBD)) present on the surface of the virus. A simple, low-cost, and one-step electrochemical anodization route was used for synthesizing TNTs, followed by an incipient wetting method for cobalt functionalization of the TNTs platform, which was connected to a potentiostat for data collection. This sensor specifically detected the S-RBD protein of SARS-CoV-2 even at very low concentration (range of 14 to 1400 nM (nano molar)). Additionally, our sensor showed a linear response in the detection of viral protein over the concentration range. Thus, our Co-TNT sensor is highly effective in detecting SARS-CoV-2 S-RBD protein in approximately 30 s, which can be explored for developing a point of care diagnostics for rapid detection of SARS-CoV-2 in nasal secretions and saliva samples.
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Affiliation(s)
- Bhaskar S Vadlamani
- Chemical and Materials Engineering Department, University of Nevada, Reno, NV 89557, USA
| | - Timsy Uppal
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Subhash C Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Mano Misra
- Chemical and Materials Engineering Department, University of Nevada, Reno, NV 89557, USA
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49
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Nchioua R, Kmiec D, Müller JA, Conzelmann C, Groß R, Swanson CM, Neil SJD, Stenger S, Sauter D, Münch J, Sparrer KMJ, Kirchhoff F. SARS-CoV-2 Is Restricted by Zinc Finger Antiviral Protein despite Preadaptation to the Low-CpG Environment in Humans. mBio 2020; 11:e01930-20. [PMID: 33067384 PMCID: PMC7569149 DOI: 10.1128/mbio.01930-20] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022] Open
Abstract
Recent evidence shows that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is sensitive to interferons (IFNs). However, the most effective types of IFNs and the underlying antiviral effectors remain to be defined. Here, we show that zinc finger antiviral protein (ZAP), which preferentially targets CpG dinucleotides in viral RNA sequences, restricts SARS-CoV-2. We further demonstrate that ZAP and its cofactors KHNYN and TRIM25 are expressed in human lung cells. Type I, II, and III IFNs all strongly inhibited SARS-CoV-2 and further induced ZAP expression. Comprehensive sequence analyses revealed that SARS-CoV-2 and its closest relatives from horseshoe bats showed the strongest CpG suppression among all known human and bat coronaviruses, respectively. Nevertheless, endogenous ZAP expression restricted SARS-CoV-2 replication in human lung cells, particularly upon treatment with IFN-α or IFN-γ. Both the long and the short isoforms of human ZAP reduced SARS-CoV-2 RNA expression levels, but the former did so with greater efficiency. Finally, we show that the ability to restrict SARS-CoV-2 is conserved in ZAP orthologues of the reservoir bat and potential intermediate pangolin hosts of human coronaviruses. Altogether, our results show that ZAP is an important effector of the innate response against SARS-CoV-2, although this pandemic pathogen emerged from zoonosis of a coronavirus that was preadapted to the low-CpG environment in humans.IMPORTANCE Although interferons inhibit SARS-CoV-2 and have been evaluated for treatment of coronavirus disease 2019 (COVID-19), the most effective types and antiviral effectors remain to be defined. Here, we show that IFN-γ is particularly potent in restricting SARS-CoV-2 and in inducing expression of the antiviral factor ZAP in human lung cells. Knockdown experiments revealed that endogenous ZAP significantly restricts SARS-CoV-2. We further show that CpG dinucleotides which are specifically targeted by ZAP are strongly suppressed in the SARS-CoV-2 genome and that the two closest horseshoe bat relatives of SARS-CoV-2 show the lowest genomic CpG content of all coronavirus sequences available from this reservoir host. Nonetheless, both the short and long isoforms of human ZAP reduced SARS-CoV-2 RNA levels, and this activity was conserved in horseshoe bat and pangolin ZAP orthologues. Our findings indicating that type II interferon is particularly efficient against SARS-CoV-2 and that ZAP restricts this pandemic viral pathogen might promote the development of effective immune therapies against COVID-19.
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Affiliation(s)
- Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Carina Conzelmann
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Chad M Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Steffen Stenger
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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50
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Komatsu TS, Okimoto N, Koyama YM, Hirano Y, Morimoto G, Ohno Y, Taiji M. Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation. Sci Rep 2020; 10:16986. [PMID: 33046764 PMCID: PMC7550358 DOI: 10.1038/s41598-020-74099-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/24/2020] [Indexed: 11/14/2022] Open
Abstract
We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (Mpro) to examine the binding dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir, were used as the potential lead drugs to investigate access to the drug binding sites in Mpro. The frequently accessed sites on Mpro were classified based on contacts between the ligands and the protein, and the differences in site distributions of the encounter complex were observed among the ligands. All seven ligands showed binding to the active site at least twice in 28 simulations of 200 ns each. We further investigated the variations in the complex structure of the active site with the ligands, using microsecond order simulations. Results revealed a wide variation in the shapes of the binding sites and binding poses of the ligands. Additionally, the C-terminal region of the other chain often interacted with the ligands and the active site. Collectively, these findings indicate the importance of dynamic sampling of protein-ligand complexes and suggest the possibilities of further drug optimisations.
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Affiliation(s)
- Teruhisa S Komatsu
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Noriaki Okimoto
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yohei M Koyama
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yoshinori Hirano
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Gentaro Morimoto
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yousuke Ohno
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Makoto Taiji
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
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