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Lee JH, Sergi C, Kast RE, Kanwar BA, Bourbeau J, Oh S, Sohn MG, Lee CJ, Coleman MD. Basic implications on three pathways associated with SARS-CoV-2. Biomed J 2024:100766. [PMID: 39004185 DOI: 10.1016/j.bj.2024.100766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 07/16/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interacts between the host and virus and govern induction, resulting in multiorgan impacts. Its pathophysiology involves the followings: 1) the angiotensin-converting enzyme (ACE2) and Toll-like receptor (TLR) pathways: 2) the neuropilin (NRP) pathway: 3) the spike protein pathway. Therefore, it is necessary to block the pathological course with modulating innate lymphoid cells against diverse corona variants in the future.
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Affiliation(s)
- Jong Hoon Lee
- Science and Research Center, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu Seoul 03080, Republic of Korea.
| | - Consolato Sergi
- Division of Anatomical Pathology, Children's Hospital of Eastern Ontario (CHEO), University of Ottawa, 401 Smyth Road Ottawa, ON K1H 8L1 Canada
| | - Richard E Kast
- IIAIGC Study Center, 11 Arlington Ct, Burlington, 05408 VT USA
| | - Badar A Kanwar
- Haider Associates, 1999 Forest Ridge Dr, Bedford, TX 76021, United States
| | - Jean Bourbeau
- Respiratory Epidemiology and Clinical Research Unit, McGill University Health Centre, Montréal, QC, Canada
| | - Sangsuk Oh
- Department of Food Engineering, Food Safety Laboratory, Memory Unit, Ewha Womans University, Seoul 03670, Korea
| | - Mun-Gi Sohn
- Department of Food Science, KyungHee University College of Life Science, Seoul 17104, Republic of Korea
| | - Chul Joong Lee
- Department of Anesthesiology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Michael D Coleman
- College of Health and Life Sciences, Aston University, Birmingham, B4 7ET UK.
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2
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Moore GJ, Ridway H, Gadanec LK, Apostolopoulos V, Zulli A, Swiderski J, Kelaidonis K, Vidali VP, Matsoukas MT, Chasapis CT, Matsoukas JM. Structural Features Influencing the Bioactive Conformation of Angiotensin II and Angiotensin A: Relationship between Receptor Desensitization, Addiction, and the Blood-Brain Barrier. Int J Mol Sci 2024; 25:5779. [PMID: 38891966 PMCID: PMC11171751 DOI: 10.3390/ijms25115779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 06/21/2024] Open
Abstract
The N-terminal portion of the octapeptide angiotensin II (DRVYIHPF; AngII), a vasopressor peptide that favorably binds to, and activates, AngII type 1 receptor (AT1R), has an important role in maintaining bioactive conformation. It involves all three charged groups, namely (i) the N-terminal amino group cation, (ii) the Asp sidechain anion and (iii) the Arg guanidino cation. Neutralization of any one of these three charged groups results in a substantial reduction (<5%) in bioactivity, implicating a specialized function for this cluster. In contrast, angiotensin A (ARVYIHPF; AngA) has reduced bioactivity at AT1R; however, replacement of Asp in AngII with sarcosine (N-methyl-glycine) not only restores bioactivity but increases the activity of agonist, antagonist, and inverse agonist analogues. A bend produced at the N-terminus by the introduction of the secondary amino acid sarcosine is thought to realign the functional groups that chaperone the C-terminal portion of AngII, allowing transfer of the negative charge originating at the C-terminus to be transferred to the Tyr hydroxyl-forming tyrosinate anion, which is required to activate the receptor and desensitizes the receptor (tachyphylaxis). Peptide (sarilesin) and nonpeptide (sartans) moieties, which are long-acting inverse agonists, appear to desensitize the receptor by a mechanism analogous to tachyphylaxis. Sartans/bisartans were found to bind to alpha adrenergic receptors resulting in structure-dependent desensitization or resensitization. These considerations have provided information on the mechanisms of receptor desensitization/tolerance and insights into possible avenues for treating addiction. In this regard sartans, which appear to cross the blood-brain barrier more readily than bisartans, are the preferred drug candidates.
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Affiliation(s)
- Graham J. Moore
- Pepmetics Inc., 772 Murphy Place, Victoria, BC V8Y 3H4, Canada;
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Harry Ridway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia;
| | - Laura Kate Gadanec
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (V.A.); (A.Z.); (J.S.)
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (V.A.); (A.Z.); (J.S.)
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - Anthony Zulli
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (V.A.); (A.Z.); (J.S.)
| | - Jordan Swiderski
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (V.A.); (A.Z.); (J.S.)
| | | | - Veroniki P. Vidali
- Institute of Nanoscience and Nanotechnology, National Centre for Scientific Research “Demokritos”, 15341 Athens, Greece;
| | | | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece;
| | - John M. Matsoukas
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (V.A.); (A.Z.); (J.S.)
- NewDrug/NeoFar PC, Patras Science Park, 26504 Patras, Greece;
- Department of Chemistry, University of Patras, 26504 Patras, Greece
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3
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Wang S, Ran W, Sun L, Fan Q, Zhao Y, Wang B, Yang J, He Y, Wu Y, Wang Y, Chen L, Chuchuay A, You Y, Zhu X, Wang X, Chen Y, Wang Y, Chen YQ, Yuan Y, Zhao J, Mao Y. Sequential glycosylations at the multibasic cleavage site of SARS-CoV-2 spike protein regulate viral activity. Nat Commun 2024; 15:4162. [PMID: 38755139 PMCID: PMC11099032 DOI: 10.1038/s41467-024-48503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
The multibasic furin cleavage site at the S1/S2 boundary of the spike protein is a hallmark of SARS-CoV-2 and plays a crucial role in viral infection. However, the mechanism underlying furin activation and its regulation remain poorly understood. Here, we show that GalNAc-T3 and T7 jointly initiate clustered O-glycosylations in the furin cleavage site of the SARS-CoV-2 spike protein, which inhibit furin processing, suppress the incorporation of the spike protein into virus-like-particles and affect viral infection. Mechanistic analysis reveals that the assembly of the spike protein into virus-like particles relies on interactions between the furin-cleaved spike protein and the membrane protein of SARS-CoV-2, suggesting a possible mechanism for furin activation. Interestingly, mutations in the spike protein of the alpha and delta variants of the virus confer resistance against glycosylation by GalNAc-T3 and T7. In the omicron variant, additional mutations reverse this resistance, making the spike protein susceptible to glycosylation in vitro and sensitive to GalNAc-T3 and T7 expression in human lung cells. Our findings highlight the role of glycosylation as a defense mechanism employed by host cells against SARS-CoV-2 and shed light on the evolutionary interplay between the host and the virus.
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Affiliation(s)
- Shengjun Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Wei Ran
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lingyu Sun
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qingchi Fan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanqi Zhao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Foshan Institute for Food and Drug Control, Foshan, China
| | - Bowen Wang
- College of Life Science, Northwest University, Xi'an, China
| | - Jinghong Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuqi He
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanyuan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Luoyi Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Arpaporn Chuchuay
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuyu You
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xinhai Zhu
- Instrumental Analysis & Research Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaojuan Wang
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ye Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yanqiu Yuan
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou Laboratory, Bio-island, Guangzhou, China.
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China.
| | - Yang Mao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangzhou, China.
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4
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Jeong GU, Hwang I, Lee W, Choi JH, Yoon GY, Kim HS, Yang JS, Kim KC, Lee JY, Kim SJ, Kwon YC, Kim KD. Generation of a lethal mouse model expressing human ACE2 and TMPRSS2 for SARS-CoV-2 infection and pathogenesis. Exp Mol Med 2024; 56:1221-1229. [PMID: 38816566 PMCID: PMC11148094 DOI: 10.1038/s12276-024-01197-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 06/01/2024] Open
Abstract
Mouse models expressing human ACE2 for coronavirus disease 2019 have been frequently used to understand its pathogenesis and develop therapeutic strategies against SARS-CoV-2. Given that human TMPRSS2 supports viral entry, replication, and pathogenesis, we established a double-transgenic mouse model expressing both human ACE2 and TMPRSS2 for SARS-CoV-2 infection. Co-overexpression of both genes increased viral infectivity in vitro and in vivo. Double-transgenic mice showed significant body weight loss, clinical disease symptoms, acute lung injury, lung inflammation, and lethality in response to viral infection, indicating that they were highly susceptible to SARS-CoV-2. Pretreatment with the TMPRSS2 inhibitor, nafamostat, effectively reduced virus-induced weight loss, viral replication, and mortality in the double-transgenic mice. Moreover, the susceptibility and differential pathogenesis of SARS-CoV-2 variants were demonstrated in this animal model. Together, our results demonstrate that double-transgenic mice could provide a highly susceptible mouse model for viral infection to understand SARS-CoV-2 pathogenesis and evaluate antiviral therapeutics against coronavirus disease 2019.
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Affiliation(s)
- Gi Uk Jeong
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Insu Hwang
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
- Division of Vaccine Development Coordination, Center for Vaccine Research, National Institute of Infectious Diseases, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Wooseong Lee
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Ji Hyun Choi
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Gun Young Yoon
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Hae Soo Kim
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Jeong-Sun Yang
- Center for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Kyung-Chang Kim
- Center for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Joo-Yeon Lee
- Center for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Seong-Jun Kim
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Young-Chan Kwon
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea.
- Medical Chemistry and Pharmacology, University of Science and Technology (UST), Daejeon, Republic of Korea.
| | - Kyun-Do Kim
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea.
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5
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Chan CWF, Wang B, Nan L, Huang X, Mao T, Chu HY, Luo C, Chu H, Choi GCG, Shum HC, Wong ASL. High-throughput screening of genetic and cellular drivers of syncytium formation induced by the spike protein of SARS-CoV-2. Nat Biomed Eng 2024; 8:291-309. [PMID: 37996617 DOI: 10.1038/s41551-023-01140-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 10/18/2023] [Indexed: 11/25/2023]
Abstract
Mapping mutations and discovering cellular determinants that cause the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to induce infected cells to form syncytia would facilitate the development of strategies for blocking the formation of such cell-cell fusion. Here we describe high-throughput screening methods based on droplet microfluidics and the size-exclusion selection of syncytia, coupled with large-scale mutagenesis and genome-wide knockout screening via clustered regularly interspaced short palindromic repeats (CRISPR), for the large-scale identification of determinants of cell-cell fusion. We used the methods to perform deep mutational scans in spike-presenting cells to pinpoint mutable syncytium-enhancing substitutions in two regions of the spike protein (the fusion peptide proximal region and the furin-cleavage site). We also used a genome-wide CRISPR screen in cells expressing the receptor angiotensin-converting enzyme 2 to identify inhibitors of clathrin-mediated endocytosis that impede syncytium formation, which we validated in hamsters infected with SARS-CoV-2. Finding genetic and cellular determinants of the formation of syncytia may reveal insights into the physiological and pathological consequences of cell-cell fusion.
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Affiliation(s)
- Charles W F Chan
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Bei Wang
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Lang Nan
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Xiner Huang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tianjiao Mao
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Hoi Yee Chu
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Cuiting Luo
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People's Republic of China.
| | - Gigi C G Choi
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
| | - Alan S L Wong
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
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6
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Zech F, Jung C, Jacob T, Kirchhoff F. Causes and Consequences of Coronavirus Spike Protein Variability. Viruses 2024; 16:177. [PMID: 38399953 PMCID: PMC10892391 DOI: 10.3390/v16020177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Coronaviruses are a large family of enveloped RNA viruses found in numerous animal species. They are well known for their ability to cross species barriers and have been transmitted from bats or intermediate hosts to humans on several occasions. Four of the seven human coronaviruses (hCoVs) are responsible for approximately 20% of common colds (hCoV-229E, -NL63, -OC43, -HKU1). Two others (SARS-CoV-1 and MERS-CoV) cause severe and frequently lethal respiratory syndromes but have only spread to very limited extents in the human population. In contrast the most recent human hCoV, SARS-CoV-2, while exhibiting intermediate pathogenicity, has a profound impact on public health due to its enormous spread. In this review, we discuss which initial features of the SARS-CoV-2 Spike protein and subsequent adaptations to the new human host may have helped this pathogen to cause the COVID-19 pandemic. Our focus is on host forces driving changes in the Spike protein and their consequences for virus infectivity, pathogenicity, immune evasion and resistance to preventive or therapeutic agents. In addition, we briefly address the significance and perspectives of broad-spectrum therapeutics and vaccines.
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Affiliation(s)
- Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christoph Jung
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; (C.J.); (T.J.)
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; (C.J.); (T.J.)
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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7
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Xiao S, Yuan Z, Huang Y. The Potential Role of Nitric Oxide as a Therapeutic Agent against SARS-CoV-2 Infection. Int J Mol Sci 2023; 24:17162. [PMID: 38138990 PMCID: PMC10742813 DOI: 10.3390/ijms242417162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
The global coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become the greatest worldwide public health threat of this century, which may predispose multi-organ failure (especially the lung) and death despite numerous mild and moderate symptoms. Recent studies have unraveled the molecular and clinical characteristics of the infectivity, pathogenicity, and immune evasion of SARS-CoV-2 and thus improved the development of many different therapeutic strategies to combat COVID-19, including treatment and prevention. Previous studies have indicated that nitric oxide (NO) is an antimicrobial and anti-inflammatory molecule with key roles in pulmonary vascular function in the context of viral infections and other pulmonary disease states. This review summarized the recent advances of the pathogenesis of SARS-CoV-2, and accordingly elaborated on the potential application of NO in the management of patients with COVID-19 through antiviral activities and anti-inflammatory properties, which mitigate the propagation of this disease. Although there are some limits of NO in the treatment of COVID-19, it might be a worthy candidate in the multiple stages of COVID-19 prevention or therapy.
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Affiliation(s)
| | | | - Yi Huang
- National Biosafety Laboratory, Chinese Academy of Sciences, Wuhan 430020, China
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8
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Su WC, Chen ZY, Chang YS, Jeng KS, Le UNP, Chou YC, Kuo LL, Melano I, Jesse, Wang WJ, Song YC, Li SR, Hung MC, Lai MMC, Lin CW. Functional assessments of SARS-CoV-2 single-round infectious particles with variant-specific spike proteins on infectivity, drug sensitivity, and antibody neutralization. Antiviral Res 2023; 220:105744. [PMID: 37944823 DOI: 10.1016/j.antiviral.2023.105744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Working with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is restricted to biosafety level III (BSL-3) laboratory. The study used a trans-complementation system consisting of virus-like particles (VLPs) and DNA-launched replicons to generate SARS-CoV-2 single-round infectious particles (SRIPs) with variant-specific spike (S) proteins. S gene of Wuhan-Hu-1 strain (SWH1) or Omicron BA.1 variant (SBA.1), along with the envelope (E) and membrane (M) genes, were cloned into a tricistronic vector, co-expressed in the cells to produce variant-specific S-VLPs. Additionally, the replicon of the WH1-like strain without S, E, M and accessory genes, was engineered under the control by a CMV promoter to produce self-replicating RNAs within VLP-producing cells, led to create SWH1- and SBA.1-based SARS-CoV-2 SRIPs. The SBA.1-based SRIP showed lower virus yield, replication, N protein expression, fusogenicity, and infectivity compared to SWH1-based SRIPs. SBA.1-based SRIP also exhibited intermediate resistance to neutralizing antibodies produced by SWH1-based vaccines, but were effective at infecting cells with low ACE2 expression. Importantly, both S-based SRIPs responded similarly to remdesivir and GC376, with EC50 values ranging from 0.17 to 1.46 μM, respectively. The study demonstrated that this trans-complementation system is a reliable and efficient tool for generating SARS-CoV-2 SRIPs with variant-specific S proteins. SARS-CoV-2 SRIPs, mimicking authentic live viruses, facilitate comprehensive analysis of variant-specific virological characteristics, including antibody neutralization, and drug sensitivity in non-BSL-3 laboratories.
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Affiliation(s)
- Wen-Chi Su
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan; International Master's Program of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan; Department of Medical Research, China Medical University Hospital, Taichung, 404327, Taiwan; Drug Development Center, China Medical University, Taichung, 404333, Taiwan
| | - Zan-Yu Chen
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 404333, Taiwan
| | - Young-Sheng Chang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan; Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 404333, Taiwan
| | - King-Song Jeng
- Department of Medical Research, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Uyen Nguyen Phuong Le
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 404333, Taiwan; Department of Biological Science and Technology, China Medical University, Taichung, 404333, Taiwan
| | - Yu-Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Li-Lan Kuo
- International Master's Program of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan
| | - Ivonne Melano
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan
| | - Jesse
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan
| | - Wei-Jan Wang
- Department of Biological Science and Technology, China Medical University, Taichung, 404333, Taiwan
| | - Ying-Chyi Song
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Sin-Rong Li
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 404333, Taiwan; Department of Laboratory Medicine, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan; Research Center for Cancer Biology, China Medical University, Taichung, 404327, Taiwan; Center for Molecular Medicine, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Michael M C Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei, 115201, Taiwan.
| | - Cheng-Wen Lin
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan; Drug Development Center, China Medical University, Taichung, 404333, Taiwan; Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 404333, Taiwan; Department of Biological Science and Technology, China Medical University, Taichung, 404333, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Wufeng, Taichung, 413305, Taiwan.
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9
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de Vries M, Ciabattoni GO, Rodriguez-Rodriguez BA, Crosse KM, Papandrea D, Samanovic MI, Dimartino D, Marier C, Mulligan MJ, Heguy A, Desvignes L, Duerr R, Dittmann M. Generation of quality-controlled SARS-CoV-2 variant stocks. Nat Protoc 2023; 18:3821-3855. [PMID: 37833423 DOI: 10.1038/s41596-023-00897-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/28/2023] [Indexed: 10/15/2023]
Abstract
One of the main challenges in the fight against coronavirus disease 2019 (COVID-19) stems from the ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into multiple variants. To address this hurdle, research groups around the world have independently developed protocols to isolate these variants from clinical samples. These isolates are then used in translational and basic research-for example, in vaccine development, drug screening or characterizing SARS-CoV-2 biology and pathogenesis. However, over the course of the COVID-19 pandemic, we have learned that the introduction of artefacts during both in vitro isolation and subsequent propagation to virus stocks can lessen the validity and reproducibility of data. We propose a rigorous pipeline for the generation of high-quality SARS-CoV-2 variant clonal isolates that minimizes the acquisition of mutations and introduces stringent controls to detect them. Overall, the process includes eight stages: (i) cell maintenance, (ii) isolation of SARS-CoV-2 from clinical specimens, (iii) determination of infectious virus titers by plaque assay, (iv) clonal isolation by plaque purification, (v) whole-virus-genome deep-sequencing, (vi and vii) amplification of selected virus clones to master and working stocks and (viii) sucrose purification. This comprehensive protocol will enable researchers to generate reliable SARS-CoV-2 variant inoculates for in vitro and in vivo experimentation and will facilitate comparisons and collaborative work. Quality-controlled working stocks for most applications can be generated from acquired biorepository virus within 1 month. An additional 5-8 d are required when virus is isolated from clinical swab material, and another 6-7 d is needed for sucrose-purifying the stocks.
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Affiliation(s)
- Maren de Vries
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Grace O Ciabattoni
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Keaton M Crosse
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Dominick Papandrea
- High Containment Laboratories-Office of Science and Research, NYU Langone Health, New York, NY, USA
| | - Marie I Samanovic
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Dacia Dimartino
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY, USA
| | - Christian Marier
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY, USA
| | - Mark J Mulligan
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Adriana Heguy
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Ludovic Desvignes
- High Containment Laboratories-Office of Science and Research, NYU Langone Health, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Ralf Duerr
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Meike Dittmann
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA.
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10
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Dabrell SN, Li YC, Yamaguchi H, Chen HF, Hung MC. Herbal Compounds Dauricine and Isoliensinine Impede SARS-CoV-2 Viral Entry. Biomedicines 2023; 11:2914. [PMID: 38001915 PMCID: PMC10669532 DOI: 10.3390/biomedicines11112914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Targeting viral entry has been the focal point for the last 3 years due to the continued threat posed by SARS-CoV-2. SARS-CoV-2's entry is highly dependent on the interaction between the virus's Spike protein and host receptors. The virus's Spike protein is a key modulator of viral entry, allowing sequential cleavage of ACE2 at the S1/S2 and S2 sites, resulting in the amalgamation of membranes and subsequent entry of the virus. A Polybasic insertion (PRRAR) conveniently located at the S1/S2 site can also be cleaved by furin or by serine protease, TMPRSS2, at the cell surface. Since ACE2 and TMPRSS2 are conveniently located on the surface of host cells, targeting one or both receptors may inhibit receptor-ligand interaction. Here, we show that Dauricine and Isoliensinine, two commonly used herbal compounds, were capable of inhibiting SARS-CoV-2 viral entry by reducing Spike-ACE2 interaction but not suppressing TMPRSS2 protease activity. Further, our biological assays using pseudoviruses engineered to express Spike proteins of different variants revealed a reduction in infection rates following treatment with these compounds. The molecular modeling revealed an interconnection between R403 of Spike protein and both two compounds. Spike mutations at residue R403 are critical, and often utilized by ACE2 to gain cell access. Overall, our findings strongly suggest that Dauricine and Isoliensinine are effective in blocking Spike-ACE2 interaction and may serve as effective therapeutic agents for targeting SARS-CoV-2's viral entry.
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Affiliation(s)
- Shaneek Natoya Dabrell
- International Master's Program of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
| | - Yi-Chuan Li
- Department of Biological Science and Technology, China Medical University, Taichung 406040, Taiwan
| | - Hirohito Yamaguchi
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
| | - Hsiao-Fan Chen
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, China Medical University, Taichung 406040, Taiwan
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 406040, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung 406040, Taiwan
- Department of Biotechnology, Asia University, Taichung 413305, Taiwan
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11
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Megha KB, Reshma S, Amir S, Krishnan MJA, Shimona A, Alka R, Mohanan PV. Comprehensive Risk Assessment of Infection Induced by SARS-CoV-2. Mol Neurobiol 2023:10.1007/s12035-023-03682-4. [PMID: 37817031 DOI: 10.1007/s12035-023-03682-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
The pandemic COVID-19 (coronavirus disease 2019) is caused by the severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), which devastated the global economy and healthcare system. The infection caused an unforeseen rise in COVID-19 patients and increased the mortality rate globally. This study gives an overall idea about host-pathogen interaction, immune responses to COVID-19, recovery status of infection, targeted organs and complications associated, and comparison of post-infection immunity in convalescent subjects and non-infected individuals. The emergence of the variants and episodes of COVID-19 infections made the situation worsen. The timely introduction of vaccines and precautionary measures helped control the infection's severity. Later, the population that recovered from COVID-19 grew significantly. However, understanding the impact of healthcare issues resulting after infection is paramount for improving an individual's health status. It is now recognised that COVID-19 infection affects multiple organs and exhibits a broad range of clinical manifestations. So, post COVID-19 infection creates a high risk in individuals with already prevailing health complications. The identification of post-COVID-19-related health issues and their appropriate management is of greater importance to improving patient's quality of life. The persistence, sequelae and other medical complications that normally last from weeks to months after the recovery of the initial infection are involved with COVID-19. A multi-disciplinary approach is necessary for the development of preventive measures, techniques for rehabilitation and strategies for clinical management when it comes to long-term care.
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Affiliation(s)
- K B Megha
- Toxicology Division, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology (Govt. of India), Poojapura, Trivandrum, Kerala, 695 012, India
| | - S Reshma
- Toxicology Division, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology (Govt. of India), Poojapura, Trivandrum, Kerala, 695 012, India
| | - S Amir
- Toxicology Division, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology (Govt. of India), Poojapura, Trivandrum, Kerala, 695 012, India
| | - M J Ajai Krishnan
- Toxicology Division, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology (Govt. of India), Poojapura, Trivandrum, Kerala, 695 012, India
| | - A Shimona
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad, 201002, India
| | - Rao Alka
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad, 201002, India
| | - P V Mohanan
- Toxicology Division, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology (Govt. of India), Poojapura, Trivandrum, Kerala, 695 012, India.
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12
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Yanagisawa H, Kita Y, Oda T, Kikkawa M. Cryo-EM elucidates the uroplakin complex structure within liquid-crystalline lipids in the porcine urothelial membrane. Commun Biol 2023; 6:1018. [PMID: 37805589 PMCID: PMC10560298 DOI: 10.1038/s42003-023-05393-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/27/2023] [Indexed: 10/09/2023] Open
Abstract
The urothelium, a distinct epithelial tissue lining the urinary tract, serves as an essential component in preserving urinary tract integrity and thwarting infections. The asymmetric unit membrane (AUM), primarily composed of the uroplakin complex, constitutes a critical permeability barrier in fulfilling this role. However, the molecular architectures of both the AUM and the uroplakin complex have remained enigmatic due to the paucity of high-resolution structural data. In this study, we utilized cryo-electron microscopy to elucidate the three-dimensional structure of the uroplakin complex within the porcine AUM. While the global resolution achieved was 3.5 Å, we acknowledge that due to orientation bias, the resolution in the vertical direction was determined to be 6.3 Å. Our findings unveiled that the uroplakin complexes are situated within hexagonally arranged crystalline lipid membrane domains, rich in hexosylceramides. Moreover, our research rectifies a misconception in a previous model by confirming the existence of a domain initially believed to be absent, and pinpointing the accurate location of a crucial Escherichia coli binding site implicated in urinary tract infections. These discoveries offer valuable insights into the molecular underpinnings governing the permeability barrier function of the urothelium and the orchestrated lipid phase formation within the plasma membrane.
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Affiliation(s)
- Haruaki Yanagisawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoshihiro Kita
- Life Sciences Core Facility, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Toshiyuki Oda
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan.
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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13
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Hou YJ, Chiba S, Leist SR, Meganck RM, Martinez DR, Schäfer A, Catanzaro NJ, Sontake V, West A, Edwards CE, Yount B, Lee RE, Gallant SC, Zost SJ, Powers J, Adams L, Kong EF, Mattocks M, Tata A, Randell SH, Tata PR, Halfmann P, Crowe JE, Kawaoka Y, Baric RS. Host range, transmissibility and antigenicity of a pangolin coronavirus. Nat Microbiol 2023; 8:1820-1833. [PMID: 37749254 PMCID: PMC10522490 DOI: 10.1038/s41564-023-01476-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 08/14/2023] [Indexed: 09/27/2023]
Abstract
The pathogenic and cross-species transmission potential of SARS-CoV-2-related coronaviruses (CoVs) remain poorly characterized. Here we recovered a wild-type pangolin (Pg) CoV GD strain including derivatives encoding reporter genes using reverse genetics. In primary human cells, PgCoV replicated efficiently but with reduced fitness and showed less efficient transmission via airborne route compared with SARS-CoV-2 in hamsters. PgCoV was potently inhibited by US Food and Drug Administration approved drugs, and neutralized by COVID-19 patient sera and SARS-CoV-2 therapeutic antibodies in vitro. A pan-Sarbecovirus antibody and SARS-CoV-2 S2P recombinant protein vaccine protected BALB/c mice from PgCoV infection. In K18-hACE2 mice, PgCoV infection caused severe clinical disease, but mice were protected by a SARS-CoV-2 human antibody. Efficient PgCoV replication in primary human cells and hACE2 mice, coupled with a capacity for airborne spread, highlights an emergence potential. However, low competitive fitness, pre-immune humans and the benefit of COVID-19 countermeasures should impede its ability to spread globally in human populations.
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Affiliation(s)
- Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Moderna Inc., Cambridge, MA, USA
| | - Shiho Chiba
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rita M Meganck
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vishwaraj Sontake
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Catlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rhianna E Lee
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel C Gallant
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lily Adams
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Edgar F Kong
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa Mattocks
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aleksandra Tata
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Purushothama R Tata
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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14
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Gupte SA, Bakshi CS, Blackham E, Duhamel GE, Jordan A, Salgame P, D'silva M, Khan MY, Nadler J, Gupte R. The severity of SARS-CoV-2 infection in K18-hACE2 mice is attenuated by a novel steroid-derivative in a gender-specific manner. Br J Pharmacol 2023; 180:2677-2693. [PMID: 37259182 PMCID: PMC10999099 DOI: 10.1111/bph.16155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND AND PURPOSE COVID-19 infections caused by SARS-CoV-2 disseminated through human-to-human transmission can evoke severe inflammation. Treatments to reduce the SARS-CoV-2-associated inflammation are needed and are the focus of much research. In this study, we investigated the effect of N-ethyl-N'-[(3β,5α)-17-oxoandrostan-3-yl] urea (NEOU), a novel 17α-ketosteroid derivative, on the severity of COVID-19 infections. EXPERIMENTAL APPROACH Studies were conducted in SARS-CoV-2-infected K18-hACE2 mice. KEY RESULTS SARS-CoV-2-infected K18-hACE2 mice developed severe inflammatory crises and immune responses along with up-regulation of genes in associated signalling pathways in male more than female mice. Notably, SARS-CoV-2 infection down-regulated genes encoding drug metabolizing cytochrome P450 enzymes in male but not female mice. Treatment with NEOU (1 mg·kg-1 ·day-1 ) 24 or 72 h post-viral infection alleviated lung injury by decreasing expression of genes encoding inflammatory cytokines and chemokines while increasing expression of genes encoding immunoglobins. In situ hybridization using RNA scope™ probes and immunohistochemical assays revealed that NEOU increased resident CD169+ immunoregulatory macrophages and IBA-1 immunoreactive macrophage-dendritic cells within alveolar spaces in the lungs of infected mice. Consequentially, NEOU reduced morbidity more prominently in male than female mice. However, NEOU increased median survival time and accelerated recovery from infection by 6 days in both males and females. CONCLUSIONS AND IMPLICATIONS These findings demonstrate that SARS-CoV-2 exhibits gender bias by differentially regulating genes encoding inflammatory cytokines, immunogenic factors and drug-metabolizing enzymes, in male versus female mice. Most importantly, we identified a novel 17α-ketosteroid that reduces the severity of COVID-19 infection and could be beneficial for reducing impact of COVID-19.
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Affiliation(s)
- Sachin A Gupte
- Department of Pharmacology, New York Medical College, Valhalla, New York, USA
| | - Chandra Shekhar Bakshi
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, New York, USA
| | | | - Gerald E Duhamel
- Department of Biomedical Sciences and New York State Animal Health Diagnostic Center and Section of Anatomic Pathology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | | | - Padmini Salgame
- Department of Medicine, Division of Infectious Diseases and The Center for Emerging Pathogens, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Melinee D'silva
- Department of Pharmacology, New York Medical College, Valhalla, New York, USA
| | - Mohammad Y Khan
- Department of Pharmacology, New York Medical College, Valhalla, New York, USA
| | - Jerry Nadler
- Department of Pharmacology, New York Medical College, Valhalla, New York, USA
- Department of Medicine, New York Medical College, Valhalla, New York, USA
| | - Rakhee Gupte
- Department of Pharmacology, New York Medical College, Valhalla, New York, USA
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15
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Guo BC, Wu KH, Chen CY, Lin WY, Chang YJ, Lee TA, Lin MJ, Wu HP. Mesenchymal Stem Cells in the Treatment of COVID-19. Int J Mol Sci 2023; 24:14800. [PMID: 37834246 PMCID: PMC10573267 DOI: 10.3390/ijms241914800] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/21/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Since the emergence of the coronavirus disease 2019 (COVID-19) pandemic, many lives have been tragically lost to severe infections. The COVID-19 impact extends beyond the respiratory system, affecting various organs and functions. In severe cases, it can progress to acute respiratory distress syndrome (ARDS) and multi-organ failure, often fueled by an excessive immune response known as a cytokine storm. Mesenchymal stem cells (MSCs) have considerable potential because they can mitigate inflammation, modulate immune responses, and promote tissue regeneration. Accumulating evidence underscores the efficacy and safety of MSCs in treating severe COVID-19 and ARDS. Nonetheless, critical aspects, such as optimal routes of MSC administration, appropriate dosage, treatment intervals, management of extrapulmonary complications, and potential pediatric applications, warrant further exploration. These research avenues hold promise for enriching our understanding and refining the application of MSCs in confronting the multifaceted challenges posed by COVID-19.
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Affiliation(s)
- Bei-Cyuan Guo
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan;
| | - Kang-Hsi Wu
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung 40201, Taiwan;
- School of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Chun-Yu Chen
- Department of Emergency Medicine, Tungs’ Taichung Metro Harbor Hospital, Taichung 43503, Taiwan;
- Department of Nursing, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli 35664, Taiwan
| | - Wen-Ya Lin
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung 43503, Taiwan
| | - Yu-Jun Chang
- Laboratory of Epidemiology and Biostastics, Changhua Christian Hospital, Changhua 50006, Taiwan;
| | - Tai-An Lee
- Department of Emergency Medicine, Chang Bing Show Chwan Memorial Hospital, Changhua 50544, Taiwan;
| | - Mao-Jen Lin
- Division of Cardiology, Department of Medicine, Taichung Tzu Chi Hospital, The Buddhist Tzu Chi Medical Foundation, Taichung 42743, Taiwan
- Department of Medicine, College of Medicine, Tzu Chi University, Hualien 97002, Taiwan
| | - Han-Ping Wu
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Pediatrics, Chiayi Chang Gung Memorial Hospital, Chiayi 61363, Taiwan
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16
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Kyriakopoulos AM, Nigh G, McCullough PA, Olivier MD, Seneff S. Bell's palsy or an aggressive infiltrating basaloid carcinoma post-mRNA vaccination for COVID-19? A case report and review of the literature. EXCLI JOURNAL 2023; 22:992-1011. [PMID: 37927346 PMCID: PMC10620857 DOI: 10.17179/excli2023-6145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/15/2023] [Indexed: 11/07/2023]
Abstract
We report on an aggressive, infiltrating, metastatic, and ultimately lethal basaloid type of carcinoma arising shortly after an mRNA vaccination for COVID-19. The wife of the patient, since deceased, gave the consent for publishing the case. The malignancy was of cutaneous origin and the case showed symptoms consistent with Bell's palsy and trigeminal neuralgia beginning four days post-vaccination (right side head temporal pain). The temporal pain was suggestive for inflammation and impairment of T cell immune activation. Magnetic Resonance Imaging (MRI) showed a vascular loop on the left lateral aspect of the 5th cranial root exit of cerebellopontine angle constituting presumably a normal variant and was considered as an unrelated factor to the right-sided palsy and pain symptoms that corresponded to cranial nerves V (trigeminal nerve) and VII (facial nerve). In this study we describe all aspects of this case and discuss possible causal links between the rapid emergence of this metastatic cancer and mRNA vaccination. We place this within the context of multiple immune impairments potentially related to the mRNA injections that would be expected to potentiate more aggressive presentation and progression of cancer. The type of malignancy we describe suggests a population risk for occurrence of a large variety of relatively common basaloid phenotype cancer cells, which may have the potential for metastatic disease. This can be avoidable with early diagnosis and adequate treatment. Since facial paralysis/pain is one of the more common adverse neurological events following mRNA injection, careful inspection of cutaneous/soft tissue should be conducted to rule out malignancy. An extensive literature review is carried out, in order to elucidate the toxicity of mRNA vaccination that may have led to the death of this patient. Preventive and precise routine clinical investigations can potentially avoid future mortalities. See also Figure 1(Fig. 1).
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Affiliation(s)
- Anthony M. Kyriakopoulos
- Director and Head of Research and Development, Nasco AD Biotechnology Laboratory, Department of Research and Development, Sachtouri 11, 18536, Piraeus, Greece
| | - Greg Nigh
- Naturopathic Oncologist, Immersion Health, Portland, OR 97214, USA
| | | | - Maria D. Olivier
- Director and medical practitioner, Dr. Maré Olivier, Inc., Kuils River, South Africa
| | - Stephanie Seneff
- Senior Research Scientist, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
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17
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Ridgway H, Orbell JD, Matsoukas MT, Kelaidonis K, Moore GJ, Tsiodras S, Gorgoulis VG, Chasapis CT, Apostolopoulos V, Matsoukas JM. W254 in furin functions as a molecular gate promoting anti-viral drug binding: Elucidation of putative drug tunneling and docking by non-equilibrium molecular dynamics. Comput Struct Biotechnol J 2023; 21:4589-4612. [PMID: 37817778 PMCID: PMC10561063 DOI: 10.1016/j.csbj.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023] Open
Abstract
Furins are serine endoproteases that process precursor proteins into their biologically active forms, and they play essential roles in normal metabolism and disease presentation, including promoting expression of bacterial virulence factors and viral pathogenesis. Thus, furins represent vital targets for development of antimicrobial and antiviral therapeutics. Recent experimental evidence indicated that dichlorophenyl (DCP)-pyridine "BOS" drugs (e.g., BOS-318) competitively inhibit human furin by an induced-fit mechanism in which tryptophan W254 in the furin catalytic cleft (FCC) functions as a molecular gate, rotating nearly 180o through a steep energy barrier about its chi-1 dihedral to an "open" orientation, exposing a buried (i.e., cryptic) hydrophobic pocket 1. Once exposed, the non-polar DCP group of BOS-318, and similar halo-phenyl groups of analogs, enter the cryptic pocket, stabilizing drug binding. Here, we demonstrate flexible-receptor docking of BOS-318 (and various analogs) was unable to emulate the induced-fit motif, even when tryptophan was replaced with less bulky phenylalanine or glycine. While either substitution allowed access to the hydrophobic pocket for most ligands tested, optimal binding was observed only for W254, inferring a stabilizing effect of the indole sidechain. Furthermore, non-equilibrium steered molecular dynamics (sMD) in which the bound drugs (or their fragments) were extracted from the FCC did not cause closure of the open W254 gate, consistent with the thermodynamic stability of the open or closed W254 orientations. Finally, interactive molecular dynamics (iMD) revealed two putative conduits of drug entry and binding into the FCC, each coupled with W254 dihedral rotation and opening of the cryptic pocket. The iMD simulations further revealed ligand entry and binding in the FCC is likely driven in part by energy fluxes stemming from disruption and re-formation of ligand and protein solvation shells during drug migration from the solution phase into the FCC.
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Affiliation(s)
- Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia
- AquaMem Consultants, Rodeo, NM 88056, USA
| | - John D. Orbell
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia
- College of Sport, Health & Engineering, Victoria University, Melbourne, VIC 8001, Australia
| | | | | | - Graham J. Moore
- Pepmetics Inc., 772 Murphy Place, Victoria, BC V8Y 3H4, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sotiris Tsiodras
- Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Vasilis G. Gorgoulis
- Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, GR-11527 Athens, Greece
- Faculty Institute for Cancer Sciences, Manchester Academic Health Sciences Centre, University of Manchester, M20 4GJ Manchester, UK
- Biomedical Research Foundation, Academy of Athens, GR-11527 Athens, Greece
- Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Surrey, UK
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne 3030, VIC, Australia
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne 3021, VIC, Australia
| | - John M. Matsoukas
- NewDrug/NeoFar PC, Patras Science Park, Patras 26504, Greece
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne 3030, VIC, Australia
- Department of Chemistry, University of Patras, 26504 Patras, Greece
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18
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Yanagisawa H, Kita Y, Oda T, Kikkawa M. Unveiling Liquid-Crystalline Lipids in the Urothelial Membrane through Cryo-EM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542358. [PMID: 37398191 PMCID: PMC10312457 DOI: 10.1101/2023.05.29.542358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The urothelium, a distinct epithelial tissue lining the urinary tract, serves as an essential component in preserving urinary tract integrity and thwarting infections. The asymmetric unit membrane (AUM), primarily composed of the uroplakin complex, constitutes a critical permeability barrier in fulfilling this role. However, the molecular architectures of both the AUM and the uroplakin complex have remained enigmatic due to the paucity of high-resolution structural data. In this study, we utilized cryo-electron microscopy to elucidate the three-dimensional structure of the uroplakin complex within the porcine AUM. While the global resolution achieved was 3.5 Å, we acknowledge that due to orientation bias, the resolution in the vertical direction was determined to be 6.3 Å. Our findings unveiled that the uroplakin complexes are situated within hexagonally arranged crystalline lipid membrane domains, rich in hexosylceramides. Moreover, our research rectifies a misconception in a previous model by confirming the existence of a domain initially believed to be absent, and pinpointing the accurate location of a crucial Escherichia coli binding site implicated in urinary tract infections. These discoveries offer valuable insights into the molecular underpinnings governing the permeability barrier function of the urothelium and the orchestrated lipid phase formation within the plasma membrane.
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Affiliation(s)
- Haruaki Yanagisawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoshihiro Kita
- Life Sciences Core Facility, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiyuki Oda
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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19
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Mondol SM, Hasib M, Limon MBH, Alam ASMRU. Insights into Omicron's Low Fusogenicity through In Silico Molecular Studies on Spike-Furin Interactions. Bioinform Biol Insights 2023; 17:11779322231189371. [PMID: 37529484 PMCID: PMC10387760 DOI: 10.1177/11779322231189371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant and its subvariants have a unique set of mutations. Two of those mutations (N679 K and P681 H) reside close to the S1 /S2 furin cleavage site (FCS; 685-686). When these mutations reside together, they exert less-efficient membrane fusion than wild type and most other variants of concern such as the Delta variant. Here, we in silico targeted these mutations to find out which of the amino acids and interactions change plays the key role in fusion. To comprehend the epistatic effect of N679 K and P681 H mutations on the spike protein, we in silico constructed three types of spike protein sequences by changing the respective amino acids on 679 and 681 positions (P681 H, N679 K, K679 N-H681 P variants). We then analyzed the binding affinity of furin and spike (Furin-Wild, Furin-Omicron, Furin-P681 H, Furin-N679 K, and Furin-K679 N/H681 P) complexes. Omicron and P681 H variants showed a similar higher binding energy trend compared to the wild type and N679 K. The variation in hydrogen, hydrophobic, and salt bridge bonds between spike protein and furin provided an explanation for the observed low fusogenicity of Omicron. The fate of the epistasis in furin binding and possible cleavage depends on the efficient interaction between FCS in spike and furin catalytic triad, and in addition, the loss of the hydrogen bond between Arg 681 (spike) and Asn 295 (furin) along with inhibitor-like ineffective higher affinity plays an important role in the enzymatic activity.
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Affiliation(s)
| | - Md Hasib
- Department of Biochemistry and Biotechnology, University of Barishal, Barishal, Bangladesh
| | | | - A S M Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
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20
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Jiao Y, Xing Y, Sun Y. Impact of E484Q and L452R Mutations on Structure and Binding Behavior of SARS-CoV-2 B.1.617.1 Using Deep Learning AlphaFold2, Molecular Docking and Dynamics Simulation. Int J Mol Sci 2023; 24:11564. [PMID: 37511322 PMCID: PMC10380202 DOI: 10.3390/ijms241411564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/04/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
During the outbreak of COVID-19, many SARS-CoV-2 variants presented key amino acid mutations that influenced their binding abilities with angiotensin-converting enzyme 2 (hACE2) and neutralizing antibodies. For the B.1.617 lineage, there had been fears that two key mutations, i.e., L452R and E484Q, would have additive effects on the evasion of neutralizing antibodies. In this paper, we systematically investigated the impact of the L452R and E484Q mutations on the structure and binding behavior of B.1.617.1 using deep learning AlphaFold2, molecular docking and dynamics simulation. We firstly predicted and verified the structure of the S protein containing L452R and E484Q mutations via the AlphaFold2-calculated pLDDT value and compared it with the experimental structure. Next, a molecular simulation was performed to reveal the structural and interaction stabilities of the S protein of the double mutant variant with hACE2. We found that the double mutations, L452R and E484Q, could lead to a decrease in hydrogen bonds and higher interaction energy between the S protein and hACE2, demonstrating the lower structural stability and the worse binding affinity in the long dynamic evolutional process, even though the molecular docking showed the lower binding energy score of the S1 RBD of the double mutant variant with hACE2 than that of the wild type (WT) with hACE2. In addition, docking to three approved neutralizing monoclonal antibodies (mAbs) showed a reduced binding affinity of the double mutant variant, suggesting a lower neutralization ability of the mAbs against the double mutant variant. Our study helps lay the foundation for further SARS-CoV-2 studies and provides bioinformatics and computational insights into how the double mutations lead to immune evasion, which could offer guidance for subsequent biomedical studies.
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Affiliation(s)
- Yanqi Jiao
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yichen Xing
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yao Sun
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
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21
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Oda T, Yanagisawa H, Kikkawa M, Kita Y. Unveiling Liquid-Crystalline Lipids in the Urothelial Membrane through Cryo-EM. RESEARCH SQUARE 2023:rs.3.rs-3080731. [PMID: 37503277 PMCID: PMC10371089 DOI: 10.21203/rs.3.rs-3080731/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The urothelium, a distinct epithelial tissue lining the urinary tract, serves as an essential component in preserving urinary tract integrity and thwarting infections. The asymmetric unit membrane (AUM), primarily composed of the uroplakin complex, constitutes a critical permeability barrier in fulfilling this role. However, the molecular architectures of both the AUM and the uroplakin complex have remained enigmatic due to the paucity of high-resolution structural data. In this investigation, we employed cryo-electron microscopy to elucidate the three-dimensional structure of the uroplakin complex embedded within the porcine AUM at a resolution of 3.5 Å. Our findings unveiled that the uroplakin complexes are situated within hexagonally arranged crystalline lipid membrane domains, rich in hexosylceramides. Moreover, our research rectifies a misconception in a previous model by confirming the existence of a domain initially believed to be absent, and pinpointing the accurate location of a crucial Escherichia coli binding site implicated in urinary tract infections. These discoveries offer valuable insights into the molecular underpinnings governing the permeability barrier function of the urothelium and the orchestrated lipid phase formation within the plasma membrane.
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22
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Low Z, Lani R, Tiong V, Poh C, AbuBakar S, Hassandarvish P. COVID-19 Therapeutic Potential of Natural Products. Int J Mol Sci 2023; 24:ijms24119589. [PMID: 37298539 DOI: 10.3390/ijms24119589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Despite the fact that coronavirus disease 2019 (COVID-19) treatment and management are now considerably regulated, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still one of the leading causes of death in 2022. The availability of COVID-19 vaccines, FDA-approved antivirals, and monoclonal antibodies in low-income countries still poses an issue to be addressed. Natural products, particularly traditional Chinese medicines (TCMs) and medicinal plant extracts (or their active component), have challenged the dominance of drug repurposing and synthetic compound libraries in COVID-19 therapeutics. Their abundant resources and excellent antiviral performance make natural products a relatively cheap and readily available alternative for COVID-19 therapeutics. Here, we deliberately review the anti-SARS-CoV-2 mechanisms of the natural products, their potency (pharmacological profiles), and application strategies for COVID-19 intervention. In light of their advantages, this review is intended to acknowledge the potential of natural products as COVID-19 therapeutic candidates.
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Affiliation(s)
- Zhaoxuan Low
- Tropical Infectious Diseases Research & Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Rafidah Lani
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Vunjia Tiong
- Tropical Infectious Diseases Research & Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Chitlaa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Petaling Jaya 47500, Malaysia
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research & Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Pouya Hassandarvish
- Tropical Infectious Diseases Research & Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia
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23
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Kaewchim K, Glab-ampai K, Mahasongkram K, Saenlom T, Thepsawat W, Chulanetra M, Choowongkomon K, Sookrung N, Chaicumpa W. Neutralizing and Enhancing Epitopes of the SARS-CoV-2 Receptor-Binding Domain (RBD) Identified by Nanobodies. Viruses 2023; 15:1252. [PMID: 37376552 PMCID: PMC10301551 DOI: 10.3390/v15061252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Engineered nanobodies (VHs) to the SARS-CoV-2 receptor-binding domain (RBD) were generated using phage display technology. A recombinant Wuhan RBD served as bait in phage panning to fish out nanobody-displaying phages from a VH/VHH phage display library. Sixteen phage-infected E. coli clones produced nanobodies with 81.79-98.96% framework similarity to human antibodies; thus, they may be regarded as human nanobodies. Nanobodies of E. coli clones 114 and 278 neutralized SARS-CoV-2 infectivity in a dose-dependent manner; nanobodies of clones 103 and 105 enhanced the virus's infectivity by increasing the cytopathic effect (CPE) in an infected Vero E6 monolayer. These four nanobodies also bound to recombinant Delta and Omicron RBDs and native SARS-CoV-2 spike proteins. The neutralizing VH114 epitope contains the previously reported VYAWN motif (Wuhan RBD residues 350-354). The linear epitope of neutralizing VH278 at Wuhan RBD 319RVQPTESIVRFPNITN334 is novel. In this study, for the first time, we report SARS-CoV-2 RBD-enhancing epitopes, i.e., a linear VH103 epitope at RBD residues 359NCVADVSVLYNSAPFFTFKCYG380, and the VH105 epitope, most likely conformational and formed by residues in three RBD regions that are spatially juxtaposed upon the protein folding. Data obtained in this way are useful for the rational design of subunit SARS-CoV-2 vaccines that should be devoid of enhancing epitopes. VH114 and VH278 should be tested further for clinical use against COVID-19.
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Affiliation(s)
- Kanasap Kaewchim
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand;
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Kittirat Glab-ampai
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Kodchakorn Mahasongkram
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Thanatsaran Saenlom
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Watayagorn Thepsawat
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Monrat Chulanetra
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Sciences, Kasetsart University, Bangkok 10900, Thailand;
| | - Nitat Sookrung
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
- Biomedical Research Incubator Unit, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wanpen Chaicumpa
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok 10700, Thailand; (K.G.-a.); (K.M.); (T.S.); (W.T.); (M.C.); (N.S.)
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24
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Ma Y, Li P, Hu Y, Qiu T, Wang L, Lu H, Lv K, Xu M, Zhuang J, Liu X, He S, He B, Liu S, Liu L, Wang Y, Yue X, Zhai Y, Luo W, Mai H, Kuang Y, Chen S, Ye F, Zhou N, Zhao W, Chen J, Chen S, Xiong X, Shi M, Pan JA, Chen YQ. Spike substitution T813S increases Sarbecovirus fusogenicity by enhancing the usage of TMPRSS2. PLoS Pathog 2023; 19:e1011123. [PMID: 37196033 DOI: 10.1371/journal.ppat.1011123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 05/30/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
SARS-CoV Spike (S) protein shares considerable homology with SARS-CoV-2 S, especially in the conserved S2 subunit (S2). S protein mediates coronavirus receptor binding and membrane fusion, and the latter activity can greatly influence coronavirus infection. We observed that SARS-CoV S is less effective in inducing membrane fusion compared with SARS-CoV-2 S. We identify that S813T mutation is sufficient in S2 interfering with the cleavage of SARS-CoV-2 S by TMPRSS2, reducing spike fusogenicity and pseudoparticle entry. Conversely, the mutation of T813S in SARS-CoV S increased fusion ability and viral replication. Our data suggested that residue 813 in the S was critical for the proteolytic activation, and the change from threonine to Serine at 813 position might be an evolutionary feature adopted by SARS-2-related viruses. This finding deepened the understanding of Spike fusogenicity and could provide a new perspective for exploring Sarbecovirus' evolution.
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Affiliation(s)
- Yong Ma
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Pengbin Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yunqi Hu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Tianyi Qiu
- Institute of Clinical Science, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lixiang Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hongjie Lu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Kexin Lv
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Mengxin Xu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Jiaxin Zhuang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Xue Liu
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Suhua He
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Bing He
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Shuning Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Lin Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yuanyuan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Xinyu Yue
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yanmei Zhai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Wanyu Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Haoting Mai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yu Kuang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Shifeng Chen
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Feng Ye
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Na Zhou
- The 74(th) Group Army Hospital, Guangzhou, China
| | - Wenjing Zhao
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Jun Chen
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shoudeng Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Mang Shi
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Ji-An Pan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- National Medical Products Administration Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Sun Yat-sen University, Guanzhou, China
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25
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Aganovic A. pH-dependent endocytosis mechanisms for influenza A and SARS-coronavirus. Front Microbiol 2023; 14:1190463. [PMID: 37234537 PMCID: PMC10206014 DOI: 10.3389/fmicb.2023.1190463] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
The ongoing SARS-CoV-2 pandemic and the influenza epidemics have revived the interest in understanding how these highly contagious enveloped viruses respond to alterations in the physicochemical properties of their microenvironment. By understanding the mechanisms and conditions by which viruses exploit the pH environment of the host cell during endocytosis, we can gain a better understanding of how they respond to pH-regulated anti-viral therapies but also pH-induced changes in extracellular environments. This review provides a detailed explanation of the pH-dependent viral structural changes preceding and initiating viral disassembly during endocytosis for influenza A (IAV) and SARS coronaviruses. Drawing upon extensive literature from the last few decades and latest research, I analyze and compare the circumstances in which IAV and SARS-coronavirus can undertake endocytotic pathways that are pH-dependent. While there are similarities in the pH-regulated patterns leading to fusion, the mechanisms and pH activation differ. In terms of fusion activity, the measured activation pH values for IAV, across all subtypes and species, vary between approximately 5.0 to 6.0, while SARS-coronavirus necessitates a lower pH of 6.0 or less. The main difference between the pH-dependent endocytic pathways is that the SARS-coronavirus, unlike IAV, require the presence of specific pH-sensitive enzymes (cathepsin L) during endosomal transport. Conversely, the conformational changes in the IAV virus under acidic conditions in endosomes occur due to the specific envelope glycoprotein residues and envelope protein ion channels (viroporins) getting protonated by H+ ions. Despite extensive research over several decades, comprehending the pH-triggered conformational alterations of viruses still poses a significant challenge. The precise mechanisms of protonation mechanisms of certain during endosomal transport for both viruses remain incompletely understood. In absence of evidence, further research is needed.
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Barkhordarian M, Behbood A, Ranjbar M, Rahimian Z, Prasad A. Overview of the cardio-metabolic impact of the COVID-19 pandemic. Endocrine 2023; 80:477-490. [PMID: 37103684 PMCID: PMC10133915 DOI: 10.1007/s12020-023-03337-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/21/2023] [Indexed: 04/28/2023]
Abstract
Evidence has shown that cardiometabolic disorders (CMDs) are amongst the top contributors to COVID-19 infection morbidity and mortality. The reciprocal impact of COVID-19 infection and the most common CMDs, the risk factors for poor composite outcome among patients with one or several underlying diseases, the effect of common medical management on CMDs and their safety in the context of acute COVID-19 infection are reviewed. Later on, the changes brought by the COVID-19 pandemic quarantine on the general population's lifestyle (diet, exercise patterns) and metabolic health, acute cardiac complications of different COVID-19 vaccines and the effect of CMDs on the vaccine efficacy are discussed. Our review identified that the incidence of COVID-19 infection is higher among patients with underlying CMDs such as hypertension, diabetes, obesity and cardiovascular disease. Also, CMDs increase the risk of COVID-19 infection progression to severe disease phenotypes (e.g. hospital and/or ICU admission, use of mechanical ventilation). Lifestyle modification during COVID-19 era had a great impact on inducing and worsening of CMDs. Finally, the lower efficacy of COVID-19 vaccines was found in patients with metabolic disease.
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Affiliation(s)
- Maryam Barkhordarian
- Department of Medicine, Division of Cardiology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Arezoo Behbood
- MPH department, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Maryam Ranjbar
- Student Research Committee, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Zahra Rahimian
- Student Research Committee, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Anand Prasad
- Division of Cardiology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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27
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Gonzalez-Rodriguez E, Zol-Hanlon M, Bineva-Todd G, Marchesi A, Skehel M, Mahoney KE, Roustan C, Borg A, Di Vagno L, Kjær S, Wrobel AG, Benton DJ, Nawrath P, Flitsch SL, Joshi D, González-Ramírez A, Wilkinson KA, Wilkinson RJ, Wall EC, Hurtado-Guerrero R, Malaker SA, Schumann B. O-Linked Sialoglycans Modulate the Proteolysis of SARS-CoV-2 Spike and Likely Contribute to the Mutational Trajectory in Variants of Concern. ACS CENTRAL SCIENCE 2023; 9:393-404. [PMID: 36968546 PMCID: PMC10037455 DOI: 10.1021/acscentsci.2c01349] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Indexed: 06/18/2023]
Abstract
The emergence of a polybasic cleavage motif for the protease furin in SARS-CoV-2 spike has been established as a major factor for human viral transmission. The region N-terminal to that motif is extensively mutated in variants of concern (VOCs). Besides furin, spikes from these variants appear to rely on other proteases for maturation, including TMPRSS2. Glycans near the cleavage site have raised questions about proteolytic processing and the consequences of variant-borne mutations. Here, we identify that sialic acid-containing O-linked glycans on Thr678 of SARS-CoV-2 spike influence furin and TMPRSS2 cleavage and posit O-linked glycosylation as a likely driving force for the emergence of VOC mutations. We provide direct evidence that the glycosyltransferase GalNAc-T1 primes glycosylation at Thr678 in the living cell, an event that is suppressed by mutations in the VOCs Alpha, Delta, and Omicron. We found that the sole incorporation of N-acetylgalactosamine did not impact furin activity in synthetic O-glycopeptides, but the presence of sialic acid reduced the furin rate by up to 65%. Similarly, O-glycosylation with a sialylated trisaccharide had a negative impact on TMPRSS2 cleavage. With a chemistry-centered approach, we substantiate O-glycosylation as a major determinant of spike maturation and propose disruption of O-glycosylation as a substantial driving force for VOC evolution.
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Affiliation(s)
- Edgar Gonzalez-Rodriguez
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Mia Zol-Hanlon
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Signalling
and Structural Biology Lab, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Ganka Bineva-Todd
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
| | - Andrea Marchesi
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Mark Skehel
- Proteomics
Science Technology Platform, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Keira E. Mahoney
- Department
of Chemistry, Yale University, 275 Prospect Street, 06511 New Haven, Connecticut, United States
| | - Chloë Roustan
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Annabel Borg
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Lucia Di Vagno
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Proteomics
Science Technology Platform, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Svend Kjær
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Antoni G. Wrobel
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Donald J. Benton
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Philipp Nawrath
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Sabine L. Flitsch
- Manchester
Institute of Biotechnology, University of
Manchester, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - Dhira Joshi
- Chemical
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Katalin A. Wilkinson
- Tuberculosis
Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Wellcome
Centre for Infectious Diseases Research in Africa, University of Cape Town, 7925 Observatory, Cape Town, South Africa
| | - Robert J. Wilkinson
- Tuberculosis
Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Wellcome
Centre for Infectious Diseases Research in Africa, University of Cape Town, 7925 Observatory, Cape Town, South Africa
- Department
of Infectious Diseases, Imperial College
London, W12 0NN London, United Kingdom
- Institute
of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, 7925 Observatory, Cape Town, South Africa
| | - Emma C. Wall
- The Francis
Crick Institute, NW1 1AT London, United Kingdom
- University
College London Hospitals (UCLH) Biomedical Research Centre, W1T 7DN London, United Kingdom
| | - Ramón Hurtado-Guerrero
- Institute
of Biocomputation and Physics of Complex Systems, University of Zaragoza, 50018 Zaragoza, Spain
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Fundación
ARAID, 50018 Zaragoza, Spain
| | - Stacy A. Malaker
- Department
of Chemistry, Yale University, 275 Prospect Street, 06511 New Haven, Connecticut, United States
| | - Benjamin Schumann
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
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28
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COVID-19-Induced Myocarditis: Pathophysiological Roles of ACE2 and Toll-like Receptors. Int J Mol Sci 2023; 24:ijms24065374. [PMID: 36982447 PMCID: PMC10049267 DOI: 10.3390/ijms24065374] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
The clinical manifestations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection responsible for coronavirus disease 2019 (COVID-19) commonly include dyspnoea and fatigue, and they primarily involve the lungs. However, extra-pulmonary organ dysfunctions, particularly affecting the cardiovascular system, have also been observed following COVID-19 infection. In this context, several cardiac complications have been reported, including hypertension, thromboembolism, arrythmia and heart failure, with myocardial injury and myocarditis being the most frequent. These secondary myocardial inflammatory responses appear to be associated with a poorer disease course and increased mortality in patients with severe COVID-19. In addition, numerous episodes of myocarditis have been reported as a complication of COVID-19 mRNA vaccinations, especially in young adult males. Changes in the cell surface expression of angiotensin-converting enzyme 2 (ACE2) and direct injury to cardiomyocytes resulting from exaggerated immune responses to COVID-19 are just some of the mechanisms that may explain the pathogenesis of COVID-19-induced myocarditis. Here, we review the pathophysiological mechanisms underlying myocarditis associated with COVID-19 infection, with a particular focus on the involvement of ACE2 and Toll-like receptors (TLRs).
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Borkotoky S, Dey D, Hazarika Z. Interactions of angiotensin-converting enzyme-2 (ACE2) and SARS-CoV-2 spike receptor-binding domain (RBD): a structural perspective. Mol Biol Rep 2023; 50:2713-2721. [PMID: 36562937 PMCID: PMC9786537 DOI: 10.1007/s11033-022-08193-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since its discovery in late 2019 in Wuhan, China. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme-2 (ACE2) receptor, a critical component of the renin-angiotensin system (RAS) that initiates the viral transmission. Most of the critical mutations found in SARS-CoV-2 are associated with the RBD of the spike protein. These mutations have the potential to reduce the efficacy of vaccines and neutralizing antibodies. METHODS In this review, the structural details of ACE2, RBD and their interactions are discussed. In addition, some critical mutations of RBD and their impact on ACE2-RBD interactions are also discussed. CONCLUSION Preventing the interaction between Spike RBD and ACE2 is considered a viable therapeutic strategy since ACE2 binding by RBD is the first step in virus infection. Because the interactions between the two entities are critical for both viral transmission and therapeutic development, it is essential to understand their interactions in detail.
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Affiliation(s)
- Subhomoi Borkotoky
- Department of Biotechnology, Faculty of Biosciences, Invertis University, Bareilly, Uttar Pradesh, 243123, India.
| | - Debajit Dey
- School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, United States of America
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Cassari L, Pavan A, Zoia G, Chinellato M, Zeni E, Grinzato A, Rothenberger S, Cendron L, Dettin M, Pasquato A. SARS-CoV-2 S Mutations: A Lesson from the Viral World to Understand How Human Furin Works. Int J Mol Sci 2023; 24:4791. [PMID: 36902222 PMCID: PMC10003014 DOI: 10.3390/ijms24054791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the etiological agent responsible for the worldwide pandemic and has now claimed millions of lives. The virus combines several unusual characteristics and an extraordinary ability to spread among humans. In particular, the dependence of the maturation of the envelope glycoprotein S from Furin enables the invasion and replication of the virus virtually within the entire body, since this cellular protease is ubiquitously expressed. Here, we analyzed the naturally occurring variation of the amino acids sequence around the cleavage site of S. We found that the virus grossly mutates preferentially at P positions, resulting in single residue replacements that associate with gain-of-function phenotypes in specific conditions. Interestingly, some combinations of amino acids are absent, despite the evidence supporting some cleavability of the respective synthetic surrogates. In any case, the polybasic signature is maintained and, as a consequence, Furin dependence is preserved. Thus, no escape variants to Furin are observed in the population. Overall, the SARS-CoV-2 system per se represents an outstanding example of the evolution of substrate-enzyme interaction, demonstrating a fast-tracked optimization of a protein stretch towards the Furin catalytic pocket. Ultimately, these data disclose important information for the development of drugs targeting Furin and Furin-dependent pathogens.
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Affiliation(s)
- Leonardo Cassari
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Angela Pavan
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Giulia Zoia
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Monica Chinellato
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Elena Zeni
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Alessandro Grinzato
- European Synchrotron Radiation Facility, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Sylvia Rothenberger
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
| | - Laura Cendron
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Monica Dettin
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Antonella Pasquato
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
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31
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Tornesello AL, Botti C, Micillo A, Labonia F, Arpino S, Isgrò MA, Meola S, Russo L, Cavalcanti E, Sale S, Nicastro C, Atripaldi L, Starita N, Cerasuolo A, Reimer U, Holenya P, Buonaguro L, Buonaguro FM, Tornesello ML. Immune profiling of SARS-CoV-2 epitopes in asymptomatic and symptomatic pediatric and adult patients. J Transl Med 2023; 21:123. [PMID: 36788606 PMCID: PMC9927035 DOI: 10.1186/s12967-023-03963-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND The infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has unpredictable manifestations of coronavirus disease (COVID-19) and variable clinical course with some patients being asymptomatic whereas others experiencing severe respiratory distress, or even death. We aimed to evaluate the immunoglobulin G (IgG) response towards linear peptides on a peptide array containing sequences from SARS-CoV-2, Middle East respiratory syndrome-related coronavirus (MERS) and common-cold coronaviruses 229E, OC43, NL63 and HKU1 antigens, in order to identify immunological indicators of disease outcome in SARS-CoV-2 infected patients. METHODS We included in the study 79 subjects, comprising 19 pediatric and 30 adult SARS-CoV-2 infected patients with increasing disease severity, from mild to critical illness, and 30 uninfected subjects who were vaccinated with one dose of SARS-CoV-2 spike mRNA BNT162b2 vaccine. Serum samples were analyzed by a peptide microarray containing 5828 overlapping 15-mer synthetic peptides corresponding to the full SARS-CoV-2 proteome and selected linear epitopes of spike (S), envelope (E) and membrane (M) glycoproteins as well as nucleoprotein (N) of MERS, SARS and coronaviruses 229E, OC43, NL63 and HKU1 (isolates 1, 2 and 5). RESULTS All patients exhibited high IgG reactivity against the central region and C-terminus peptides of both SARS-CoV-2 N and S proteins. Setting the threshold value for serum reactivity above 25,000 units, 100% and 81% of patients with severe disease, 36% and 29% of subjects with mild symptoms, and 8% and 17% of children younger than 8-years reacted against N and S proteins, respectively. Overall, the total number of peptides in the SARS-CoV-2 proteome targeted by serum samples was much higher in children compared to adults. Notably, we revealed a differential antibody response to SARS-CoV-2 peptides of M protein between adults, mainly reacting against the C-terminus epitopes, and children, who were highly responsive to the N-terminus of M protein. In addition, IgG signals against NS7B, NS8 and ORF10 peptides were found elevated mainly among adults with mild (63%) symptoms. Antibodies towards S and N proteins of other coronaviruses (MERS, 229E, OC43, NL63 and HKU1) were detected in all groups without a significant correlation with SARS-CoV-2 antibody levels. CONCLUSIONS Overall, our results showed that antibodies elicited by specific linear epitopes of SARS-CoV-2 proteome are age dependent and related to COVID-19 clinical severity. Cross-reaction of antibodies to epitopes of other human coronaviruses was evident in all patients with distinct profiles between children and adult patients. Several SARS-CoV-2 peptides identified in this study are of particular interest for the development of vaccines and diagnostic tests to predict the clinical outcome of SARS-CoV-2 infection.
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Affiliation(s)
- Anna Lucia Tornesello
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", 80131, Naples, Italy.
| | - Chiara Botti
- grid.415247.10000 0004 1756 8081Laboratory of Clinical Pathology, Santobono-Pausilipon Children’s Hospital, 80129 Napoli, Italy
| | - Alberto Micillo
- grid.415247.10000 0004 1756 8081Laboratory of Clinical Pathology, Santobono-Pausilipon Children’s Hospital, 80129 Napoli, Italy
| | - Francesco Labonia
- grid.508451.d0000 0004 1760 8805Laboratory Medicine Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Sergio Arpino
- grid.508451.d0000 0004 1760 8805Laboratory Medicine Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Maria Antonietta Isgrò
- grid.508451.d0000 0004 1760 8805Laboratory Medicine Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Serena Meola
- grid.508451.d0000 0004 1760 8805Laboratory Medicine Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Luigi Russo
- grid.508451.d0000 0004 1760 8805Laboratory Medicine Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Ernesta Cavalcanti
- grid.508451.d0000 0004 1760 8805Laboratory Medicine Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Silvia Sale
- UOC Biochimica Chimica, AORN Ospedali dei Colli P.O. Monaldi, Naples, Italy
| | - Carmine Nicastro
- UOC Biochimica Chimica, AORN Ospedali dei Colli P.O. Monaldi, Naples, Italy
| | - Luigi Atripaldi
- UOC Biochimica Chimica, AORN Ospedali dei Colli P.O. Monaldi, Naples, Italy
| | - Noemy Starita
- grid.508451.d0000 0004 1760 8805Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Andrea Cerasuolo
- grid.508451.d0000 0004 1760 8805Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Ulf Reimer
- grid.435562.3JPT Peptide Technologies GmbH, Berlin, Germany
| | - Pavlo Holenya
- grid.435562.3JPT Peptide Technologies GmbH, Berlin, Germany
| | - Luigi Buonaguro
- grid.508451.d0000 0004 1760 8805Innovative Immunological Models, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, Via Mariano Semmola, 80131 Naples, Italy
| | - Franco M. Buonaguro
- grid.508451.d0000 0004 1760 8805Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
| | - Maria Lina Tornesello
- grid.508451.d0000 0004 1760 8805Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, 80131 Naples, Italy
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Khatri R, Siddqui G, Sadhu S, Maithil V, Vishwakarma P, Lohiya B, Goswami A, Ahmed S, Awasthi A, Samal S. Intrinsic D614G and P681R/H mutations in SARS-CoV-2 VoCs Alpha, Delta, Omicron and viruses with D614G plus key signature mutations in spike protein alters fusogenicity and infectivity. Med Microbiol Immunol 2023; 212:103-122. [PMID: 36583790 PMCID: PMC9801140 DOI: 10.1007/s00430-022-00760-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 12/03/2022] [Indexed: 12/31/2022]
Abstract
The SARS-CoV-2 virus has been rapidly evolving over the time and the genetic variation has led to the generation of Variants of Concerns (VoC), which have shown increased fitness. These VoC viruses contain the key mutations in the spike protein which have allowed better survival and evasion of host defense mechanisms. The D614G mutation in the spike domain is found in the majority of VoC; additionally, the P681R/H mutation at the S1/S2 furin cleavage site junction is also found to be highly conserved in major VoCs; Alpha, Delta, Omicron, and its' current variants. The impact of these genetic alterations of the SARS-CoV-2 VoCs on the host cell entry, transmissibility, and infectivity has not been clearly identified. In our study, Delta and D614G + P681R synthetic double mutant pseudoviruses showed a significant increase in the cell entry, cell-to-cell fusion and infectivity. In contrast, the Omicron and P681H synthetic single mutant pseudoviruses showed TMPRSS2 independent cell entry, less fusion and infectivity as compared to Delta and D614G + P681R double mutants. Addition of exogenous trypsin further enhanced fusion in Delta viruses as compared to Omicron. Furthermore, Delta viruses showed susceptibility to both E64d and Camostat mesylate inhibitors suggesting, that the Delta virus could exploit both endosomal and TMPRSS2 dependent entry pathways as compared to the Omicron virus. Taken together, these results indicate that the D614G and P681R/H mutations in the spike protein are pivotal which might be favoring the VoC replication in different host compartments, and thus allowing a balance of mutation vs selection for better long-term adaptation.
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Affiliation(s)
- Ritika Khatri
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Gazala Siddqui
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Srikanth Sadhu
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
- Immunobiology and Immunology Core Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Vikas Maithil
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Preeti Vishwakarma
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Bharat Lohiya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Abhishek Goswami
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Shubbir Ahmed
- Centralized Core Research Facility (CCRF), All India Institute of Medical Science (AIIMS), Delhi, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
- Immunobiology and Immunology Core Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Sweety Samal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India.
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Sattar S, Kabat J, Jerome K, Feldmann F, Bailey K, Mehedi M. Nuclear translocation of spike mRNA and protein is a novel feature of SARS-CoV-2. Front Microbiol 2023; 14:1073789. [PMID: 36778849 PMCID: PMC9909199 DOI: 10.3389/fmicb.2023.1073789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/12/2023] [Indexed: 01/27/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes severe pathophysiology in vulnerable older populations and appears to be highly pathogenic and more transmissible than other coronaviruses. The spike (S) protein appears to be a major pathogenic factor that contributes to the unique pathogenesis of SARS-CoV-2. Although the S protein is a surface transmembrane type 1 glycoprotein, it has been predicted to be translocated into the nucleus due to the novel nuclear localization signal (NLS) "PRRARSV," which is absent from the S protein of other coronaviruses. Indeed, S proteins translocate into the nucleus in SARS-CoV-2-infected cells. S mRNAs also translocate into the nucleus. S mRNA colocalizes with S protein, aiding the nuclear translocation of S mRNA. While nuclear translocation of nucleoprotein (N) has been shown in many coronaviruses, the nuclear translocation of both S mRNA and S protein reveals a novel feature of SARS-CoV-2.
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Affiliation(s)
- Sarah Sattar
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
| | - Juraj Kabat
- Biological Imaging Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kailey Jerome
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
| | - Friederike Feldmann
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Kristina Bailey
- Department of Internal Medicine, Pulmonary, Critical Care, and Sleep and Allergy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Masfique Mehedi
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
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34
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Wang E. Prediction of antibody binding to SARS-CoV-2 RBDs. BIOINFORMATICS ADVANCES 2023; 3:vbac103. [PMID: 36698760 PMCID: PMC9868522 DOI: 10.1093/bioadv/vbac103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/18/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
Abstract
Summary The ability to predict antibody-antigen binding is essential for computational models of antibody affinity maturation and protein design. While most models aim to predict binding for arbitrary antigens and antibodies, the global impact of SARS-CoV-2 on public health and the availability of associated data suggest that a SARS-CoV-2-specific model would be highly beneficial. In this work, we present a neural network model, trained on ∼315 000 datapoints from deep mutational scanning experiments, that predicts escape fractions of SARS-CoV-2 RBDs binding to arbitrary antibodies. The antibody embeddings within the model constitute an effective sequence space, which correlates with the Hamming distance, suggesting that these embeddings may be useful for downstream tasks such as binding prediction. Indeed, the model achieves Spearman correlation coefficients of 0.46 and 0.52 on two held-out test sets. By comparison, correlation coefficients calculated using existing structure and sequence-based models do not exceed 0.28. The correlation coefficient against dissociation constants of antibodies binding to SARS-CoV-2 RBD variants is 0.46. Additionally, the residue-level escapes are highest in the antibody epitope, correlating well with experimentally measured escapes. We further study the effect of antibody chain use, embedding dimension size and feed-forward and convolutional architectures on the model results. Lastly, we find that the inference time of our model is significantly faster than previous models, suggesting that it could be a useful tool for the accurate and rapid prediction of antibodies binding to SARS-CoV-2 RBDs. Availability and implementation The model and associated code are available for download at https://github.com/ericzwang/RBD_AB. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Eric Wang
- To whom correspondence should be addressed.
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35
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Pereira GC. An Automated Strategy to Handle Antigenic Variability in Immunisation Protocols, Part I: Nanopore Sequencing of Infectious Agent Variants. Methods Mol Biol 2023; 2575:305-321. [PMID: 36301483 DOI: 10.1007/978-1-0716-2716-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Infectious agents often challenge therapeutics, from antibiotics resistance to antigenic variability affecting inoculation measures. Over the last decades, genome sequencing arose as an important ally to address such challenges. In bacterial infection, whole-genome-sequencing (WGS) supports tracking pathogenic alterations affecting the human microbiome. In viral infection, the analysis of the relevant sequence of nucleotides helps with determining historical variants of a virus and elucidates details about infection clusters and their distribution. Additionally, genome sequencing is now an important step in inoculation protocols, isolating target genes to design more robust immunisation assays. Ultimately, genetic engineering has empowered repurposing at scale, allowing long-lasting repeating clinical trials to be automated within a much shorter time-frame, by adjusting existing protocols. This is particularly important during sanitary emergencies as the ones caused by the 2014 West African Ebola outbreak, the Zika virus rapid spread in both South and North America in 2015, followed by Asia in 2016, and the pandemic caused by the SARS-CoV-2, which has infected more than 187 million people and caused more than 4 million deaths, worldwide, as per July 2021 statistics. In this scenery, this chapter presents a novel fully automated strategy to handle antigenic variability in immunisation protocols. The methodology comprises of two major steps (1) nanopore sequencing of infectious agent variants - the focus is on the SARS-CoV-2 and its variants; followed by (2) mRNA vector design for immunotherapy. This chapter presents the nanopore sequencing step and Chapter 17 introduces a protocol for mRNA vector design.
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36
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Chee J, Chern B, Loh WS, Mullol J, Wang DY. Pathophysiology of SARS-CoV-2 Infection of Nasal Respiratory and Olfactory Epithelia and Its Clinical Impact. Curr Allergy Asthma Rep 2023; 23:121-131. [PMID: 36598732 PMCID: PMC9811886 DOI: 10.1007/s11882-022-01059-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2022] [Indexed: 01/05/2023]
Abstract
PURPOSE OF REVIEW While the predominant cause for morbidity and mortality with SARS-CoV-2 infection is the lower respiratory tract manifestations of the disease, the effects of SARS-CoV-2 infection on the sinonasal tract have also come to the forefront especially with the increased recognition of olfactory symptom. This review presents a comprehensive summary of the mechanisms of action of the SARS-CoV-2 virus, sinonasal pathophysiology of COVID-19, and the correlation with the clinical and epidemiological impact on olfactory dysfunction. RECENT FINDINGS ACE2 and TMPRSS2 receptors are key players in the mechanism of infection of SARS-CoV-2. They are present within both the nasal respiratory as well as olfactory epithelia. There are however differences in susceptibility between different groups of individuals, as well as between the different SARS-CoV-2 variants. The sinonasal cavity is an important route for SARS-CoV-2 infection. While the mechanism of infection of SARS-CoV-2 in nasal respiratory and olfactory epithelia is similar, there exist small but significant differences in the susceptibility of these epithelia and consequently clinical manifestations of the disease. Understanding the differences and nuances in sinonasal pathophysiology in COVID-19 would allow the clinician to predict and counsel patients suffering from COVID-19. Future research into molecular pathways and cytokine responses at different stages of infection and different variants of SARS-CoV-2 would evaluate the individual clinical phenotype, prognosis, and possibly response to vaccines and therapeutics.
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Affiliation(s)
- Jeremy Chee
- grid.410759.e0000 0004 0451 6143Department of Otolaryngology - Head & Neck Surgery, National University Health System, 1E Kent Ridge Road, Singapore, 119228 Singapore
| | - Beverlyn Chern
- grid.410759.e0000 0004 0451 6143Department of Otolaryngology - Head & Neck Surgery, National University Health System, 1E Kent Ridge Road, Singapore, 119228 Singapore
| | - Woei Shyang Loh
- grid.410759.e0000 0004 0451 6143Department of Otolaryngology - Head & Neck Surgery, National University Health System, 1E Kent Ridge Road, Singapore, 119228 Singapore ,grid.4280.e0000 0001 2180 6431Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Joaquim Mullol
- grid.10403.360000000091771775Rhinology Unit & Smell Clinic, Department of Otorhinolaryngology, Hospital Clinic Barcelona, Universitat de Barcelona, IDIBAPS, CIBERES, Barcelona, Catalonia Spain
| | - De Yun Wang
- Department of Otolaryngology - Head & Neck Surgery, National University Health System, 1E Kent Ridge Road, Singapore, 119228, Singapore. .,Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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37
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Li X, Yuan H, Li X, Wang H. Spike protein mediated membrane fusion during SARS-CoV-2 infection. J Med Virol 2023; 95:e28212. [PMID: 36224449 PMCID: PMC9874878 DOI: 10.1002/jmv.28212] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/15/2022] [Accepted: 10/10/2022] [Indexed: 01/27/2023]
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a serious threat to public health and has quickly become a global concern. The infection of SARS-CoV-2 begins with the binding of its spike protein to the receptor-angiotensin-converting enzyme 2 (ACE2), which, after a series of conformation changes, results in the fusion of viral-cell membranes and the release of the viral RNA genome into the cytoplasm. In addition, infected host cells can express spike protein on their cell surface, which will interact with ACE2 on neighboring cells, leading to cell membrane fusion and the formation of multinucleated cells or syncytia. Both viral entry and syncytia formation are mediated by spike-ACE2 interaction and share some common mechanisms of membrane fusion. Here in this review, we will summarize our current understanding of spike-mediated membrane fusion, which may shed light on future broad-spectrum antiviral development.
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Affiliation(s)
- Xinyu Li
- Department of Pathogen Biology and ImmunologyXi'an Jiaotong University Health Science CenterXi'anChina
| | - Huijun Yuan
- Department of Pathogen Biology and ImmunologyXi'an Jiaotong University Health Science CenterXi'anChina
| | - Xiaozhen Li
- Department of Pathogen Biology and ImmunologyXi'an Jiaotong University Health Science CenterXi'anChina
| | - Hongliang Wang
- Department of Pathogen Biology and ImmunologyXi'an Jiaotong University Health Science CenterXi'anChina
- Key Laboratory of Environment and Genes Related to DiseasesXi'an Jiaotong UniversityXi'anChina
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Development of Fluorescence-Tagged SARS-CoV-2 Virus-like Particles by a Tri-Cistronic Vector Expression System for Investigating the Cellular Entry of SARS-CoV-2. Viruses 2022; 14:v14122825. [PMID: 36560829 PMCID: PMC9786960 DOI: 10.3390/v14122825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) has caused the pandemic that began late December 2019. The co-expression of SARS-CoV-2 structural proteins in cells could assemble into several types of virus-like particles (VLPs) without a viral RNA genome. VLPs containing S proteins with the structural and functional properties of authentic virions are safe materials to exploit for virus-cell entry and vaccine development. In this study, to generate SARS-CoV-2 VLPs (SCoV2-SEM VLPs) composed of three structural proteins including spike (S), envelop (E) protein and membrane (M) protein, a tri-cistronic vector expression system was established in a cell line co-expressing SARS-CoV-2 S, E and M proteins. The SCoV2-SEM VLPs were harvested from the cultured medium, and three structure proteins were confirmed by Western blot assay. A negative-stain TEM assay demonstrated the size of the SCoV2-SEM VLPs with a diameter of about 90 nm. To further characterize the infectious properties of SCoV2-SEM VLPs, the VLPs (atto647N-SCoV2-SEM VLPs) were fluorescence-labeled by conjugation with atto-647N and visualized under confocal microscopy at a single-particle resolution. The results of the infection assay revealed that atto647N-SCoV2-SEM VLPs attached to the surface of the HEK293T cells at the pre-binding phase in a ACE2-dependent manner. At the post-infection phase, atto647N-SCoV2-SEM VLPs either fused with the cellular membrane or internalized into the cytoplasm with mCherry-rab5-positive early endosomes. Moreover, fusion with the cellular membrane and the internalization with early endosomes could be inhibited by the treatment of camostat (a pharmacological inhibitor of TMPRSS2) and chlorpromazine (an endocytosis inhibitor), respectively. These results elucidated that SCoV2-SEM VLPs behave similarly to the authentic live SARS-CoV-2 virus, suggesting that the development of SCoV2-SEM VLPs provide a realistic and safe experimental model for studying the infectious mechanism of SARS-CoV-2.
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Meyer zu Natrup C, Tscherne A, Dahlke C, Ciurkiewicz M, Shin DL, Fathi A, Rohde C, Kalodimou G, Halwe S, Limpinsel L, Schwarz JH, Klug M, Esen M, Schneiderhan-Marra N, Dulovic A, Kupke A, Brosinski K, Clever S, Schünemann LM, Beythien G, Armando F, Mayer L, Weskamm ML, Jany S, Freudenstein A, Tuchel T, Baumgärtner W, Kremsner P, Fendel R, Addo MM, Becker S, Sutter G, Volz A. Stabilized recombinant SARS-CoV-2 spike antigen enhances vaccine immunogenicity and protective capacity. J Clin Invest 2022; 132:159895. [PMID: 36301637 PMCID: PMC9754005 DOI: 10.1172/jci159895] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/21/2022] [Indexed: 12/24/2022] Open
Abstract
The SARS-CoV-2 spike (S) glycoprotein is synthesized as a large precursor protein and must be activated by proteolytic cleavage into S1 and S2. A recombinant modified vaccinia virus Ankara (MVA) expressing native, full-length S protein (MVA-SARS-2-S) is currently under investigation as a candidate vaccine in phase I clinical studies. Initial results from immunogenicity monitoring revealed induction of S-specific antibodies binding to S2, but low-level antibody responses to the S1 domain. Follow-up investigations of native S antigen synthesis in MVA-SARS-2-S-infected cells revealed limited levels of S1 protein on the cell surface. In contrast, we found superior S1 cell surface presentation upon infection with a recombinant MVA expressing a stabilized version of SARS-CoV-2 S protein with an inactivated S1/S2 cleavage site and K986P and V987P mutations (MVA-SARS-2-ST). When comparing immunogenicity of MVA vector vaccines, mice vaccinated with MVA-SARS-2-ST mounted substantial levels of broadly reactive anti-S antibodies that effectively neutralized different SARS-CoV-2 variants. Importantly, intramuscular MVA-SARS-2-ST immunization of hamsters and mice resulted in potent immune responses upon challenge infection and protected from disease and severe lung pathology. Our results suggest that MVA-SARS-2-ST represents an improved clinical candidate vaccine and that the presence of plasma membrane-bound S1 is highly beneficial to induce protective antibody levels.
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Affiliation(s)
| | - Alina Tscherne
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany.,German Center for Infection Research, partner site Munich, and
| | - Christine Dahlke
- partner site Hamburg-Lübeck-Borstel-Riems.,University Medical Center Hamburg-Eppendorf, Institute for Infection Research and Vaccine Development (IIRVD), Hamburg, Germany
| | - Malgorzata Ciurkiewicz
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Dai-Lun Shin
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Anahita Fathi
- partner site Hamburg-Lübeck-Borstel-Riems.,University Medical Center Hamburg-Eppendorf, Institute for Infection Research and Vaccine Development (IIRVD), Hamburg, Germany.,University Medical Center Hamburg-Eppendorf, Division of Infectious Diseases, Hamburg, Germany
| | - Cornelius Rohde
- German Center for Infection Research, partner site Gießen-Marburg-Langen.,Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Georgia Kalodimou
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany.,German Center for Infection Research, partner site Munich, and
| | - Sandro Halwe
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Leonard Limpinsel
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Jan H. Schwarz
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Martha Klug
- German Center for Infection Research, partner site Tübingen.,Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Meral Esen
- German Center for Infection Research, partner site Tübingen.,Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | | | - Alex Dulovic
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Alexandra Kupke
- German Center for Infection Research, partner site Gießen-Marburg-Langen.,Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Katrin Brosinski
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Sabrina Clever
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Lisa-Marie Schünemann
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Georg Beythien
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Federico Armando
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Leonie Mayer
- partner site Hamburg-Lübeck-Borstel-Riems.,University Medical Center Hamburg-Eppendorf, Institute for Infection Research and Vaccine Development (IIRVD), Hamburg, Germany.,University Medical Center Hamburg-Eppendorf, Division of Infectious Diseases, Hamburg, Germany
| | - Marie L. Weskamm
- partner site Hamburg-Lübeck-Borstel-Riems.,University Medical Center Hamburg-Eppendorf, Institute for Infection Research and Vaccine Development (IIRVD), Hamburg, Germany.,University Medical Center Hamburg-Eppendorf, Division of Infectious Diseases, Hamburg, Germany
| | - Sylvia Jany
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Astrid Freudenstein
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Tamara Tuchel
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Peter Kremsner
- German Center for Infection Research, partner site Tübingen.,Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany.,Centre de Recherches Médicales de Lambarene, Gabon
| | - Rolf Fendel
- German Center for Infection Research, partner site Tübingen.,Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Marylyn M. Addo
- University Medical Center Hamburg-Eppendorf, Institute for Infection Research and Vaccine Development (IIRVD), Hamburg, Germany.,German Center for Infection Research, partner site Tübingen
| | - Stephan Becker
- German Center for Infection Research, partner site Gießen-Marburg-Langen.,Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Gerd Sutter
- Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany.,German Center for Infection Research, partner site Munich, and
| | - Asisa Volz
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany.,German Center for Infection Research, partner site Hanover-Braunschweig
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40
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Shapira T, Vimalanathan S, Rens C, Pichler V, Peña-Díaz S, Jordana G, Rees W, Winkler DFH, Sarai I, Steiner T, Jean F, Pelech S, Av-Gay Y. Inhibition of glycogen synthase kinase-3-beta (GSK3β) blocks nucleocapsid phosphorylation and SARS-CoV-2 replication. MOLECULAR BIOMEDICINE 2022; 3:43. [PMID: 36508083 PMCID: PMC9742639 DOI: 10.1186/s43556-022-00111-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/19/2022] [Indexed: 12/14/2022] Open
Abstract
GSK3β has been proposed to have an essential role in Coronaviridae infections. Screening of a targeted library of GSK3β inhibitors against both SARS-CoV-2 and HCoV-229E to identify broad-spectrum anti-Coronaviridae inhibitors resulted in the identification of a high proportion of active compounds with low toxicity to host cells. A selected lead compound, T-1686568, showed low micromolar, dose-dependent activity against SARS-CoV-2 and HCoV-229E. T-1686568 showed efficacy in viral-infected cultured cells and primary 2D organoids. T-1686568 also inhibited SARS-CoV-2 variants of concern Delta and Omicron. Importantly, while inhibition by T-1686568 resulted in the overall reduction of viral load and protein translation, GSK3β inhibition resulted in cellular accumulation of the nucleocapsid protein relative to the spike protein. Following identification of potential phosphorylation sites of Coronaviridae nucleocapsid, protein kinase substrate profiling assays combined with Western blotting analysis of nine host kinases showed that the SARS-CoV-2 nucleocapsid could be phosphorylated by GSK3β and PKCa. GSK3β phosphorylated SARS-CoV-2 nucleocapsid on the S180/S184, S190/S194 and T198 phospho-sites, following previous priming in the adjacent S188, T198 and S206, respectively. Such inhibition presents a compelling target for broad-spectrum anti-Coronaviridae compound development, and underlies the mechanism of action of GSK3β host-directed therapy against this class of obligate intracellular pathogens.
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Affiliation(s)
- Tirosh Shapira
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada ,grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Selvarani Vimalanathan
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Celine Rens
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Virginia Pichler
- grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Sandra Peña-Díaz
- grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Grace Jordana
- grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - William Rees
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Dirk F. H. Winkler
- grid.292479.3Kinexus Bioinformatics Corporation, Suite 1 – 8755 Ash Street, Vancouver, BC V6P 6T3 Canada
| | - Iqbal Sarai
- grid.292479.3Kinexus Bioinformatics Corporation, Suite 1 – 8755 Ash Street, Vancouver, BC V6P 6T3 Canada
| | - Theodore Steiner
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - François Jean
- grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
| | - Steven Pelech
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada ,grid.292479.3Kinexus Bioinformatics Corporation, Suite 1 – 8755 Ash Street, Vancouver, BC V6P 6T3 Canada
| | - Yossef Av-Gay
- grid.17091.3e0000 0001 2288 9830Division of Infectious Disease, Department of Medicine, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada ,grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
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Song S, Kim H, Jang EY, Jeon H, Diao H, Khan MRI, Lee M, Lee YJ, Nam J, Kim S, Kim Y, Sohn E, Hwang I, Choi J. SARS-CoV-2 spike trimer vaccine expressed in Nicotiana benthamiana adjuvanted with Alum elicits protective immune responses in mice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2298-2312. [PMID: 36062974 PMCID: PMC9538723 DOI: 10.1111/pbi.13908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/30/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic has spurred rapid development of vaccines as part of the public health response. However, the general strategy used to construct recombinant trimeric severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) proteins in mammalian cells is not completely adaptive to molecular farming. Therefore, we generated several constructs of recombinant S proteins for high expression in Nicotiana benthamiana. Intramuscular injection of N. benthamiana-expressed Sct vaccine (NSct Vac) into Balb/c mice elicited both humoral and cellular immune responses, and booster doses increased neutralizing antibody titres. In human angiotensin-converting enzyme knock-in mice, two doses of NSct Vac induced anti-S and neutralizing antibodies, which cross-neutralized Alpha, Beta, Delta and Omicron variants. Survival rates after lethal challenge with SARS-CoV-2 were up to 80%, without significant body weight loss, and viral titres in lung tissue fell rapidly, with no infectious virus detectable at 7-day post-infection. Thus, plant-derived NSct Vac could be a candidate COVID-19 vaccine.
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Affiliation(s)
- Shi‐Jian Song
- Department of Life SciencePohang University of Science and TechnologyPohangKorea
| | - Heeyeon Kim
- Division of Acute Viral Disease, Center for Emerging Virus ResearchNational Institute of Infectious Diseases, Korea National Institute of HealthCheongjuKorea
| | - Eun Young Jang
- Division of Vaccine Research, Vaccine Research CenterNational Institute of Infectious Diseases, Korea National Institute of HealthCheongjuKorea
| | - Hyungmin Jeon
- Department of Life SciencePohang University of Science and TechnologyPohangKorea
| | - Hai‐Ping Diao
- Department of Life SciencePohang University of Science and TechnologyPohangKorea
| | - Md Rezaul Islam Khan
- Department of Life SciencePohang University of Science and TechnologyPohangKorea
| | - Mi‐Seon Lee
- Division of Infectious Diseases InspectionJeju Special Self‐Governing Province Institute of Environment ResearchJejuKorea
| | - Young Jae Lee
- Division of Vaccine Research, Vaccine Research CenterNational Institute of Infectious Diseases, Korea National Institute of HealthCheongjuKorea
| | - Jeong‐hyun Nam
- Division of Vaccine Research, Vaccine Research CenterNational Institute of Infectious Diseases, Korea National Institute of HealthCheongjuKorea
| | - Seong‐Ryeol Kim
- Division of Acute Viral Disease, Center for Emerging Virus ResearchNational Institute of Infectious Diseases, Korea National Institute of HealthCheongjuKorea
| | - Young‐Jin Kim
- Department of Life SciencePohang University of Science and TechnologyPohangKorea
| | - Eun‐Ju Sohn
- BioApplications Inc.Pohang Technopark ComplexPohangSouth Korea
| | - Inhwan Hwang
- Department of Life SciencePohang University of Science and TechnologyPohangKorea
| | - Jang‐Hoon Choi
- Division of Acute Viral Disease, Center for Emerging Virus ResearchNational Institute of Infectious Diseases, Korea National Institute of HealthCheongjuKorea
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Sattar S, Kabat J, Jerome K, Feldmann F, Bailey K, Mehedi M. Nuclear translocation of spike mRNA and protein is a novel pathogenic feature of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.27.509633. [PMID: 36203551 PMCID: PMC9536038 DOI: 10.1101/2022.09.27.509633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes severe pathophysiology in vulnerable older populations and appears to be highly pathogenic and more transmissible than SARS-CoV or MERS-CoV [1, 2]. The spike (S) protein appears to be a major pathogenic factor that contributes to the unique pathogenesis of SARS-CoV-2. Although the S protein is a surface transmembrane type 1 glycoprotein, it has been predicted to be translocated into the nucleus due to the novel nuclear localization signal (NLS) "PRRARSV", which is absent from the S protein of other coronaviruses. Indeed, S proteins translocate into the nucleus in SARS-CoV-2-infected cells. To our surprise, S mRNAs also translocate into the nucleus. S mRNA colocalizes with S protein, aiding the nuclear translocation of S mRNA. While nuclear translocation of nucleoprotein (N) has been shown in many coronaviruses, the nuclear translocation of both S mRNA and S protein reveals a novel pathogenic feature of SARS-CoV-2. Author summary One of the novel sequence insertions resides at the S1/S2 boundary of Spike (S) protein and constitutes a functional nuclear localization signal (NLS) motif "PRRARSV", which may supersede the importance of previously proposed polybasic furin cleavage site "RRAR". Indeed, S protein's NLS-driven nuclear translocation and its possible role in S mRNA's nuclear translocation reveal a novel pathogenic feature of SARS-CoV-2.
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Affiliation(s)
- Sarah Sattar
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, USA
| | - Juraj Kabat
- Biological Imaging Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kailey Jerome
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, USA
| | - Friederike Feldmann
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kristina Bailey
- Department of Internal Medicine, Pulmonary, Critical Care, and Sleep and Allergy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Masfique Mehedi
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, USA
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Wang E, Chakraborty AK. Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants. PLoS Comput Biol 2022; 18:e1010563. [PMID: 36156540 PMCID: PMC9536555 DOI: 10.1371/journal.pcbi.1010563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 10/06/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022] Open
Abstract
The rise of SARS-CoV-2 variants and the history of outbreaks caused by zoonotic coronaviruses point to the need for next-generation vaccines that confer protection against variant strains. Here, we combined analyses of diverse sequences and structures of coronavirus spikes with data from deep mutational scanning to design SARS-CoV-2 variant antigens containing the most significant mutations that may emerge. We trained a neural network to predict RBD expression and ACE2 binding from sequence, which allowed us to determine that these antigens are stable and bind to ACE2. Thus, they represent viable variants. We then used a computational model of affinity maturation (AM) to study the antibody response to immunization with different combinations of the designed antigens. The results suggest that immunization with a cocktail of the antigens is likely to promote evolution of higher titers of antibodies that target SARS-CoV-2 variants than immunization or infection with the wildtype virus alone. Finally, our analysis of 12 coronaviruses from different genera identified the S2’ cleavage site and fusion peptide as potential pan-coronavirus vaccine targets. SARS-CoV-2 variants have already emerged and future variants may pose greater threats to the efficacy of current vaccines. Rather than using a reactive approach to vaccine development that would lag behind the evolution of the virus, such as updating the sequence in the vaccine with a current variant, we sought to use a proactive approach that predicts some of the mutations that could arise that could evade current immune responses. Then, by including these mutations in a new vaccine antigen, we might be able to protect against those potential variants before they appear. Toward this end, we used various computational methods including sequence analysis and machine learning to design such antigens. We then used simulations of antibody development, and the results suggest that immunization with our designed antigens is likely to result in an antibody response that is better able to target SARS-CoV-2 variants than current vaccines. We also leveraged our sequence analysis to suggest that a particular site on the spike protein could serve as a useful target for a pan-coronavirus vaccine.
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Affiliation(s)
- Eric Wang
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Arup K. Chakraborty
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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44
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Non-coding RNA in SARS-CoV-2: Progress toward therapeutic significance. Int J Biol Macromol 2022; 222:1538-1550. [PMID: 36152703 PMCID: PMC9492401 DOI: 10.1016/j.ijbiomac.2022.09.105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 12/18/2022]
Abstract
The recently developed pathogenic virus, SARS-CoV-2, was found in the Hubei Province, China. Giving rise to a broad spectrum of symptoms, SARS-CoV-2 rapidly spread across the globe, causing multi-systemic and dangerous complications, with death in extreme cases. Thereby, the number of research cases increases every day on preventing infection and treating its resulting damage. Accumulating evidence suggests noncoding RNAs (ncRNAs) are necessary for modifying virus infection and antiviral immune reaction, along with biological processes regulating SARS-CoV-2 and subsequent disease states. Therefore, understanding these mechanisms might provide a further understanding of the pathogenesis and feasible therapy alternatives against SARS-CoV2. Consequently, the molecular biology of SARS-CoV-2, ncRNA's role in its infection, and various RNA therapy tactics against the virus have been presented in this review section.
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Tyrkalska SD, Martínez-López A, Arroyo AB, Martínez-Morcillo FJ, Candel S, García-Moreno D, Mesa-del-Castillo P, Cayuela ML, Mulero V. Differential proinflammatory activities of Spike proteins of SARS-CoV-2 variants of concern. SCIENCE ADVANCES 2022; 8:eabo0732. [PMID: 36112681 PMCID: PMC9481140 DOI: 10.1126/sciadv.abo0732] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic turned the whole world upside down in a short time. One of the main challenges faced has been to understand COVID-19-associated life-threatening hyperinflammation, the so-called cytokine storm syndrome (CSS). We report here the proinflammatory role of Spike (S) proteins from different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern in zebrafish. We found that wild-type/Wuhan variant S1 (S1WT) promoted neutrophil and macrophage recruitment, local and systemic hyperinflammation, emergency myelopoiesis, and hemorrhages. In addition, S1γ was more proinflammatory S1δ was less proinflammatory than S1WT, and, notably, S1β promoted delayed and long-lasting inflammation. Pharmacological inhibition of the canonical inflammasome alleviated S1-induced inflammation and emergency myelopoiesis. In contrast, genetic inhibition of angiotensin-converting enzyme 2 strengthened the proinflammatory activity of S1, and angiotensin (1-7) fully rescued S1-induced hyperinflammation and hemorrhages. These results shed light into the mechanisms orchestrating the COVID-19-associated CSS and the host immune response to different SARS-CoV-2 S protein variants.
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Affiliation(s)
- Sylwia D. Tyrkalska
- Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Corresponding author. (S.D.T.); (M.L.C); (V.M.)
| | - Alicia Martínez-López
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana B. Arroyo
- Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Francisco J. Martínez-Morcillo
- Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Sergio Candel
- Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Diana García-Moreno
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Pablo Mesa-del-Castillo
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain
| | - María L. Cayuela
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain
- Corresponding author. (S.D.T.); (M.L.C); (V.M.)
| | - Victoriano Mulero
- Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Corresponding author. (S.D.T.); (M.L.C); (V.M.)
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Kumar S, Dutta D, Ravichandiran V, Sukla S. Monoclonal antibodies: a remedial approach to prevent SARS-CoV-2 infection. 3 Biotech 2022; 12:227. [PMID: 35982759 PMCID: PMC9383686 DOI: 10.1007/s13205-022-03281-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 07/26/2022] [Indexed: 11/07/2022] Open
Abstract
SARS-CoV-2, the newly emerged virus of the Coronaviridae family is causing havoc worldwide. The novel coronavirus 2019 was first reported in Wuhan, China marked as the third highly infectious pathogenic virus of the twenty-first century. The typical manifestations of COVID-19 include cough, sore throat, fever, fatigue, loss of sense of taste and difficulties in breathing. Large numbers of SARS-CoV-2 infected patients have mild to moderate symptoms, however severe and life-threatening cases occur in about 5-10% of infections with an approximately 2% mortality rate. For the treatment of SARS-CoV-2, the use of neutralizing monoclonal antibodies (mAbs) could be one approach. The receptor binding domain (RBD) and N-terminal domain (NTD) situated on the peak of the spike protein (S-Protein) of SARS-CoV-2 are immunogenic in nature, therefore, can be targeted by neutralizing monoclonal antibodies. Several bioinformatics approaches highlight the identification of novel SARS-CoV-2 epitopes which can be targeted for the development of COVID-19 therapeutics. Here we present a summary of neutralizing mAbs isolated from COVID-19 infected patients which are anticipated to be a better therapeutic alternative against SARS-CoV-2. However, provided the vast escalation of the disease worldwide affecting people from all strata, affording expensive mAb therapy will not be feasible. Hence other strategies are also being employed to find suitable vaccine candidates and antivirals against SARS-CoV-2 that can be made easily available to the population.
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Affiliation(s)
- Sonu Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
| | - Debrupa Dutta
- Department of Pharmacology and Toxicology, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
| | - Soumi Sukla
- Department of Pharmacology and Toxicology, National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata, 700054 West Bengal India
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Beaudoin CA, Pandurangan AP, Kim SY, Hamaia SW, Huang CL, Blundell TL, Vedithi SC, Jackson AP. In silico analysis of mutations near S1/S2 cleavage site in SARS-CoV-2 spike protein reveals increased propensity of glycosylation in Omicron strain. J Med Virol 2022; 94:4181-4192. [PMID: 35575289 PMCID: PMC9348480 DOI: 10.1002/jmv.27845] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/06/2022]
Abstract
Cleavage of the severe respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein has been demonstrated to contribute to viral-cell fusion and syncytia formation. Studies have shown that variants of concern (VOC) and variants of interest (VOI) show differing membrane fusion capacity. Mutations near cleavage motifs, such as the S1/S2 and S2' sites, may alter interactions with host proteases and, thus, the potential for fusion. The biochemical basis for the differences in interactions with host proteases for the VOC/VOI spike proteins has not yet been explored. Using sequence and structure-based bioinformatics, mutations near the VOC/VOI spike protein cleavage sites were inspected for their structural effects. All mutations found at the S1/S2 sites were predicted to increase affinity to the furin protease but not TMPRSS2. Mutations at the spike residue P681 in several strains, such P681R in the Delta strain, resulted in the disruption of a proline-directed kinase phosphorylation motif at the S1/S2 site, which may lessen the impact of phosphorylation for these variants. However, the unique N679K mutation in the Omicron strain was found to increase the propensity for O-linked glycosylation at the S1/S2 cleavage site, which may prevent recognition by proteases. Such glycosylation in the Omicron strain may hinder entry at the cell surface and, thus, decrease syncytia formation and induce cell entry through the endocytic pathway as has been shown in previous studies. Further experimental work is needed to confirm the effect of mutations and posttranslational modifications on SARS-CoV-2 spike protein cleavage sites.
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Affiliation(s)
| | - Arun P. Pandurangan
- Department of Biochemistry, Sanger BuildingUniversity of CambridgeCambridgeUnited Kingdom
| | - So Yeon Kim
- Department of Biochemistry, Sanger BuildingUniversity of CambridgeCambridgeUnited Kingdom
| | - Samir W. Hamaia
- Department of Biochemistry, Hopkins BuildingUniversity of CambridgeCambridgeUnited Kingdom
| | - Christopher L.‐H. Huang
- Department of Biochemistry, Hopkins BuildingUniversity of CambridgeCambridgeUnited Kingdom
- Physiological LaboratoryUniversity of CambridgeCambridgeUnited Kingdom
| | - Tom L. Blundell
- Department of Biochemistry, Sanger BuildingUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Antony P. Jackson
- Department of Biochemistry, Hopkins BuildingUniversity of CambridgeCambridgeUnited Kingdom
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48
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Bian DJH, Sabri S, Abdulkarim BS. Interactions between COVID-19 and Lung Cancer: Lessons Learned during the Pandemic. Cancers (Basel) 2022; 14:cancers14153598. [PMID: 35892857 PMCID: PMC9367272 DOI: 10.3390/cancers14153598] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary COVID-19 is a respiratory infectious disease caused by the coronavirus SARS-CoV-2. Lung cancer is the leading cause of all cancer-related deaths worldwide. As both SARS-CoV-2 and lung cancer affect the lungs, the aim of this narrative review is to provide a consolidation of lessons learned throughout the pandemic regarding lung cancer and COVID-19. Risk factors found in lung cancer patients, such as advanced cancers, smoking, male, etc., have been associated with severe COVID-19. The cancer treatments hormonal therapy, immunotherapy, and targeted therapy have shown no association with severe COVID-19 disease, but chemotherapy and radiation therapy have shown conflicting results. Logistical changes and modifications in treatment plans were instituted during the pandemic to minimize SARS-CoV-2 exposure while maintaining life-saving cancer care. Finally, medications have been developed to treat early COVID-19, which can be highly beneficial in vulnerable cancer patients, with paxlovid being the most efficacious drug currently available. Abstract Cancer patients, specifically lung cancer patients, show heightened vulnerability to severe COVID-19 outcomes. The immunological and inflammatory pathophysiological similarities between lung cancer and COVID-19-related ARDS might explain the predisposition of cancer patients to severe COVID-19, while multiple risk factors in lung cancer patients have been associated with worse COVID-19 outcomes, including smoking status, older age, etc. Recent cancer treatments have also been urgently evaluated during the pandemic as potential risk factors for severe COVID-19, with conflicting findings regarding systemic chemotherapy and radiation therapy, while other therapies were not associated with altered outcomes. Given this vulnerability of lung cancer patients for severe COVID-19, the delivery of cancer care was significantly modified during the pandemic to both proceed with cancer care and minimize SARS-CoV-2 infection risk. However, COVID-19-related delays and patients’ aversion to clinical settings have led to increased diagnosis of more advanced tumors, with an expected increase in cancer mortality. Waning immunity and vaccine breakthroughs related to novel variants of concern threaten to further impede the delivery of cancer services. Cancer patients have a high risk of severe COVID-19, despite being fully vaccinated. Numerous treatments for early COVID-19 have been developed to prevent disease progression and are crucial for infected cancer patients to minimize severe COVID-19 outcomes and resume cancer care. In this literature review, we will explore the lessons learned during the COVID-19 pandemic to specifically mitigate COVID-19 treatment decisions and the clinical management of lung cancer patients.
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Affiliation(s)
- David J. H. Bian
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3G 2M1, Canada;
| | - Siham Sabri
- Cancer Research Program, Research Institute, McGill University Health Center Glen Site, McGill University, Montreal, QC H4A 3J1, Canada;
| | - Bassam S. Abdulkarim
- Cancer Research Program, Research Institute, and Department of Oncology, Cedars Cancer Center, McGill University Health Center Glen Site, McGill University, Montreal, QC H4A 3J1, Canada
- Correspondence:
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Quaglia F, Salladini E, Carraro M, Minervini G, Tosatto SCE, Le Mercier P. SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion. FEBS J 2022; 289:4240-4250. [PMID: 35108439 PMCID: PMC9542094 DOI: 10.1111/febs.16379] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/21/2022] [Accepted: 01/31/2022] [Indexed: 12/13/2022]
Abstract
The SARS‐CoV‐2 pandemic is maintained by the emergence of successive variants, highlighting the flexibility of the protein sequences of the virus. We show that experimentally determined intrinsically disordered regions (IDRs) are abundant in the SARS‐CoV‐2 viral proteins, making up to 28% of disorder content for the S1 subunit of spike and up to 51% for the nucleoprotein, with the vast majority of mutations occurring in the 13 major variants mapped to these IDRs. Strikingly, antigenic sites are enriched in IDRs, in the receptor‐binding domain (RBD) and in the N‐terminal domain (NTD), suggesting a key role of structural flexibility in the antigenicity of the SARS‐CoV‐2 protein surface. Mutations occurring in the S1 subunit and nucleoprotein (N) IDRs are critical for immune evasion and antibody escape, suggesting potential additional implications for vaccines and monoclonal therapeutic strategies. Overall, this suggests the presence of variable regions on S1 and N protein surfaces, which confer sequence and antigenic flexibility to the virus without altering its protein functions.
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Affiliation(s)
- Federica Quaglia
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR-IBIOM), Bari, Italy.,Department of Biomedical Sciences, University of Padova, Italy
| | | | - Marco Carraro
- Department of Biomedical Sciences, University of Padova, Italy
| | | | | | - Philippe Le Mercier
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
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50
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Kastenhuber ER, Johnson JL, Yaron TM, Mercadante M, Cantley LC. Evolution of host protease interactions among SARS-CoV-2 variants of concern and related coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.16.496428. [PMID: 35734085 PMCID: PMC9216717 DOI: 10.1101/2022.06.16.496428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Previously, we showed that coagulation factors directly cleave SARS-CoV-2 spike and promote viral entry (Kastenhuber et al., 2022). Here, we show that substitutions in the S1/S2 cleavage site observed in SARS-CoV-2 variants of concern (VOCs) exhibit divergent interactions with host proteases, including factor Xa and furin. Nafamostat remains effective to block coagulation factor-mediated cleavage of variant spike sequences. Furthermore, host protease usage has likely been a selection pressure throughout coronavirus evolution, and we observe convergence of distantly related coronaviruses to attain common host protease interactions, including coagulation factors. Interpretation of genomic surveillance of emerging SARS-CoV-2 variants and future zoonotic spillover is supported by functional characterization of recurrent emerging features.
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Affiliation(s)
- Edward R. Kastenhuber
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jared L. Johnson
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Tomer M. Yaron
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marisa Mercadante
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Lewis C. Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Dana Farber Cancer Institute, Boston, MA, USA
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