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Purves K, Reynolds LJ, Sala-Comorera L, Martin NA, Dahly DL, Meijer WG, Fletcher NF. Decay of RNA and infectious SARS-CoV-2 and murine hepatitis virus in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173877. [PMID: 38871327 DOI: 10.1016/j.scitotenv.2024.173877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]
Abstract
Wastewater-based epidemiology (WBE) has been an important tool for population surveillance during the COVID-19 pandemic and continues to play a key role in monitoring SARS-CoV-2 infection levels following reductions in national clinical testing schemes. Studies measuring decay profiles of SARS-CoV-2 in wastewater have underscored the value of WBE, however investigations have been hampered by high biosafety requirements for SARS-CoV-2 infection studies. Therefore, surrogate viruses with lower biosafety standards have been used for SARS-CoV-2 decay studies, such as murine hepatitis virus (MHV), but few studies have directly compared decay rates of both viruses. We compared the persistence of SARS-CoV-2 and MHV in wastewater, using 50 % tissue culture infectious dose (TCID50) and reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays to assess infectious virus titre and viral gene markers, respectively. Infectious SARS-CoV-2 and MHV indicate similar endpoints, however observed early decay characteristics differed, with infectious SARS-CoV-2 decaying more rapidly than MHV. We find that MHV is an appropriate infectious virus surrogate for viable SARS-CoV-2, however inconsistencies exist in viral RNA decay parameters, indicating MHV may not be a suitable nucleic acid surrogate across certain temperature regimes. This study highlights the importance of sample preparation and the potential for decay rate overestimation in wastewater surveillance for SARS-CoV-2 and other pathogens.
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Affiliation(s)
- Kevin Purves
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Ireland
| | - Liam J Reynolds
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Ireland
| | - Laura Sala-Comorera
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain
| | - Niamh A Martin
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Ireland
| | - Darren L Dahly
- Health Research Board Clinical Research Facility, University College Cork, Ireland; School of Public Health, University College Cork, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Ireland
| | - Nicola F Fletcher
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Ireland.
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2
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Wang H, Liu X, Zhang X, Zhao Z, Lu Y, Pu D, Zhang Z, Chen J, Wang Y, Li M, Dong X, Duan Y, He Y, Mao Q, Guo H, Sun H, Zhou Y, Yang Q, Gao Y, Yang X, Cao H, Guddat L, Sun L, Rao Z, Yang H. TMPRSS2 and glycan receptors synergistically facilitate coronavirus entry. Cell 2024:S0092-8674(24)00656-1. [PMID: 38964329 DOI: 10.1016/j.cell.2024.06.016] [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: 02/28/2024] [Revised: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024]
Abstract
The entry of coronaviruses is initiated by spike recognition of host cellular receptors, involving proteinaceous and/or glycan receptors. Recently, TMPRSS2 was identified as the proteinaceous receptor for HCoV-HKU1 alongside sialoglycan as a glycan receptor. However, the underlying mechanisms for viral entry remain unknown. Here, we investigated the HCoV-HKU1C spike in the inactive, glycan-activated, and functionally anchored states, revealing that sialoglycan binding induces a conformational change of the NTD and promotes the neighboring RBD of the spike to open for TMPRSS2 recognition, exhibiting a synergistic mechanism for the entry of HCoV-HKU1. The RBD of HCoV-HKU1 features an insertion subdomain that recognizes TMPRSS2 through three previously undiscovered interfaces. Furthermore, structural investigation of HCoV-HKU1A in combination with mutagenesis and binding assays confirms a conserved receptor recognition pattern adopted by HCoV-HKU1. These studies advance our understanding of the complex viral-host interactions during entry, laying the groundwork for developing new therapeutics against coronavirus-associated diseases.
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Affiliation(s)
- Haofeng Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Xiaoce Liu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Xiang Zhang
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zhuoqian Zhao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; Lingang Laboratory, Shanghai 200031, China
| | - Yuchi Lu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; Lingang Laboratory, Shanghai 200031, China
| | - Dingzhe Pu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; Guangzhou Laboratory, Guangzhou 510005, China
| | - Zeyang Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; Lingang Laboratory, Shanghai 200031, China
| | - Jie Chen
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Yajie Wang
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Mengfei Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Xuxue Dong
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; Guangzhou Laboratory, Guangzhou 510005, China
| | - Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Yujia He
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Qiyu Mao
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Hangtian Guo
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Haoran Sun
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Yihan Zhou
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Qi Yang
- Guangzhou Laboratory, Guangzhou 510005, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Hongzhi Cao
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Luke Guddat
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Lei Sun
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China; Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin 300353, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China.
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3
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Schäfer A, Gralinski LE, Leist SR, Hampton BK, Mooney MA, Jensen KL, Graham RL, Agnihothram S, Jeng S, Chamberlin S, Bell TA, Scobey DT, Linnertz CL, VanBlargan LA, Thackray LB, Hock P, Miller DR, Shaw GD, Diamond MS, de Villena FPM, McWeeney SK, Heise MT, Menachery VD, Ferris MT, Baric RS. Genetic loci regulate Sarbecovirus pathogenesis: A comparison across mice and humans. Virus Res 2024; 344:199357. [PMID: 38508400 PMCID: PMC10981091 DOI: 10.1016/j.virusres.2024.199357] [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: 09/28/2023] [Revised: 02/15/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
Coronavirus (CoV) cause considerable morbidity and mortality in humans and other mammals, as evidenced by the emergence of Severe Acute Respiratory CoV (SARS-CoV) in 2003, Middle East Respiratory CoV (MERS-CoV) in 2012, and SARS-CoV-2 in 2019. Although poorly characterized, natural genetic variation in human and other mammals modulate virus pathogenesis, as reflected by the spectrum of clinical outcomes ranging from asymptomatic infections to lethal disease. Using multiple human epidemic and zoonotic Sarbecoviruses, coupled with murine Collaborative Cross genetic reference populations, we identify several dozen quantitative trait loci that regulate SARS-like group-2B CoV pathogenesis and replication. Under a Chr4 QTL, we deleted a candidate interferon stimulated gene, Trim14 which resulted in enhanced SARS-CoV titers and clinical disease, suggesting an antiviral role during infection. Importantly, about 60 % of the murine QTL encode susceptibility genes identified as priority candidates from human genome-wide association studies (GWAS) studies after SARS-CoV-2 infection, suggesting that similar selective forces have targeted analogous genes and pathways to regulate Sarbecovirus disease across diverse mammalian hosts. These studies provide an experimental platform in rodents to investigate the molecular-genetic mechanisms by which potential cross mammalian susceptibility loci and genes regulate type-specific and cross-SARS-like group 2B CoV replication, immunity, and pathogenesis in rodent models. Our study also provides a paradigm for identifying susceptibility loci for other highly heterogeneous and virulent viruses that sporadically emerge from zoonotic reservoirs to plague human and animal populations.
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Affiliation(s)
- Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael A Mooney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Kara L Jensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rachel L Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sudhakar Agnihothram
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sophia Jeng
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Steven Chamberlin
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Timothy A Bell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D Trevor Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology & Immunology2, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology3, Washington University School of Medicine, St. Louis, MO, USA
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shannon K McWeeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Mark T Heise
- Department of Genetics, 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; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill NC, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA; Department of Pathology and Center for Biodefense & Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - 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; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill NC, USA.
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4
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Bayyurt B, Baltacı S, Şahin NÖ, Arslan S, Bakır M. Relationship of Toll-Like Receptor 7, 9, and 10 Polymorphisms and the Severity of Coronavirus Disease 2019. Jpn J Infect Dis 2024; 77:161-168. [PMID: 38296538 DOI: 10.7883/yoken.jjid.2023.411] [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: 05/24/2024]
Abstract
Coronavirus disease 2019 (COVID-19) is a pandemic that is still affecting people and has caused many deaths. Toll-like receptors (TLRs) have an important role in the binding of disease agents to the host cell, disease susceptibility and severity, and host disease resistance. In this study, we investigated the frequencies of TLR7 (C.4-151 A/G), TLR9 (T-1486C and G2848A), and TLR10 (720A/C and 992T/A) single nucleotide polymorphisms in 150 cases with COVID-19 and 171 control samples. We also examined whether TLR7, TLR9, and TLR10 were related to COVID-19 severity. Furthermore, we analyzed the association between COVID-19 and some clinical parameters. Polymerase chain reaction based on restriction fragment length polymorphisms performed for the TLR7, TLR9, and TLR10 single nucleotide polymorphisms. TLR7 C.4-151 A/G G allele and GG genotype; TLR9 T-1486C C allele and TC, CC genotypes; and TLR10 720A/C C allele; TLR10 992T/A A allele and AA genotype frequencies were statistically significant in cases with COVID-19 compared with controls (P < 0.05*). In addition, there was a statistically significant difference in the distribution of TLR7, TLR9, and TLR10 allele and genotype frequencies between the severity groups (P < 0.05*). Our findings suggest that TLR7, TLR9, and TLR10 polymorphisms may be crucial for the clinical course and susceptibility to infection.
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Affiliation(s)
- Burcu Bayyurt
- Department of Medical Biology, Faculty of Medicine, Sivas Cumhuriyet University, Turkey
| | - Sevgi Baltacı
- Departments of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Sivas Cumhuriyet University, Turkey
| | - Nil Özbilüm Şahin
- Department of Molecular Biology and Genetic, Faculty of Science, Sivas Cumhuriyet University, Turkey
| | - Serdal Arslan
- Department of Medical Biology, Faculty of Medicine, Mersin University, Turkey
| | - Mehmet Bakır
- Departments of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Sivas Cumhuriyet University, Turkey
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5
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Liu C, Huang W, He X, Feng Z, Chen Q. Research Advances on Swine Acute Diarrhea Syndrome Coronavirus. Animals (Basel) 2024; 14:448. [PMID: 38338091 PMCID: PMC10854734 DOI: 10.3390/ani14030448] [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: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a virulent pathogen that causes acute diarrhea in piglets. The virus was first discovered in Guangdong Province, China, in 2017 and has since emerged in Jiangxi, Fujian, and Guangxi Provinces. The outbreak exhibited a localized and sporadic pattern, with no discernable temporal continuity. The virus can infect human progenitor cells and demonstrates considerable potential for cross-species transmission, representing a potential risk for zoonotic transmission. Therefore, continuous surveillance of and comprehensive research on SADS-CoV are imperative. This review provides an overview of the temporal and evolutionary features of SADS-CoV outbreaks, focusing on the structural characteristics of the virus, which serve as the basis for discussing its potential for interspecies transmission. Additionally, the review summarizes virus-host interactions, including the effects on host cells, as well as apoptotic and autophagic behaviors, and discusses prevention and treatment modalities for this viral infection.
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Affiliation(s)
- Chuancheng Liu
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Weili Huang
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Xinyan He
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Zhihua Feng
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Qi Chen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
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6
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Kant R, Kaushik R, Chopra M, Saluja D. Structure-based drug discovery to identify SARS-CoV2 spike protein-ACE2 interaction inhibitors. J Biomol Struct Dyn 2024:1-19. [PMID: 38174578 DOI: 10.1080/07391102.2023.2300060] [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: 07/15/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024]
Abstract
After the emergence of the COVID-19 pandemic in late 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has undergone a dynamic evolution driven by the acquisition of genetic modifications, resulting in several variants that are further classified as variants of interest (VOIs), variants under monitoring (VUM) and variants of concern (VOC) by World Health Organization (WHO). Currently, there are five SARS-CoV-2 VOCs (Alpha, Beta, Delta, Gamma and Omicron), two VOIs (Lambda and Mu) and several other VOIs that have been reported globally. In this study, we report a natural compound, Curcumin, as the potential inhibitor to the interactions between receptor binding domain (RBD(S1)) and human angiotensin-converting enzyme 2 (hACE2) domains and showcased its inhibitory potential for the Delta and Omicron variants through a computational approach by implementing state of the art methods. The study for the first time revealed a higher efficiency of Curcumin, especially for hindering the interaction between RBD(S1) and hACE-2 domains of Delta and Omicron variants as compared to other lead compounds. We investigated that the mutations in the RBD(S1) of VOC especially Delta and Omicron variants affect its structure compared to that of the wild type and other variants and therefore altered its binding to the hACE2 receptor. Molecular docking and molecular dynamics (MD) simulation analyses substantially supported the findings in terms of the stability of the docked complexes. This study offers compelling evidence, warranting a more in-depth exploration into the impact of these alterations on the binding of identified drug molecules with the Spike protein. Further investigation into their potential therapeutic effects in vivo is highly recommended.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Kant
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research &Delhi School of Public Health, IoE, University of Delhi, Delhi, India
| | - Rahul Kaushik
- Biotechology Research Center, Technology Innovation Institute, Masdar City, UAE
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Daman Saluja
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research &Delhi School of Public Health, IoE, University of Delhi, Delhi, India
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7
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Geng Q, Wan Y, Hsueh FC, Shang J, Ye G, Bu F, Herbst M, Wilkens R, Liu B, Li F. Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein. eLife 2023; 12:e74060. [PMID: 37991488 PMCID: PMC10695562 DOI: 10.7554/elife.74060] [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: 09/20/2021] [Accepted: 11/21/2023] [Indexed: 11/23/2023] Open
Abstract
SARS-CoV-2 spike protein plays a key role in mediating viral entry and inducing host immune responses. It can adopt either an open or closed conformation based on the position of its receptor-binding domain (RBD). It is yet unclear what causes these conformational changes or how they influence the spike's functions. Here, we show that Lys417 in the RBD plays dual roles in the spike's structure: it stabilizes the closed conformation of the trimeric spike by mediating inter-spike-subunit interactions; it also directly interacts with ACE2 receptor. Hence, a K417V mutation has opposing effects on the spike's function: it opens up the spike for better ACE2 binding while weakening the RBD's direct binding to ACE2. The net outcomes of this mutation are to allow the spike to bind ACE2 with higher probability and mediate viral entry more efficiently, but become more exposed to neutralizing antibodies. Given that residue 417 has been a viral mutational hotspot, SARS-CoV-2 may have been evolving to strike a balance between infection potency and immune evasion, contributing to its pandemic spread.
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Affiliation(s)
- Qibin Geng
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Yushun Wan
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Fu-Chun Hsueh
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Jian Shang
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Gang Ye
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Fan Bu
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Morgan Herbst
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Rowan Wilkens
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Bin Liu
- Hormel Institute, University of MinnesotaAustinUnited States
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
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8
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Justo Arevalo S, Castillo-Chávez A, Uribe Calampa CS, Zapata Sifuentes D, Huallpa CJ, Landa Bianchi G, Garavito-Salini Casas R, Quiñones Aguilar M, Pineda Chavarría R. What do we know about the function of SARS-CoV-2 proteins? Front Immunol 2023; 14:1249607. [PMID: 37790934 PMCID: PMC10544941 DOI: 10.3389/fimmu.2023.1249607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 10/05/2023] Open
Abstract
The COVID-19 pandemic has highlighted the importance in the understanding of the biology of SARS-CoV-2. After more than two years since the first report of COVID-19, it remains crucial to continue studying how SARS-CoV-2 proteins interact with the host metabolism to cause COVID-19. In this review, we summarize the findings regarding the functions of the 16 non-structural, 6 accessory and 4 structural SARS-CoV-2 proteins. We place less emphasis on the spike protein, which has been the subject of several recent reviews. Furthermore, comprehensive reviews about COVID-19 therapeutic have been also published. Therefore, we do not delve into details on these topics; instead we direct the readers to those other reviews. To avoid confusions with what we know about proteins from other coronaviruses, we exclusively report findings that have been experimentally confirmed in SARS-CoV-2. We have identified host mechanisms that appear to be the primary targets of SARS-CoV-2 proteins, including gene expression and immune response pathways such as ribosome translation, JAK/STAT, RIG-1/MDA5 and NF-kβ pathways. Additionally, we emphasize the multiple functions exhibited by SARS-CoV-2 proteins, along with the limited information available for some of these proteins. Our aim with this review is to assist researchers and contribute to the ongoing comprehension of SARS-CoV-2's pathogenesis.
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Affiliation(s)
- Santiago Justo Arevalo
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru
- Departmento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Daniela Zapata Sifuentes
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru
- Departmento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | - César J. Huallpa
- Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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9
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Hadni H, Fitri A, Touimi Benjelloun A, Benzakour M, Mcharfi M, Benbrahim M. Identification of terpenoids as potential inhibitors of SARS-CoV-2 (main protease) and spike (RBD) via computer-aided drug design. J Biomol Struct Dyn 2023:1-14. [PMID: 37548619 DOI: 10.1080/07391102.2023.2245051] [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: 04/02/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023]
Abstract
The scientific community has been faced with a major challenge in the fight against the SARS-CoV-2 virus responsible for the COVID-19 pandemic, due to the lack of targeted antiviral drugs. To address this issue, we used an in silico approach to screen 23 natural compounds from the terpenoid class for their ability to target key SARS-CoV-2 therapeutic proteins. The results revealed that several compounds showed promising interactions with SARS-CoV-2 proteins, specifically the main protease and the spike receptor binding domain. The molecular docking analysis revealed the importance of certain residues, such as GLY143, SER144, CYS145 and GLU166, in the main protease of the SARS-CoV-2 protein, which play a crucial role in interactions with the ligand. In addition, our study highlighted the importance of interactions with residues GLY496, ARG403, SER494 and ARG393 of the spike receptor-binding domain within the SARS-CoV-2 protein. ADMET and drug similarity analyses were also performed, followed by molecular dynamics and MM-GBSA calculations, to identify potential drugs could be repurposed to combat COVID-19. Indeed, the results suggest that certain terpenoid compounds of plant origin have promising potential as therapeutic targets for SARS-CoV-2. However, additional experimental studies are required to confirm their efficacy as drugs against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hanine Hadni
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Asmae Fitri
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Adil Touimi Benjelloun
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Benzakour
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Mcharfi
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Benbrahim
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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10
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Cheng Y, Zheng D, Zhang D, Guo D, Wang Y, Liu W, Liang L, Hu J, Luo T. Molecular recognition of SARS-CoV-2 spike protein with three essential partners: exploring possible immune escape mechanisms of viral mutants. J Mol Model 2023; 29:109. [PMID: 36964244 PMCID: PMC10038388 DOI: 10.1007/s00894-023-05509-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023]
Abstract
OBJECTIVE The COVID-19 epidemic is raging around the world, with the emergence of viral mutant strains such as Delta and Omicron, posing severe challenges to people's health and quality of life. A full understanding life cycle of the virus in host cells helps to reveal inactivation mechanism of antibody and provide inspiration for the development of a new-generation vaccines. METHODS In this work, molecular recognitions and conformational changes of SARS-CoV-2 spike protein mutants (i.e., Delta, Mu, and Omicron) and three essential partners (i.e., membrane receptor hACE2, protease TMPRSS2, and antibody C121) both were compared and analyzed using molecular simulations. RESULTS Water basin and binding free energy calculations both show that the three mutants possess higher affinity for hACE2 than WT, exhibiting stronger virus transmission. The descending order of cleavage ability by TMPRSS2 is Mu, Delta, Omicron, and WT, which is related to the new S1/S2 cutting site induced by transposition effect. The inefficient utilization of TMPRSS2 by Omicron is consistent with its primary entry into cells via the endosomal pathway. In addition, RBD-directed antibody C121 showed obvious resistance to Omicron, which may have originated from high fluctuation of approaching angles, high flexibility of I472-F490 loop, and reduced binding ability. CONCLUSIONS According to the overall characteristics of the three mutants, high infectivity, high immune escape, and low virulence may be the future evolutionary selection of SARS-CoV-2. In a word, this work not only proposes the possible resistance mechanism of SARS-CoV-2 mutants, but also provides theoretical guidance for the subsequent drug design against COVID-19 based on S protein structure.
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Affiliation(s)
- Yan Cheng
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China
| | - Dan Zheng
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China
| | - Derong Zhang
- School of Marxism, Chengdu Vocational & Technical College of Industry, Chengdu, China
| | - Du Guo
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China
| | - Yueteng Wang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Wei Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Ting Luo
- Breast Disease Center, West China Hospital, Sichuan University, Cancer CenterChengdu, 610000, China.
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11
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Evaluation of flavonoids as potential inhibitors of the SARS-CoV-2 main protease and spike RBD: Molecular docking, ADMET evaluation and molecular dynamics simulations. J INDIAN CHEM SOC 2022. [PMCID: PMC9428111 DOI: 10.1016/j.jics.2022.100697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The 3CLpro main protease and the RDB spike (s) protein of SARS-CoV-2 are critical targets in the treatment of coronavirus 19 disease (COVID-19), as they are responsible for the COVID-19 replication and infection. With this in mind, Molecular docking of 26 natural compounds belonging to the flavonoid family with the 3CLpro and RBD sites of SARS-CoV-2 has been performed. The docking results revealed that the ligands Silibinin, Tomentin A, Tomentin B, 4′-O-methyldiplacone, Hesperidin Amentoflavone and Bilobetin act as a potential inhibitor of SARS-CoV-2 3CLpro, and that the ligands Herbacetin, Morin, Silibinin, Tomentin E, Amentoflavone, Bilobetin, Baicalein and Quercetin can be potential inhibitors of SARS-CoV-2 RBD. It has been noticed that three ligands can inhibit both sites of SARS-CoV-2, indicating a great potential of these compounds to combat COVID-19. Moreover, molecular docking has been validated by a new validation method based on visual inspiration. Evaluation of ADMET pharmacokinetic properties and the drug likeness in silico revealed that six compounds could be effective drugs against COVID-19. Finally, the docking results were verified by molecular dynamics simulations and MM-GBSA calculation to confirm the stability of hydrogen bonding interactions with crucial residues, which are essential to overcome SARS-CoV-2. These results could direct researchers toward plant-derived compounds that could be further investigated as therapeutic targets against COVID-19 replication and infection.
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12
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Bio-Guided Isolation of SARS-CoV-2 Main Protease Inhibitors from Medicinal Plants: In Vitro Assay and Molecular Dynamics. PLANTS 2022; 11:plants11151914. [PMID: 35893619 PMCID: PMC9332707 DOI: 10.3390/plants11151914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/24/2022]
Abstract
Since the emergence of the pandemic of the coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the discovery of antiviral phytoconstituents from medicinal plants against SARS-CoV-2 has been comprehensively researched. In this study, thirty-three plants belonging to seventeen different families used traditionally in Saudi Arabia were tested in vitro for their ability to inhibit the SARS-CoV-2 main protease (MPRO). Major constituents of the bio-active extracts were isolated and tested for their inhibition potential against this enzyme; in addition, their antiviral activity against the SARS-CoV-2 Egyptian strain was assessed. Further, the thermodynamic stability of the best active compounds was studied through focused comparative insights for the active metabolites regarding ligand–target binding characteristics at the molecular level. Additionally, the obtained computational findings provided useful directions for future drug optimization and development. The results revealed that Psiadia punctulata, Aframomum melegueta, and Nigella sativa extracts showed a high percentage of inhibition of 66.4, 58.7, and 31.5%, against SARS-CoV-2 MPRO, respectively. The major isolated constituents of these plants were identified as gardenins A and B (from P. punctulata), 6-gingerol and 6-paradol (from A. melegueta), and thymoquinone (from N. sativa). These compounds are the first to be tested invitro against SARS-CoV-2 MPRO. Among the isolated compounds, only thymoquinone (THY), gardenin A (GDA), 6-gingerol (GNG), and 6-paradol (PAD) inhibited the SARS-CoV-2 MPRO enzyme with inhibition percentages of 63.21, 73.80, 65.2, and 71.8%, respectively. In vitro assessment of SARS-CoV-2 (hCoV-19/Egypt/NRC-03/2020 (accession number on GSAID: EPI_ISL_430820) revealed a strong-to-low antiviral activity of the isolated compounds. THY showed relatively high cytotoxicity and was anti-SARS-CoV-2, while PAD demonstrated a cytotoxic effect on the tested VERO cells with a selectivity index of CC50/IC50 = 1.33 and CC50/IC50 = 0.6, respectively. Moreover, GNG had moderate activity at non-cytotoxic concentrations in vitro with a selectivity index of CC50/IC50 = 101.3/43.45 = 2.3. Meanwhile, GDA showed weak activity with a selectivity index of CC50/IC50 = 246.5/83.77 = 2.9. The thermodynamic stability of top-active compounds revealed preferential stability and SARS-CoV-2 MPRO binding affinity for PAD through molecular-docking-coupled molecular dynamics simulation. The obtained results suggest the treating potential of these plants and/or their active metabolites for COVID-19. However, further in-vivo and clinical investigations are required to establish the potential preventive and treatment effectiveness of these plants and/or their bio-active compounds in COVID-19.
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13
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The Glycan-Binding Trait of the Sarbecovirus Spike N-Terminal Domain Reveals an Evolutionary Footprint. J Virol 2022; 96:e0095822. [PMID: 35852351 PMCID: PMC9364788 DOI: 10.1128/jvi.00958-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The spike protein on sarbecovirus virions contains two external, protruding domains: an N-terminal domain (NTD) with unclear function and a C-terminal domain (CTD) that binds the host receptor, allowing for viral entry and infection. While the CTD is well studied for therapeutic interventions, the role of the NTD is far less well understood for many coronaviruses. Here, we demonstrate that the spike NTD from SARS-CoV-2 and other sarbecoviruses binds to unidentified glycans in vitro similarly to other members of the Coronaviridae family. We also show that these spike NTD (S-NTD) proteins adhere to Calu3 cells, a human lung cell line, although the biological relevance of this is unclear. In contrast to what has been shown for Middle East respiratory syndrome coronavirus (MERS-CoV), which attaches sialic acids during cell entry, sialic acids present on Calu3 cells inhibited sarbecovirus infection. Therefore, while sarbecoviruses can interact with cell surface glycans similarly to other coronaviruses, their reliance on glycans for entry is different from that of other respiratory coronaviruses, suggesting sarbecoviruses and MERS-CoV have adapted to different cell types, tissues, or hosts during their divergent evolution. Our findings provide important clues for further exploring the biological functions of sarbecovirus glycan binding and adds to our growing understanding of the complex forces that shape coronavirus spike evolution. IMPORTANCE Spike N-terminal domains (S-NTD) of sarbecoviruses are highly diverse; however, their function remains largely understudied compared with the receptor-binding domains (RBD). Here, we show that sarbecovirus S-NTD can be phylogenetically clustered into five clades and exhibit various levels of glycan binding in vitro. We also show that, unlike some coronaviruses, including MERS-CoV, sialic acids present on the surface of Calu3, a human lung cell culture, inhibit SARS-CoV-2 and other sarbecoviruses. These results suggest that while glycan binding might be an ancestral trait conserved across different coronavirus families, the functional outcome during infection can vary, reflecting divergent viral evolution. Our results expand our knowledge on the biological functions of the S-NTD across diverse sarbecoviruses and provide insight on the evolutionary history of coronavirus spike.
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14
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Behl T, Kumar S, Singh S, Bhatia S, Albarrati A, Albratty M, Meraya AM, Najmi A, Bungau S. Reviving the mutual impact of SARS-COV-2 and obesity on patients: From morbidity to mortality. Biomed Pharmacother 2022; 151:113178. [PMID: 35644117 PMCID: PMC9127128 DOI: 10.1016/j.biopha.2022.113178] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 01/25/2023] Open
Abstract
Obesity-related metabolic dysfunction, endothelium imbalance, chronic inflammation, immune dysregulation, and its comorbidities may all have a role in systemic inflammation, leading to the pulmonary fibrosis and cytokine storm, which leads to failure of lung function, which is a hallmark of severe SARS-CoV-2 infection. Obesity may also disrupt the function of mucociliary escalators and cooperation of epithelial cell's motile cilia in the airway, limiting the clearance of the coronavirus that causes severe acute respiratory syndrome (SARS-CoV-2). Adipose tissues in obese patients have a greater number of proteases and receptors for SARS-CoV-2 admittance, proposing that they could serve as an accelerator and reservoir for this virus, boosting immunological response and systemic inflammation. Lastly, anti-inflammatory cytokines such as anti-IL-6 and the infusion of mesenchymal stem cells could be used as a modulation therapy of immunity to help COVID-19 patients. Obesity, on the other hand, is linked to the progress of COVID-19 through a variety of molecular pathways, and obese people are part of the SARS-CoV-2 susceptible individuals, necessitating more protective measures.
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Affiliation(s)
- Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India,Corresponding author
| | - Sachin Kumar
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Sukhbir Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Saurabh Bhatia
- Natural & Medical Sciences Research Centre, University of Nizwa, Birkat Al Mauz, Nizwa, Oman,School of Health Science, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India
| | - Ali Albarrati
- Rehabilitation Health Sciences College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Albratty
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Abdulkarim M. Meraya
- Pharmacy Practice Research Unit, Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Asim Najmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania,Doctoral School of Biomedical Sciences, University of Oradea, Oradea, Romania,Corresponding author at: Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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15
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Yang X, Dickmander RJ, Bayati A, Taft-Benz SA, Smith JL, Wells CI, Madden EA, Brown JW, Lenarcic EM, Yount BL, Chang E, Axtman AD, Baric RS, Heise MT, McPherson PS, Moorman NJ, Willson TM. Host Kinase CSNK2 is a Target for Inhibition of Pathogenic SARS-like β-Coronaviruses. ACS Chem Biol 2022; 17:1937-1950. [PMID: 35723434 PMCID: PMC9236220 DOI: 10.1021/acschembio.2c00378] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inhibition of the protein kinase CSNK2 with any of 30 specific and selective inhibitors representing different chemotypes, blocked replication of pathogenic human, bat, and murine β-coronaviruses. The potency of in-cell CSNK2A target engagement across the set of inhibitors correlated with antiviral activity and genetic knockdown confirmed the essential role of the CSNK2 holoenzyme in β-coronavirus replication. Spike protein endocytosis was blocked by CSNK2A inhibition, indicating that antiviral activity was due in part to a suppression of viral entry. CSNK2A inhibition may be a viable target for the development of anti-SARS-like β-coronavirus drugs.
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Affiliation(s)
- Xuan Yang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
| | - Rebekah J Dickmander
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Armin Bayati
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Sharon A Taft-Benz
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jeffery L Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Emily A Madden
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jason W Brown
- Takeda San Diego, San Diego, California 92121, United States
| | - Erik M Lenarcic
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Edcon Chang
- Takeda San Diego, San Diego, California 92121, United States
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
| | - Ralph S Baric
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States.,Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mark T Heise
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Peter S McPherson
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Nathaniel J Moorman
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Timothy M Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
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16
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Abstract
Coronaviruses have caused devastation in both human and animal populations, affecting both health and the economy. Amidst the emergence and re-emergence of coronaviruses, humans need to surmount the health and economic threat of coronaviruses through science and evidence-based approaches. One of these approaches is through biotechnology, particularly the heterologous production of biopharmaceutical proteins. This review article briefly describes the genome, general virion morphology, and key structural proteins of different coronaviruses affecting animals and humans. In addition, this review paper also presents the different systems in recombinant protein technology such as bacteria, yeasts, plants, mammalian cells, and insect/insect cells systems used to express key structural proteins in the development of countermeasures such as diagnostics, prophylaxis, and therapeutics in the challenging era of coronaviruses.
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17
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Qing E, Li P, Cooper L, Schulz S, Jäck HM, Rong L, Perlman S, Gallagher T. Inter-domain communication in SARS-CoV-2 spike proteins controls protease-triggered cell entry. Cell Rep 2022; 39:110786. [PMID: 35477024 PMCID: PMC9015963 DOI: 10.1016/j.celrep.2022.110786] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/11/2022] [Accepted: 04/13/2022] [Indexed: 01/29/2023] Open
Abstract
SARS-CoV-2 continues to evolve into variants of concern (VOC), with greatest variability in the multidomain, entry-facilitating spike proteins. To recognize the significance of adaptive spike protein changes, we compare variant SARS-CoV-2 virus particles in several assays reflecting authentic virus-cell entry. Virus particles with adaptive changes in spike amino-terminal domains (NTDs) are hypersensitive to proteolytic activation of membrane fusion, an essential step in virus-cell entry. Proteolysis is within fusion domains (FDs), at sites over 10 nm from the VOC-specific NTD changes, indicating allosteric inter-domain control of fusion activation. In addition, NTD-specific antibodies block FD cleavage, membrane fusion, and virus-cell entry, suggesting restriction of inter-domain communication as a neutralization mechanism. Finally, using structure-guided mutagenesis, we identify an inter-monomer β sheet structure that facilitates NTD-to-FD transmissions and subsequent fusion activation. This NTD-to-FD axis that sensitizes viruses to infection and to NTD-specific antibody neutralization provides new context for understanding selective forces driving SARS-CoV-2 evolution.
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Affiliation(s)
- Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Pengfei Li
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Laura Cooper
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Sebastian Schulz
- Division of Molecular Immunology, Friedrich-Alexander University Erlangen-Nuremberg and University Hospital Erlangen, 91054 Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Friedrich-Alexander University Erlangen-Nuremberg and University Hospital Erlangen, 91054 Erlangen, Germany
| | - Lijun Rong
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA,Corresponding author
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18
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Gaur P, Zaffran I, George T, Alekberli FR, Ben-Zimra M, Levi-Schaffer F. The regulatory role of eosinophils in viral, bacterial, and fungal infections. Clin Exp Immunol 2022; 209:72-82. [PMID: 35467728 PMCID: PMC9307229 DOI: 10.1093/cei/uxac038] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 03/15/2022] [Accepted: 04/24/2022] [Indexed: 12/14/2022] Open
Abstract
Eosinophils are innate immune cells typically associated with allergic and parasitic diseases. However, in recent years, eosinophils have also been ascribed a role in keeping homeostasis and in fighting several infectious diseases. Indeed, these cells circulate as mature cells in the blood and can be quickly recruited to the infected tissue. Moreover, eosinophils have all the necessary cellular equipment such as pattern recognition receptors (PRRs), pro-inflammatory cytokines, anti-bacterial proteins, and DNA traps to fight pathogens and promote an efficient immune response. This review summarizes some of the updated information on the role of eosinophils' direct and indirect mediated interactions with pathogens.
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Affiliation(s)
- Pratibha Gaur
- Pharmacology and Experimental Therapeutics Unit, School of Pharmacy, Institute for Drug Research, Faculty of Medicine, The Hebrew University of Jerusalem, Israel
| | - Ilan Zaffran
- Pharmacology and Experimental Therapeutics Unit, School of Pharmacy, Institute for Drug Research, Faculty of Medicine, The Hebrew University of Jerusalem, Israel
| | - Tresa George
- Pharmacology and Experimental Therapeutics Unit, School of Pharmacy, Institute for Drug Research, Faculty of Medicine, The Hebrew University of Jerusalem, Israel
| | - Fidan Rahimli Alekberli
- Pharmacology and Experimental Therapeutics Unit, School of Pharmacy, Institute for Drug Research, Faculty of Medicine, The Hebrew University of Jerusalem, Israel
| | - Micha Ben-Zimra
- Pharmacology and Experimental Therapeutics Unit, School of Pharmacy, Institute for Drug Research, Faculty of Medicine, The Hebrew University of Jerusalem, Israel
| | - Francesca Levi-Schaffer
- Pharmacology and Experimental Therapeutics Unit, School of Pharmacy, Institute for Drug Research, Faculty of Medicine, The Hebrew University of Jerusalem, Israel
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19
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Dai J, Wang H, Liao Y, Tan L, Sun Y, Song C, Liu W, Qiu X, Ding C. Coronavirus Infection and Cholesterol Metabolism. Front Immunol 2022; 13:791267. [PMID: 35529872 PMCID: PMC9069556 DOI: 10.3389/fimmu.2022.791267] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/21/2022] [Indexed: 12/19/2022] Open
Abstract
Host cholesterol metabolism remodeling is significantly associated with the spread of human pathogenic coronaviruses, suggesting virus-host relationships could be affected by cholesterol-modifying drugs. Cholesterol has an important role in coronavirus entry, membrane fusion, and pathological syncytia formation, therefore cholesterol metabolic mechanisms may be promising drug targets for coronavirus infections. Moreover, cholesterol and its metabolizing enzymes or corresponding natural products exert antiviral effects which are closely associated with individual viral steps during coronavirus replication. Furthermore, the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 infections are associated with clinically significant low cholesterol levels, suggesting cholesterol could function as a potential marker for monitoring viral infection status. Therefore, weaponizing cholesterol dysregulation against viral infection could be an effective antiviral strategy. In this review, we comprehensively review the literature to clarify how coronaviruses exploit host cholesterol metabolism to accommodate viral replication requirements and interfere with host immune responses. We also focus on targeting cholesterol homeostasis to interfere with critical steps during coronavirus infection.
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Affiliation(s)
- Jun Dai
- College of Animal Science and Technology, Guangxi University, Nanning, China
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Experimental Animal Center, Zunyi Medical University, Zunyi City, China
| | - Huan Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ying Liao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Weiwei Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Xusheng Qiu, ; Chan Ding,
| | - Chan Ding
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- *Correspondence: Xusheng Qiu, ; Chan Ding,
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20
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Cavezzi A, Menicagli R, Troiani E, Corrao S. COVID-19, Cation Dysmetabolism, Sialic Acid, CD147, ACE2, Viroporins, Hepcidin and Ferroptosis: A Possible Unifying Hypothesis. F1000Res 2022; 11:102. [PMID: 35340277 PMCID: PMC8921693 DOI: 10.12688/f1000research.108667.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/17/2022] [Indexed: 12/15/2022] Open
Abstract
Background: iron and calcium dysmetabolism, with hyperferritinemia, hypoferremia, hypocalcemia and anemia have been documented in the majority of COVID-19 patients at later/worse stages. Furthermore, complementary to ACE2, both sialic acid (SA) molecules and CD147 proved relevant host receptors for SARS-CoV-2 entry, which explains the viral attack to multiple types of cells, including erythrocytes, endothelium and neural tissue. Several authors advocated that cell ferroptosis may be the core and final cell degenerative mechanism. Methods: a literature research was performed in several scientific search engines, such as PubMed Central, Cochrane Library, Chemical Abstract Service. More than 500 articles were retrieved until mid-December 2021, to highlight the available evidence about the investigated issues. Results: based on COVID-19 literature data, we have highlighted a few pathophysiological mechanisms, associated with virus-based cation dysmetabolism, multi-organ attack, mitochondria degeneration and ferroptosis. Our suggested elucidated pathological sequence is: a) spike protein subunit S1 docking with sialylated membrane glycoproteins/receptors (ACE2, CD147), and S2 subunit fusion with the lipid layer; b) cell membrane morpho-functional changes due to the consequent electro-chemical variations and viroporin action, which induce an altered ion channel function and intracellular cation accumulation; c) additional intracellular iron concentration due to a deregulated hepcidin-ferroportin axis, with higher hepcidin levels. Viral invasion may also affect erythrocytes/erythroid precursors, endothelial cells and macrophages, through SA and CD147 receptors, with relative hemoglobin and iron/calcium dysmetabolism. AB0 blood group, hemochromatosis, or environmental elements may represent possible factors which affect individual susceptibility to COVID-19. Conclusions: our literature analysis confirms the combined role of SA molecules, ACE2, CD147, viroporins and hepcidin in determining the cation dysmetabolism and final ferroptosis in the cells infected by SARS-CoV-2. The altered ion channels and electrochemical gradients of the cell membrane have a pivotal role in the virus entry and cell dysmetabolism, with subsequent multi-organ immune-inflammatory degeneration and erythrocyte/hemoglobin alterations.
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Affiliation(s)
- Attilio Cavezzi
- Eurocenter Venalinfa, San Benedetto del Tronto, AP, 63074, Italy
| | | | - Emidio Troiani
- Cardiology Unit, Social Security Institute, State Hospital, Cailungo, 47893, San Marino
| | - Salvatore Corrao
- Department of Clinical Medicine, Internal Medicine Division,, ARNAS Civico Di Cristina Benfratelli Hospital Trust, Palermo, Italy
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21
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Nascimento ED, Fonseca WT, de Oliveira TR, de Correia CRSTB, Faça VM, de Morais BP, Silvestrini VC, Pott-Junior H, Teixeira FR, Faria RC. COVID-19 diagnosis by SARS-CoV-2 Spike protein detection in saliva using an ultrasensitive magneto-assay based on disposable electrochemical sensor. SENSORS AND ACTUATORS. B, CHEMICAL 2022; 353:131128. [PMID: 34866796 DOI: 10.1016/j.snb.2021.131148] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 05/27/2023]
Abstract
The outbreak of the COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome of Coronavirus 2 (SARS-CoV-2), has fueled the search for diagnostic tests aiming at the control and reduction of the viral transmission. The main technique used for diagnosing the Coronavirus disease (COVID-19) is the reverse transcription-polymerase chain reaction (RT-PCR) technique. However, considering the high number of cases and the underlying limitations of the RT-PCR technique, especially with regard to accessibility and cost of the test, one does not need to overemphasize the need to develop new and less expensive testing techniques that can aid the early diagnosis of the disease. With that in mind, we developed an ultrasensitive magneto-assay using magnetic beads and gold nanoparticles conjugated to human angiotensin-converting enzyme 2 (ACE2) peptide (Gln24-Gln42) for the capturing and detection of SARS-CoV-2 Spike protein in human saliva. The technique applied involved the use of a disposable electrochemical device containing eight screen-printed carbon electrodes which allow the simultaneous analysis of eight samples. The magneto-assay exhibited an ultralow limit of detection of 0.35 ag mL-1 for the detection of SARS-CoV-2 Spike protein in saliva. The magneto-assay was tested in saliva samples from healthy and SARS-CoV-2-infected individuals. In terms of efficiency, the proposed technique - which presented a sensitivity of 100.0% and specificity of 93.7% for SARS-CoV-2 Spike protein-exhibited great similarity with the RT-PCR technique. The results obtained point to the application potential of this simple, low-cost magneto-assay for saliva-based point-of-care COVID-19 diagnosis.
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Affiliation(s)
- Evair D Nascimento
- Department of Chemistry, Federal University of São Carlos-UFSCar, Rod. Washington Luís km 235, São Carlos, SP, 13565-905, Brazil
| | - Wilson T Fonseca
- Department of Chemistry, Federal University of São Carlos-UFSCar, Rod. Washington Luís km 235, São Carlos, SP, 13565-905, Brazil
| | - Tássia R de Oliveira
- Department of Chemistry, Federal University of São Carlos-UFSCar, Rod. Washington Luís km 235, São Carlos, SP, 13565-905, Brazil
| | - Camila R S T B de Correia
- Department of Genetics and Evolution, Federal University of Sao Carlos-UFSCar, São Carlos, SP, 13565-905, Brazil
| | - Vitor M Faça
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo-USP, Brazil
| | - Beatriz P de Morais
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo-USP, Brazil
| | - Virginia C Silvestrini
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo-USP, Brazil
| | - Henrique Pott-Junior
- Department of Medicine, Federal University of São Carlos-UFSCar, São Carlos, SP, 13565-905, Brazil
| | - Felipe R Teixeira
- Department of Genetics and Evolution, Federal University of Sao Carlos-UFSCar, São Carlos, SP, 13565-905, Brazil
| | - Ronaldo C Faria
- Department of Chemistry, Federal University of São Carlos-UFSCar, Rod. Washington Luís km 235, São Carlos, SP, 13565-905, Brazil
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22
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Nascimento ED, Fonseca WT, de Oliveira TR, de Correia CRSTB, Faça VM, de Morais BP, Silvestrini VC, Pott-Junior H, Teixeira FR, Faria RC. COVID-19 diagnosis by SARS-CoV-2 Spike protein detection in saliva using an ultrasensitive magneto-assay based on disposable electrochemical sensor. SENSORS AND ACTUATORS. B, CHEMICAL 2022; 353:131128. [PMID: 34866796 PMCID: PMC8626148 DOI: 10.1016/j.snb.2021.131128] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 05/03/2023]
Abstract
The outbreak of the COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome of Coronavirus 2 (SARS-CoV-2), has fueled the search for diagnostic tests aiming at the control and reduction of the viral transmission. The main technique used for diagnosing the Coronavirus disease (COVID-19) is the reverse transcription-polymerase chain reaction (RT-PCR) technique. However, considering the high number of cases and the underlying limitations of the RT-PCR technique, especially with regard to accessibility and cost of the test, one does not need to overemphasize the need to develop new and less expensive testing techniques that can aid the early diagnosis of the disease. With that in mind, we developed an ultrasensitive magneto-assay using magnetic beads and gold nanoparticles conjugated to human angiotensin-converting enzyme 2 (ACE2) peptide (Gln24-Gln42) for the capturing and detection of SARS-CoV-2 Spike protein in human saliva. The technique applied involved the use of a disposable electrochemical device containing eight screen-printed carbon electrodes which allow the simultaneous analysis of eight samples. The magneto-assay exhibited an ultralow limit of detection of 0.35 ag mL-1 for the detection of SARS-CoV-2 Spike protein in saliva. The magneto-assay was tested in saliva samples from healthy and SARS-CoV-2-infected individuals. In terms of efficiency, the proposed technique - which presented a sensitivity of 100.0% and specificity of 93.7% for SARS-CoV-2 Spike protein-exhibited great similarity with the RT-PCR technique. The results obtained point to the application potential of this simple, low-cost magneto-assay for saliva-based point-of-care COVID-19 diagnosis.
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Affiliation(s)
- Evair D Nascimento
- Department of Chemistry, Federal University of São Carlos-UFSCar, Rod. Washington Luís km 235, São Carlos, SP, 13565-905, Brazil
| | - Wilson T Fonseca
- Department of Chemistry, Federal University of São Carlos-UFSCar, Rod. Washington Luís km 235, São Carlos, SP, 13565-905, Brazil
| | - Tássia R de Oliveira
- Department of Chemistry, Federal University of São Carlos-UFSCar, Rod. Washington Luís km 235, São Carlos, SP, 13565-905, Brazil
| | - Camila R S T B de Correia
- Department of Genetics and Evolution, Federal University of Sao Carlos-UFSCar, São Carlos, SP, 13565-905, Brazil
| | - Vitor M Faça
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo-USP, Brazil
| | - Beatriz P de Morais
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo-USP, Brazil
| | - Virginia C Silvestrini
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo-USP, Brazil
| | - Henrique Pott-Junior
- Department of Medicine, Federal University of São Carlos-UFSCar, São Carlos, SP, 13565-905, Brazil
| | - Felipe R Teixeira
- Department of Genetics and Evolution, Federal University of Sao Carlos-UFSCar, São Carlos, SP, 13565-905, Brazil
| | - Ronaldo C Faria
- Department of Chemistry, Federal University of São Carlos-UFSCar, Rod. Washington Luís km 235, São Carlos, SP, 13565-905, Brazil
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23
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Known Cellular and Receptor Interactions of Animal and Human Coronaviruses: A Review. Viruses 2022; 14:v14020351. [PMID: 35215937 PMCID: PMC8878323 DOI: 10.3390/v14020351] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/12/2022] Open
Abstract
This article aims to review all currently known interactions between animal and human coronaviruses and their cellular receptors. Over the past 20 years, three novel coronaviruses have emerged that have caused severe disease in humans, including SARS-CoV-2 (severe acute respiratory syndrome virus 2); therefore, a deeper understanding of coronavirus host-cell interactions is essential. Receptor-binding is the first stage in coronavirus entry prior to replication and can be altered by minor changes within the spike protein-the coronavirus surface glycoprotein responsible for the recognition of cell-surface receptors. The recognition of receptors by coronaviruses is also a major determinant in infection, tropism, and pathogenesis and acts as a key target for host-immune surveillance and other potential intervention strategies. We aim to highlight the need for a continued in-depth understanding of this subject area following on from the SARS-CoV-2 pandemic, with the possibility for more zoonotic transmission events. We also acknowledge the need for more targeted research towards glycan-coronavirus interactions as zoonotic spillover events from animals to humans, following an alteration in glycan-binding capability, have been well-documented for other viruses such as Influenza A.
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24
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Madden EA, Diamond MS. Host cell-intrinsic innate immune recognition of SARS-CoV-2. Curr Opin Virol 2022; 52:30-38. [PMID: 34814102 PMCID: PMC8580835 DOI: 10.1016/j.coviro.2021.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 01/04/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged at the end of 2019 and caused the pandemic of coronavirus disease 2019 (COVID-19). Basic and clinical investigations indicate that severe forms of COVID-19 are due in part to dysregulated immune responses to virus infection. The innate immune system is the first line of host defense against most virus infections, with pathogen recognition receptors detecting SARS-CoV-2 RNA and protein components and initiating pro-inflammatory and antiviral responses. Notwithstanding this response, SARS-CoV-2 proteins evade, inhibit, and skew innate immune signaling early in infection. In this review, we highlight the components of cell-based recognition of SARS-CoV-2 infection and the mechanisms employed by the virus to modulate these innate immune host defense pathways.
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Affiliation(s)
- Emily A Madden
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 631100, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA.
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25
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Li CX, Noreen S, Zhang LX, Saeed M, Wu PF, Ijaz M, Dai DF, Maqbool I, Madni A, Akram F, Naveed M, Li JH. A critical analysis of SARS-CoV-2 (COVID-19) complexities, emerging variants, and therapeutic interventions and vaccination strategies. Biomed Pharmacother 2022; 146:112550. [PMID: 34959116 PMCID: PMC8673752 DOI: 10.1016/j.biopha.2021.112550] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 01/11/2023] Open
Abstract
Coronavirus is a family of viruses that can cause diseases such as the common cold, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS). The universal outbreak of coronavirus disease 2019 (COVID-19) caused by SARS coronaviruses 2 (SARS-CoV-2) has become a global pandemic. The β-Coronaviruses, which caused SARS-CoV-2 (COVID-19), have spread in more than 213 countries, infected over 81 million people, and caused more than 1.79 million deaths. COVID-19 symptoms vary from mild fever, flu to severe pneumonia in severely ill patients. Difficult breathing, acute respiratory distress syndrome (ARDS), acute kidney disease, liver damage, and multi-organ failure ultimately lead to death. Researchers are working on different pre-clinical and clinical trials to prevent this deadly pandemic by developing new vaccines. Along with vaccines, therapeutic intervention is an integral part of healthcare response to address the ongoing threat posed by COVID-19. Despite the global efforts to understand and fight against COVID-19, many challenges need to be addressed. This article summarizes the current pandemic, different strains of SARS-CoV-2, etiology, complexities, surviving medications of COVID-19, and so far, vaccination for the treatment of COVID-19.
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Affiliation(s)
- Chang-Xing Li
- Department of Human Anatomy, Medical College of Qinghai University, 810000 Xining, China
| | - Sobia Noreen
- Department of Pharmaceutics, Faculty of Pharmacy, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Li-Xue Zhang
- School of Medicine, Northwest Minzu University, Lanzhou 730030, China
| | - Muhammad Saeed
- The Cholistan University of Veterinary and Animal Sciences, Bahawalpur 6300, Pakistan
| | - Pei-Feng Wu
- School of Medicine, Northwest Minzu University, Lanzhou 730030, China
| | - Muhammad Ijaz
- Department of Pharmacy, COMSATS University Islamabad, Lahore Campus, Lahore 54000, Pakistan
| | - Dong-Fang Dai
- Department of Human Anatomy, Medical College of Qinghai University, 810000 Xining, China
| | - Irsah Maqbool
- Department of Pharmaceutics, Faculty of Pharmacy, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Asadullah Madni
- Department of Pharmaceutics, Faculty of Pharmacy, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Faizan Akram
- Department of Pharmaceutics, Faculty of Pharmacy, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Muhammad Naveed
- Department of Clinical Pharmacy, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China.
| | - Jian-Hua Li
- Department of Human Anatomy, Medical College of Qinghai University, 810000 Xining, China.
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26
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Yang X, Dickmander RJ, Bayati A, Taft-Benz SA, Smith JL, Wells CI, Madden EA, Brown JW, Lenarcic EM, Yount BL, Chang E, Axtman AD, Baric RS, Heise MT, McPherson PS, Moorman NJ, Willson TM. Host kinase CSNK2 is a target for inhibition of pathogenic β-coronaviruses including SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 35018375 PMCID: PMC8750650 DOI: 10.1101/2022.01.03.474779] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Inhibition of the protein kinase CSNK2 with any of 30 specific and selective inhibitors representing different chemotypes, blocked replication of pathogenic human and murine β-coronaviruses. The potency of in-cell CSNK2A target engagement across the set of inhibitors correlated with antiviral activity and genetic knockdown confirmed the essential role of the CSNK2 holoenzyme in β-coronavirus replication. Spike protein uptake was blocked by CSNK2A inhibition, indicating that antiviral activity was due in part to a suppression of viral entry. CSNK2A inhibition may be a viable target for development of new broad spectrum anti-β-coronavirus drugs.
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Affiliation(s)
- Xuan Yang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.,Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States
| | - Rebekah J Dickmander
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Armin Bayati
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Sharon A Taft-Benz
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffery L Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Emily A Madden
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason W Brown
- Takeda San Diego, San Diego, CA 92121, United States
| | - Erik M Lenarcic
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Edcon Chang
- Takeda San Diego, San Diego, CA 92121, United States
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Ralph S Baric
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States.,Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Mark T Heise
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Peter S McPherson
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Nathaniel J Moorman
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Timothy M Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.,Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, United States
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27
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Abstract
The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect human cells, is the basis for many vaccines and a hotspot of concerning virus evolution. Here, we discuss the outstanding progress in structural characterization of the S-protein and how these structures facilitate analysis of virus function and evolution. We emphasize the differences in reported structures and that analysis of structure-function relationships is sensitive to the structure used. We show that the average residue solvent exposure in nearly complete structures is a good descriptor of open vs closed conformation states. Because of structural heterogeneity of functionally important surface-exposed residues, we recommend using averages of a group of high-quality protein structures rather than a single structure before reaching conclusions on specific structure-function relationships. To illustrate these points, we analyze some significant chemical tendencies of prominent S-protein mutations in the context of the available structures. In the discussion of new variants, we emphasize the selectivity of binding to ACE2 vs prominent antibodies rather than simply the antibody escape or ACE2 affinity separately. We note that larger chemical changes, in particular increased electrostatic charge or side-chain volume of exposed surface residues, are recurring in mutations of concern, plausibly related to adaptation to the negative surface potential of human ACE2. We also find indications that the fixated mutations of the S-protein in the main variants are less destabilizing than would be expected on average, possibly pointing toward a selection pressure on the S-protein. The richness of available structures for all of these situations provides an enormously valuable basis for future research into these structure-function relationships.
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Affiliation(s)
- Rukmankesh Mehra
- Department of Chemistry, Indian Institute
of Technology Bhilai, Sejbahar, Raipur 492015, Chhattisgarh,
India
| | - Kasper P. Kepp
- DTU Chemistry, Technical University of
Denmark, Building 206, 2800 Kongens Lyngby,
Denmark
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28
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Gómez-López VM, Jubinville E, Rodríguez-López MI, Trudel-Ferland M, Bouchard S, Jean J. Inactivation of Foodborne Viruses by UV Light: A Review. Foods 2021; 10:foods10123141. [PMID: 34945692 PMCID: PMC8701782 DOI: 10.3390/foods10123141] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/29/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022] Open
Abstract
Viruses on some foods can be inactivated by exposure to ultraviolet (UV) light. This green technology has little impact on product quality and, thus, could be used to increase food safety. While its bactericidal effect has been studied extensively, little is known about the viricidal effect of UV on foods. The mechanism of viral inactivation by UV results mainly from an alteration of the genetic material (DNA or RNA) within the viral capsid and, to a lesser extent, by modifying major and minor viral proteins of the capsid. In this review, we examine the potential of UV treatment as a means of inactivating viruses on food processing surfaces and different foods. The most common foodborne viruses and their laboratory surrogates; further explanation on the inactivation mechanism and its efficacy in water, liquid foods, meat products, fruits, and vegetables; and the prospects for the commercial application of this technology are discussed. Lastly, we describe UV’s limitations and legislation surrounding its use. Based on our review of the literature, viral inactivation in water seems to be particularly effective. While consistent inactivation through turbid liquid food or the entire surface of irregular food matrices is more challenging, some treatments on different food matrices seem promising.
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Affiliation(s)
- Vicente M. Gómez-López
- Catedra Alimentos para la Salud, Universidad Católica San Antonio de Murcia, Campus de los Jerónimos, E-30107 Murcia, Spain;
| | - Eric Jubinville
- Institute of Nutraceuticals and Functional Foods, Département des Sciences des Aliments, Université Laval, Québec, QC G1V 0A6, Canada; (E.J.); (M.T.-F.); (S.B.)
| | - María Isabel Rodríguez-López
- Departamento de Tecnología de la Alimentación y Nutrición, Universidad Católica San Antonio de Murcia, Campus de los Jerónimos, E-30107 Murcia, Spain;
| | - Mathilde Trudel-Ferland
- Institute of Nutraceuticals and Functional Foods, Département des Sciences des Aliments, Université Laval, Québec, QC G1V 0A6, Canada; (E.J.); (M.T.-F.); (S.B.)
| | - Simon Bouchard
- Institute of Nutraceuticals and Functional Foods, Département des Sciences des Aliments, Université Laval, Québec, QC G1V 0A6, Canada; (E.J.); (M.T.-F.); (S.B.)
| | - Julie Jean
- Institute of Nutraceuticals and Functional Foods, Département des Sciences des Aliments, Université Laval, Québec, QC G1V 0A6, Canada; (E.J.); (M.T.-F.); (S.B.)
- Correspondence: ; Tel.: +1-418-656-2131 (ext. 413849)
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29
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Evaluation of biochemical characteristics of 183 COVID-19 patients: A retrospective study. GENE REPORTS 2021; 26:101448. [PMID: 34869941 PMCID: PMC8626347 DOI: 10.1016/j.genrep.2021.101448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/01/2021] [Accepted: 11/16/2021] [Indexed: 01/08/2023]
Abstract
Introduction and aim Coronavirus disease 2019 (COVID-19), with a high mortality rate, has caught the eyes of researchers worldwide and placed a heavy burden on the health care system. Accordingly, this study aimed to evaluate the values of biochemical parameters on the outcomes of COVID-19 patients in Golestan, Iran. Materials and methods This retrospective study was conducted on 183 COVID-19 patients (i.e., 94 males and 89 females) between March and September 2020. The biochemical parameters and demographic data of the patients (including age, sex, urea, creatinine [Cr], lactate dehydrogenase [LDH], and creatine kinase [CK]) were obtained from electrical medical records. According to the outcome of COVID-19, the patients were categorized into two groups (i.e., death [n = 63] and survival [n = 120] groups), and the biochemical parameters and outcomes of COVID-19 were analyzed. Results Of the 183 patients, 120 (65.5%) had a non-severe type and recovered from COVID-19, and 63 (34.4%) developed into a critically severe type and died. The mean age of all patients was 56.5 years old. The highest mortality was observed in patients with LDH ≥280. The data obtained by the one-sample t-test showed that there were significantly higher mean values of urea, Cr, CK, and LDH in COVID-19 patients when compared to their reference intervals (P˂0.0001 for all). Conclusions Some biochemical parameters are effective in the evaluation of dynamic variations in COVID-19 patients. It can be concluded from the results that biochemical parameters and reinforce LDH may be useful for the evaluation of the COVID-19 outcome.
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Eid JI, Das B, Al‐Tuwaijri MM, Basal WT. Targeting SARS-CoV-2 with Chaga mushroom: An in silico study toward developing a natural antiviral compound. Food Sci Nutr 2021; 9:6513-6523. [PMID: 34900242 PMCID: PMC8645752 DOI: 10.1002/fsn3.2576] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 08/01/2021] [Accepted: 08/27/2021] [Indexed: 01/05/2023] Open
Abstract
The novel coronavirus (SARS-CoV-2) has caused large-scale global outbreaks and mainly mediates host cell entry through the interaction of its spike (S) protein with the human angiotensin-converting enzyme-2 (ACE-2) receptor. As there is no effective treatment for SARS-CoV-2 to date, it is imperative to explore the efficacy of new compounds that possess potential antiviral activity. In this study, we assessed the potential binding interaction of the beneficial components of Chaga mushroom, a natural anti-inflammatory and immune booster with that of the SARS-CoV-2 receptor-binding domain (RBD) using molecular docking, MD simulation, and phylogenetic analysis. Beta glycan, betulinic acid, and galactomannan constituents of Chaga mushroom exhibited strong binding interaction (-7.4 to -8.6 kcal/mol) forming multivalent hydrogen and non-polar bonds with the viral S1-carboxy-terminal domain of the RBD. Specifically, the best interacting sites for beta glycan comprised ASN-440, SER 373, TRP-436, ASN-343, and ARG 509 with average binding energy of -8.4 kcal/mol. The best interacting sites of galactomannan included ASN-437, SER 373, TRP-436, ASN-343, and ALA 344 with a mean binding energy of -7.4 kcal/mol; and the best interacting sites of betulinic acid were ASN-437, SER 373, TRP-436, PHE 342, ARG 509, and ALA 344 that strongly interacted with the S-protein (ΔG = -8.1 kcal/mol). The docking results were also compared with an S-protein binding analog, NAG and depicted similar binding affinities compared with that of the ligands (-8.67 kcal/mol). In addition, phylogenetic analysis using global isolates depicted that the current SARS-CoV-2 isolates possessed a furin cleavage site (NSPRRA) in the RBD, which was absent in the previous isolates that indicated increased efficacy of the present virus for enhanced infection through increased interaction with ACE-2. The results showed that Chaga could be an effective natural antiviral that can supplement the current anti-SARS-CoV-2 drugs.
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Affiliation(s)
| | - Biswadeep Das
- School of BiotechnologyKIIT UniversityBhubaneswarIndia
| | | | - Wesam Taha Basal
- Department of ZoologyFaculty of ScienceCairo UniversityCairoEgypt
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Pape KA, Dileepan T, Kabage AJ, Kozysa D, Batres R, Evert C, Matson M, Lopez S, Krueger PD, Graiziger C, Vaughn BP, Shmidt E, Rhein J, Schacker TW, Khoruts A, Jenkins MK. High-affinity memory B cells induced by SARS-CoV-2 infection produce more plasmablasts and atypical memory B cells than those primed by mRNA vaccines. Cell Rep 2021; 37:109823. [PMID: 34610291 PMCID: PMC8463313 DOI: 10.1016/j.celrep.2021.109823] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/16/2021] [Accepted: 09/20/2021] [Indexed: 02/03/2023] Open
Abstract
Although both infections and vaccines induce memory B cell (MBC) populations that participate in secondary immune responses, the MBCs generated in each case can differ. Here, we compare SARS-CoV-2 spike receptor binding domain (S1-RBD)-specific primary MBCs that form in response to infection or a single mRNA vaccination. Both primary MBC populations have similar frequencies in the blood and respond to a second S1-RBD exposure by rapidly producing plasmablasts with an abundant immunoglobulin (Ig)A+ subset and secondary MBCs that are mostly IgG+ and cross-react with the B.1.351 variant. However, infection-induced primary MBCs have better antigen-binding capacity and generate more plasmablasts and secondary MBCs of the classical and atypical subsets than do vaccine-induced primary MBCs. Our results suggest that infection-induced primary MBCs have undergone more affinity maturation than vaccine-induced primary MBCs and produce more robust secondary responses.
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Affiliation(s)
- Kathryn A Pape
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Thamotharampillai Dileepan
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Amanda J Kabage
- Department of Medicine, Division of Gastroenterology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Daria Kozysa
- Department of Medicine, Division of Gastroenterology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Rodolfo Batres
- Department of Medicine, Division of Infectious Disease, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Clayton Evert
- Department of Medicine, Division of Gastroenterology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Michael Matson
- Department of Medicine, Division of Gastroenterology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Sharon Lopez
- Department of Medicine, Division of Gastroenterology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Peter D Krueger
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Carolyn Graiziger
- Department of Medicine, Division of Gastroenterology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Byron P Vaughn
- Department of Medicine, Division of Gastroenterology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Eugenia Shmidt
- Department of Medicine, Division of Gastroenterology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Joshua Rhein
- Department of Medicine, Division of Infectious Disease, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Timothy W Schacker
- Department of Medicine, Division of Infectious Disease, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Alexander Khoruts
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Department of Medicine, Division of Gastroenterology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Marc K Jenkins
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA.
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Wan Y, Huang L, Zhang X, Shang J, Perlman S, Du L, Li F. Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. RESEARCH SQUARE 2021:rs.3.rs-736159. [PMID: 34611654 PMCID: PMC8491847 DOI: 10.21203/rs.3.rs-736159/v2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
SARS-CoV-2 spike protein plays a key role in viral entry and host immune responses. The conformation of the spike protein can be either open or closed, yet it is unclear how the conformations affect the protein's functions or what regulate the conformational changes. Using SARS-CoV-1 and bat RaTG13-CoV as comparisons, we identified two molecular switches that regulate the conformations of SARS-CoV-2 spike protein: (i) a furin motif loop turns SARS-CoV-2 spike from a closed conformation to a mixture of open and closed conformations, and (ii) a K417V mutation turns SARS-CoV-2 spike from mixed conformations to an open conformation. We showed that the open conformation favors viral potency by exposing the RBD for receptor binding and viral entry, whereas the closed conformation supports viral immune evasion by hiding the RBD from neutralizing antibodies. Hence SARS-CoV-2 spike has evolved to reach a balance between potency and immune evasiveness, which may contribute to the pandemic spread of SARS-CoV-2. The dynamics between viral potency and invasiveness is likely to further evolve, providing insights into future evolution of SARS-CoV-2.
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Affiliation(s)
- Yushun Wan
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
- Center for Coronavirus Research, University of Minnesota, Saint Paul, MN, USA
| | - Linfen Huang
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
- Center for Coronavirus Research, University of Minnesota, Saint Paul, MN, USA
| | - Xiujuan Zhang
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, USA
| | - Jian Shang
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
- Center for Coronavirus Research, University of Minnesota, Saint Paul, MN, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Lanying Du
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, USA
| | - Fang Li
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
- Center for Coronavirus Research, University of Minnesota, Saint Paul, MN, USA
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In silico targeting SARS-CoV-2 spike protein and main protease by biochemical compounds. Biologia (Bratisl) 2021; 76:3547-3565. [PMID: 34565804 PMCID: PMC8456686 DOI: 10.1007/s11756-021-00881-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/30/2021] [Indexed: 12/18/2022]
Abstract
Since there is no general agreement on drug treatment of SARS-CoV-2, the search for a new drug capable of treating COVID-19 is of utmost priority. This study aims to dereplicate the chemical compounds of the methanol extract of Salvia officinalis and Artemisia dracunculus, and assay the inhibitory effect of these compounds as well as the previously dereplicated components of Zingiber officinale against SARS-CoV-2 in an in-silico study. A molecular networking (MN) technique was applied to find the chemical constituents of the extracts. Docking analysis was also used to find the binding affinity of dereplicated components from S. officinalis, A. dracunculus, and Z. officinale to COV-2-SP and Mpro. 57 compounds were dereplicated from the MeOH extracts of S. officinalis and A. dracunculus which include the class of polyphenols, flavonoids, coumarins, phenylpropanoids, anthocyanins, and dihydrochalcones. Molecular docking analysis indicated a high affinity of about 27 compounds from three mentioned plants against studied targets. kaempferol 3-O-rutinoside, neodiosmin, and querciturone with docking score values of -10.575, -10.208, and - 9.904 Kcal/mol and ki values of 0.016606, 0.030921, and 0.051749, respectively were found to have the highest affinities against COV-2-SP. 2-phenylethyl beta-primeveroside, curcumin PE, and kaempferol 3-O-rutinoside also indicated the highest affinity against Mpro with docking scores of -10.34, -10.126 and - 9.705 and ki values of 0.024726, 0.035529, and 0.072494, respectively. MN can be successfully used for the dereplication of metabolites from plant extracts. In addition, the in-silico binding energies introduced several inhibitors from Z. officinale, S. officinalis, and A. dracunculus for the treatment of SARS-CoV-2 disease. Supplementary Information The online version contains supplementary material available at 10.1007/s11756-021-00881-z.
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Ghareeb DA, Saleh SR, Seadawy MG, Nofal MS, Abdulmalek SA, Hassan SF, Khedr SM, AbdElwahab MG, Sobhy AA, Abdel-Hamid ASA, Yassin AM, Elmoneam AAA, Masoud AA, Kaddah MMY, El-Zahaby SA, Al-mahallawi AM, El-Gharbawy AM, Zaki A, Seif IK, Kenawy MY, Amin M, Amer K, El Demellawy MA. Nanoparticles of ZnO/Berberine complex contract COVID-19 and respiratory co-bacterial infection in addition to elimination of hydroxychloroquine toxicity. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2021. [DOI: https://doi.org/10.1007/s40005-021-00544-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ghareeb DA, Saleh SR, Seadawy MG, Nofal MS, Abdulmalek SA, Hassan SF, Khedr SM, AbdElwahab MG, Sobhy AA, Abdel-Hamid ASA, Yassin AM, Elmoneam AAA, Masoud AA, Kaddah MMY, El-Zahaby SA, Al-Mahallawi AM, El-Gharbawy AM, Zaki A, Seif IK, Kenawy MY, Amin M, Amer K, El Demellawy MA. Nanoparticles of ZnO/Berberine complex contract COVID-19 and respiratory co-bacterial infection in addition to elimination of hydroxychloroquine toxicity. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2021; 51:735-757. [PMID: 34513113 PMCID: PMC8419391 DOI: 10.1007/s40005-021-00544-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/22/2021] [Indexed: 02/07/2023]
Abstract
Purpose A novel coronavirus (COVID-19) that has not been previously identified in humans and has no specific treatment has recently spread. Treatment trials using antiviral and immune-modulating drugs such as hydroxychloroquine (HCQ) were used to control this viral outbreak however several side effects have emerged. Berberine (BER) is an alkaloid that has been reported to reveal some pharmacological properties including antioxidant and antimicrobial activities. Additionally, Zinc oxide nanoparticles (ZnO-NPs) possess potent antioxidant and anti-inflammatory properties. Therefore, this study was undertaken to estimate the efficiency of both BER and synthetic ZnO/BER complex as an anti-COVID-19 therapy. Methods First, the ZnO/BER complex was prepared by the facile mixing method. Then in vitro studies on the two compounds were conducted including VeroE6 toxicity, anti-COVID-19 activity, determination of inhibitory activity towards papain-like proteinase (PL pro) and spike protein- and receptor- binding domain (RBD) as well as assessment of drug toxicity on RBCs. Results The results showed that ZnO/BER complex acts as an anti-COVID-19 by inhibiting spike protein binding with angiotensin-converting enzyme II (ACE II), PL pro activity, spike protein and E protein levels, and expression of both E-gene and RNA dependent RNA polymerase (RdRp) at a concentration lower than that of BER or ZnO-NPs alone. Furthermore, ZnO/BER complex had antioxidant and antimicrobial properties where it prevents the auto oxidation of 2,2-Diphenyl-1-picrylhydrazyl (DPPH) and the culture of lower respiratory system bacteria that affected Covid 19 patients. The ZnO/BER complex prevented as well the HCQ cytotoxic effect on both RBC and WBC (in vitro) and hepatotoxicity, nephrotoxicity and anemia that occurred after HCQ long administration in vivo. Conclusion The ZnO/BER complex can be accounted as promising anti-COVID 19 candidate because it inhibited the virus entry, replication, and assembly. Furthermore, it could be used to treat a second bacterial infection that took place in hospitalized COVID 19 patients. Moreover, ZnO/BER complex was found to eliminate the toxicity of long-term administration of HCQ in vivo.
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Affiliation(s)
- Doaa A Ghareeb
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Samar R Saleh
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | | | - Mohammed S Nofal
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Shaymaa A Abdulmalek
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Salma F Hassan
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Shaimaa M Khedr
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Miral G AbdElwahab
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Ahmed A Sobhy
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Clinical Pharmacy Program, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Ali Saber Ali Abdel-Hamid
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Abdelrahman Mohamed Yassin
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Alshimaa A Abd Elmoneam
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Aliaa A Masoud
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Mohamed M Y Kaddah
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Sally A El-Zahaby
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Pharos University in Alexandria, Alexandria, Egypt
| | - Abdulaziz Mohsen Al-Mahallawi
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo, Egypt
| | - Alaa M El-Gharbawy
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Ahmed Zaki
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Inas K Seif
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Marwa Y Kenawy
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Fabrication Technology Research Department, Advanced Technology and New Materials Research Institute (ATNMRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria, 21934 Egypt
| | | | - Khaled Amer
- Egypt Center for Research and Regenerative Medicine, Cairo, Egypt
| | - Maha Adel El Demellawy
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
- Medical Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
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Panigrahi D. Molecular Docking Analysis of the Phytochemicals from Tinospora Cordifolia as Potential Inhibitor Against Multi Targeted SARS-CoV-2 & Cytokine Storm. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2, a novel coronavirus, is a member of the Coronoviridae family that has spread worldwide. Developing efficacious therapeutics for the treatment of SARS-CoV-2 is of high priority. Therefore, in this study, the chemical constituents obtained from Tinospora cordifolia are investigated for their in-silico interaction with protein targets crucial for SARSCoV-2 infection and cytokine storm. The five important targets chosen for SARSCoV-2 were the main protease (Mpro), Spike receptor binding domain (Spike-RBD), RNA-dependent RNA polymerase (RdRp or Nsp12), nonstructural protein 15 (Nsp15) of SARS-CoV-2 and the host angiotensin converting enzyme-2 (ACE-2) spike-RBD binding domain and cytokine receptors TNF-[Formula: see text] (Tumor Necrosis Factor-[Formula: see text]) and IL-6 (Interleukine-6). This was accomplished using Maestro 12.4 (Schrodinger Suite) to obtain docking scores. Also, the absorption, distribution, metabolism, elimination, and toxicity parameters (ADMET) were determined using Maestro QikProp modules. The results of computational study revealed that four constituents Cordifolioside-A, Palmatoside-E, Tinocordioside and Tinosporaside significantly antagonize the five targets of SARS-CoV-2 by binding in the binding pocket with docking score ranging from −9.664 to −6.488 kcal/mol and shows drug-like property and also effectively inhibit cytokine storm by antagonizing the TNF-[Formula: see text] and IL-6 receptors. Promising drug-like properties, excellent docking scores, and binding pose against each target makes the screened compounds as possible lead candidate which can be further evaluated in future studies to assess their in vitro and in vivo efficacy against SARS-CoV-2. The structure of these compounds can be used further for optimization and design of drugs against COVID-19.
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Affiliation(s)
- Debadash Panigrahi
- Drug Research Laboratory, Nodal Research Centre, College of Pharmaceutical Sciences, Puri, Baliguali, Puri-Konark Marine Drive Road, Puri, Odisha 752002, India
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Ayele AG, Enyew EF, Kifle ZD. Roles of existing drug and drug targets for COVID-19 management. Metabol Open 2021; 11:100103. [PMID: 34222852 PMCID: PMC8239316 DOI: 10.1016/j.metop.2021.100103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 06/27/2021] [Indexed: 02/07/2023] Open
Abstract
In December 2019, a highly transmissible, pneumonia epidemic caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), erupted in China and other countries, resulting in devastation and health crisis worldwide currently. The search and using existing drugs support to curb the current highly contagious viral infection is spirally increasing since the pandemic began. This is based on these drugs had against other related RNA-viruses such as MERS-Cov, and SARS-Cov. Moreover, researchers are scrambling to identify novel drug targets and discover novel therapeutic options to vanquish the current pandemic. Since there is no definitive treatment to control Covid-19 vaccines are remain to be a lifeline. Currently, many vaccine candidates are being developed with most of them are reported to have positive results. Therapeutic targets such as helicases, transmembrane serine protease 2, cathepsin L, cyclin G-associated kinase, adaptor-associated kinase 1, two-pore channel, viral virulence factors, 3-chymotrypsin-like protease, suppression of excessive inflammatory response, inhibition of viral membrane, nucleocapsid, envelope, and accessory proteins, and inhibition of endocytosis were identified as a potential target against COVID-19 infection. This review also summarizes plant-based medicines for the treatment of COVID-19 such as saposhnikoviae divaricata, lonicerae japonicae flos, scutellaria baicalensis, lonicera japonicae, and some others. Thus, this review aimed to focus on the most promising therapeutic targets being repurposed against COVID-19 and viral elements that are used in COVID-19 vaccine candidates.
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Key Words
- 3CLpro, 3-chymotrypsin-like protease
- AAK1, adaptor-associated kinase 1
- ACE-2, Angiotensin-Converting Enzyme-2
- CEF, Cepharanthine
- COVID-19
- COVID-19, coronavirus disease-2019
- Existing drug
- GAK, cyclin G-associated kinase
- MERS-CoV, Middle East respiratory syndrome coronavirus
- Management
- Nsp, non-structure protein
- ORF, open reading frame
- PLpro, papain-like protease
- RdRp, RNA-dependence RNA-polymerase
- SARS-COV-2, severe acute respiratory syndrome coronavirus-2
- TMPRSS2, transmembrane Serine Protease 2
- TPC2, two-pore channel 2
- Therapeutic target
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Affiliation(s)
- Akeberegn Gorems Ayele
- Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Science, Addis Ababa University, Addis Ababa, Ethiopia
| | - Engidaw Fentahun Enyew
- Department of Human Anatomy, School of Medicine, College of Medicine and Health Sciences, Gondar, Ethiopia
| | - Zemene Demelash Kifle
- Department of Pharmacology, School of Pharmacy, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia
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Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has placed a global challenge on both healthcare and society. So far, studies have shown that men are more prone to become ill than women and are more likely to die compared to female patients. Higher rates of positive cases and fatality in men than women have drawn the attention of scientists to investigate the possible impacts of SARS-CoV-2 on the male reproductive system. In this review, we tried to summarise so far findings on the effect of the SARS-CoV-2 on the male reproductive function to further assess the potential risks of this novel coronavirus on male reproductive health.
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Affiliation(s)
- Marziye Farsimadan
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Mohammad Motamedifar
- Department of Bacteriology and Virology, Shiraz Medical School, Shiraz University of Medical Sciences, Shiraz, Iran
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More N, Ranglani D, Kharche S, Choppadandi M, Ghosh S, Vaidya S, Kapusetti G. Current challenges in identification of clinical characteristics and detection of COVID-19: A comprehensive review. MEASUREMENT. SENSORS 2021; 16:100052. [PMID: 36578268 PMCID: PMC8178959 DOI: 10.1016/j.measen.2021.100052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 12/31/2022]
Abstract
World Health Organization (WHO) declares the COVID-19 outbreak as a pandemic. The newly emerging infection has caused around one million deaths worldwide and still counting. There is no specific treatment for the disease, and it can only contain by breaking the spread. So that early and rapid diagnosis of the infection is the only way to control the outbreak. The COVID-19 virus affects the human respiratory system and subsequently infects other vital organs. In consideration of the diagnosis, the present review focuses on the critical diagnostic approaches for COVID-19, including RT-PCR, Chest-CT scan, some biosensor-based systems, etc. Moreover, this review is a specific bird's eye view on recent developments on the point of care devices and related technologies. Additionally, it presented a small glimpse of the pathophysiology and structural aspects of COVID-19. Therefore, the current review can motivate and help the reader to develop cutting-edge diagnostic technologies for the early and rapid detection of the COVID-19.
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Affiliation(s)
| | | | | | | | | | | | - Govinda Kapusetti
- Corresponding author. Department of Medical Devices, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, India
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Zhang L, Cao L, Gao XS, Zheng BY, Deng YQ, Li JX, Feng R, Bian Q, Guo XL, Wang N, Qiu HY, Wang L, Cui Z, Ye Q, Chen G, Lu KK, Chen Y, Chen YT, Pan HX, Yu J, Yao W, Zhu BL, Chen J, Liu Y, Qin CF, Wang X, Zhu FC. A proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2. Natl Sci Rev 2021; 8:nwab053. [PMID: 34676098 PMCID: PMC8083607 DOI: 10.1093/nsr/nwab053] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 11/12/2022] Open
Abstract
Mutations and transient conformational movements of the receptor binding domain (RBD) that make neutralizing epitopes momentarily unavailable present immune escape routes for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To mitigate viral escape, we developed a cocktail of neutralizing antibodies (NAbs) targeting epitopes located on different domains of spike (S) protein. Screening of a library of monoclonal antibodies generated from peripheral blood mononuclear cells of COVID-19 convalescent patients yielded potent NAbs, targeting the N-terminal domain (NTD) and RBD domain of S, effective at nM concentrations. Remarkably, a combination of RBD-targeting NAbs and NTD-binding NAbs, FC05, enhanced the neutralization potency in cell-based assays and an animal model. Results of competitive surface plasmon resonance assays and cryo-electron microscopy (cryo-EM) structures of antigen-binding fragments bound to S unveil determinants of immunogenicity. Combinations of immunogens, identified in the NTD and RBD of S, when immunized in rabbits and macaques, elicited potent protective immune responses against SARS-CoV-2. More importantly, two immunizations of this combination of NTD and RBD immunogens provided complete protection in macaques against a SARS-CoV-2 challenge, without observable antibody-dependent enhancement of infection. These results provide a proof of concept for neutralization-based immunogen design targeting SARS-CoV-2 NTD and RBD.
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Affiliation(s)
- Li Zhang
- National Health Commission of the People's Republic of China, Key Laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing 210009, China
| | - Lei Cao
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xing-Su Gao
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Bin-Yang Zheng
- National Health Commission of the People's Republic of China, Key Laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing 210009, China
| | - Yong-Qiang Deng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Jing-Xin Li
- National Health Commission of the People's Republic of China, Key Laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing 210009, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Rui Feng
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Bian
- National Health Commission of the People's Republic of China, Key Laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing 210009, China
| | - Xi-Ling Guo
- National Health Commission of the People's Republic of China, Key Laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing 210009, China
| | - Nan Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong-Ying Qiu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Lei Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhen Cui
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Ye
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Geng Chen
- National Health Commission of the People's Republic of China, Key Laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing 210009, China
| | - Kui-Kui Lu
- National Health Commission of the People's Republic of China, Key Laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing 210009, China
| | - Yin Chen
- National Health Commission of the People's Republic of China, Key Laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing 210009, China
| | - Yu-Tao Chen
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong-Xing Pan
- National Health Commission of the People's Republic of China, Key Laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing 210009, China
| | - Jiaping Yu
- Jiangsu Rec-biotechnology Co. Ltd, Taizhou 225300, China
| | - Wenrong Yao
- Jiangsu Rec-biotechnology Co. Ltd, Taizhou 225300, China
| | - Bao-Li Zhu
- National Health Commission of the People's Republic of China, Key Laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing 210009, China
| | - Jianping Chen
- Jiangsu Rec-biotechnology Co. Ltd, Taizhou 225300, China
| | - Yong Liu
- Jiangsu Rec-biotechnology Co. Ltd, Taizhou 225300, China
| | - Cheng-Feng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510200, China
| | - Feng-Cai Zhu
- National Health Commission of the People's Republic of China, Key Laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing 210009, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
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Mishra GP, Bhadane RN, Panigrahi D, Amawi HA, Asbhy CR, Tiwari AK. The interaction of the bioflavonoids with five SARS-CoV-2 proteins targets: An in silico study. Comput Biol Med 2021; 134:104464. [PMID: 34020130 PMCID: PMC8108478 DOI: 10.1016/j.compbiomed.2021.104464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022]
Abstract
Flavonoids have been shown to have antioxidant, anti-inflammatory, anti-proliferative, antibacterial and antiviral efficacy. Therefore, in this study, we choose 85 flavonoid compounds and screened them to determine their in-silico interaction with protein targets crucial for SARS-CoV-2 infection. The five important targets chosen were the main protease (Mpro), Spike receptor binding domain (Spike-RBD), RNA - dependent RNA polymerase (RdRp or Nsp12), non-structural protein 15 (Nsp15) of SARS-CoV-2 and the host angiotensin converting enzyme-2 (ACE-2) spike-RBD binding domain. The compounds were initially docked at the selected sites and further evaluated for binding free energy, using the molecular mechanics/generalized Born surface area (MMGBSA) method. The three compounds with the best binding scores were subjected to molecular dynamics (MD) simulations. The compound, tribuloside, had a high average binding free energy of -86.99 and -88.98 kcal/mol for Mpro and Nsp12, respectively. The compound, legalon, had an average binding free energy of -59.02 kcal/mol at the ACE2 spike-RBD binding site. The compound, isosilybin, had an average free binding energy of -63.06 kcal/mol for the Spike-RBD protein. Overall, our results suggest that tribuloside, legalon and isosilybin should be evaluated in future studies to determine their efficacy to inhibit SARS-CoV-2 infectivity.
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Affiliation(s)
- Ganesh Prasad Mishra
- Kharvel Subharti College of Pharmacy, Swami VivekanandSubharti University, Subhartipuram, NH-58, Delhi-Haridwar Bypass Road, Meerut, U.P, 250005, India,Corresponding author
| | - Rajendra N. Bhadane
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI, 20520, Turku, Finland,Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI, 20520, Turku, Finland
| | - Debadash Panigrahi
- Drug Research Laboratory, Nodal Research Centre, College of Pharmaceutical Sciences, Puri, Baliguali, Puri- Konark Marine Drive Road, Puri, Odisha, 752002, India
| | - Haneen A. Amawi
- Department of Clinical Pharmacy and Pharmacy Practice, College of Pharmacy, Yarmouk University, Shafiq Irshidat St, Irbid, Jordan
| | - Charles R. Asbhy
- Department of Pharmaceutical Sciences, College of Pharmacy & Pharmaceutical Sciences, St. John's University, Queens, NY, USA, 10049
| | - Amit K. Tiwari
- Department of Pharmacology & Experimental Therapeutics, College of Pharmacy & Pharmaceutical Sciences, The University of Toledo, Toledo, OH, 43614, USA,Department of Cancer Biology, College of Medicine & Life Sciences, The University of Toledo, Toledo, OH, 43614, USA,Corresponding author. Department of Pharmacology & Experimental Therapeutics, College of Pharmacy & Pharmaceutical Sciences, The University of Toledo, Toledo, OH, 43614, USA
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Abstract
The high SARS-CoV-2 reproductive number driving the COVID-19 pandemic has been a mystery. Our recent in vitro, and in vivo coronaviral pathogenesis studies involving Mouse Hepatitis Virus (MHV-A59) suggest a crucial role for a small host membrane-virus contact initiator region of the Spike protein, called the fusion peptide that enhances the virus fusogenicity and infectivity. Here I study the Spike from five human β-coronaviruses (HCoV) including the SARS-CoV-2, and MHV-A59 for comparison. The structural and dynamics analyses of the Spike show that its fusion loop spatially organizes three fusion peptides contiguous to each other to synergistically trigger the virus-host membrane fusion process. I propose a Contact Initiation Model based on the architecture of the Spike quaternary structure that explains the obligatory participation of the fusion loop in the initiation of the host membrane contact for the virus fusion process. Among all the HCoV Spikes in this study, SARS-CoV-2 has the most hydrophobic surface and the extent of hydrophobicity correlates with the reproductive number and infectivity of the other HCoV. Comparison between results from standard and replica exchange molecular dynamics reveal the unique physicochemical properties of the SARS-CoV-2 fusion peptides, accrued in part from the presence of consecutive prolines that impart backbone rigidity which aids the virus fusogenicity. The priming of the Spike by its cleavage and subsequent fusogenic conformational transition steered by the fusion loop may be critical for the SARS-CoV-2 spread. The importance of the fusion loop makes it an apt target for anti-virals and vaccine candidates.
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Affiliation(s)
- Debnath Pal
- Indian Institute of Science, Bengaluru 560012, India.
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43
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Beeckmans S, Van Driessche E. Scrutinizing Coronaviruses Using Publicly Available Bioinformatic Tools: The Viral Structural Proteins as a Case Study. Front Mol Biosci 2021; 8:671923. [PMID: 34109214 PMCID: PMC8181738 DOI: 10.3389/fmolb.2021.671923] [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: 02/24/2021] [Accepted: 04/15/2021] [Indexed: 01/18/2023] Open
Abstract
Since early 2020, the world suffers from a new beta-coronavirus, called SARS-CoV-2, that has devastating effects globally due to its associated disease, Covid-19. Until today, Covid-19, which not only causes life-threatening lung infections but also impairs various other organs and tissues, has killed hundreds of thousands of people and caused irreparable damage to many others. Since the very onset of the pandemic, huge efforts were made worldwide to fully understand this virus and numerous studies were, and still are, published. Many of these deal with structural analyses of the viral spike glycoprotein and with vaccine development, antibodies and antiviral molecules or immunomodulators that are assumed to become essential tools in the struggle against the virus. This paper summarizes knowledge on the properties of the four structural proteins (spike protein S, membrane protein M, envelope protein E and nucleocapsid protein N) of the SARS-CoV-2 virus and its relatives, SARS-CoV and MERS-CoV, that emerged few years earlier. Moreover, attention is paid to ways to analyze such proteins using freely available bioinformatic tools and, more importantly, to bring these proteins alive by looking at them on a computer/laptop screen with the easy-to-use but highly performant and interactive molecular graphics program DeepView. It is hoped that this paper will stimulate non-bioinformaticians and non-specialists in structural biology to scrutinize these and other macromolecules and as such will contribute to establishing procedures to fight these and maybe other forthcoming viruses.
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Affiliation(s)
- Sonia Beeckmans
- Research Unit Protein Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
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Courrol LC, de Oliveira Silva FR, Masilamani V. SARS-CoV-2, hemoglobin and protoporphyrin IX: Interactions and perspectives. Photodiagnosis Photodyn Ther 2021; 34:102324. [PMID: 33965601 PMCID: PMC8123386 DOI: 10.1016/j.pdpdt.2021.102324] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/20/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022]
Abstract
Background SARS-CoV-2 attacks hemoglobin through its structural protein ORF3a, dissociating the iron from the heme, as iron is necessary by cell machinery for virus replication. In this process protoporphyrin (PpIX) is released. Methods The decrease in the hemoglobin levels observed in patients with Covid-19 is frequently accompanied by an increase in PpIX levels. This evidence was confirmed by the quantification of PpIX by high-performance liquid chromatography (HPLC). PpIX emission is observed in its two characteristic bands at approximately 635 nm and 705 nm. Results This paper searches to understand the role of heme and PpIX inside the cells. Perspectives on the use of PpIX fluorescence as a sensor to monitor the presence of SARS-CoV-2 in the tissue, blood, urine, or feces to map the evolution and severity of the disease or to monitor the response of the Covid-19 treatment modalities were described. Conclusion Fluorescence spectroscopy could be adopted as an excellent diagnostic technique for Covid-19, of low cost and high sensitivity. This method can potentially be used as a marker to monitor the response to the treatments. Photodynamic and sonodynamic therapies using the endogenous PpIX increased in the acute phase of the disease, could be employed for Covid-19 treatment.
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Affiliation(s)
| | | | - Valdivel Masilamani
- King Saud University, Physics and Astronomy Department, Laser Group, College of Science, Riyadh, Saudi Arabia
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Li B, Wang W, Song W, Zhao Z, Tan Q, Zhao Z, Tang L, Zhu T, Yin J, Bai J, Dong X, Tan S, Hu Q, Tang BZ, Huang X. Antiviral and Anti‐Inflammatory Treatment with Multifunctional Alveolar Macrophage‐Like Nanoparticles in a Surrogate Mouse Model of COVID‐19. ADVANCED SCIENCE 2021; 8:2003556. [PMCID: PMC8209923 DOI: 10.1002/advs.202003556] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The pandemic of coronavirus disease 2019 (COVID‐19) is continually worsening. Clinical treatment for COVID‐19 remains primarily supportive with no specific medicines or regimens. Here, the development of multifunctional alveolar macrophage (AM)‐like nanoparticles (NPs) with photothermal inactivation capability for COVID‐19 treatment is reported. The NPs, made by wrapping polymeric cores with AM membranes, display the same surface receptors as AMs, including the coronavirus receptor and multiple cytokine receptors. By acting as AM decoys, the NPs block coronavirus from host cell entry and absorb various proinflammatory cytokines, thus achieving combined antiviral and anti‐inflammatory treatment. To enhance the antiviral efficiency, an efficient photothermal material based on aggregation‐induced emission luminogens is doped into the NPs for virus photothermal disruption under near‐infrared (NIR) irradiation. In a surrogate mouse model of COVID‐19 caused by murine coronavirus, treatment with multifunctional AM‐like NPs with NIR irradiation decreases virus burden and cytokine levels, reduces lung damage and inflammation, and confers a significant survival advantage to the infected mice. Crucially, this therapeutic strategy may be clinically applied for the treatment of COVID‐19 at early stage through atomization inhalation of the NPs followed by NIR irradiation of the respiratory tract, thus alleviating infection progression and reducing transmission risk.
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Affiliation(s)
- Bin Li
- Center for Infection and ImmunityGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdong519000China
- Southern Marine Science and Engineering Guangdong LaboratoryZhuhaiGuangdong519000China
| | - Wei Wang
- Center for Infection and ImmunityGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdong519000China
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of EducationXizang Minzu UniversityXianyangShaanxi712082China
| | - Weifeng Song
- Center for Infection and ImmunityGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdong519000China
| | - Zheng Zhao
- Department of ChemistryThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong Kong999077China
| | - Qingqin Tan
- Center for Infection and ImmunityGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdong519000China
- Southern Marine Science and Engineering Guangdong LaboratoryZhuhaiGuangdong519000China
| | - Zhaoyan Zhao
- Center for Infection and ImmunityGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdong519000China
- Southern Marine Science and Engineering Guangdong LaboratoryZhuhaiGuangdong519000China
| | - Lantian Tang
- Center for Infection and ImmunityGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdong519000China
- Southern Marine Science and Engineering Guangdong LaboratoryZhuhaiGuangdong519000China
| | - Tianchuan Zhu
- Center for Infection and ImmunityGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdong519000China
- Southern Marine Science and Engineering Guangdong LaboratoryZhuhaiGuangdong519000China
| | - Jialing Yin
- Center for Infection and ImmunityGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdong519000China
- Southern Marine Science and Engineering Guangdong LaboratoryZhuhaiGuangdong519000China
| | - Jun Bai
- Center for Infection and ImmunityGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdong519000China
- Southern Marine Science and Engineering Guangdong LaboratoryZhuhaiGuangdong519000China
| | - Xin Dong
- Center for Infection and ImmunityGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdong519000China
- Southern Marine Science and Engineering Guangdong LaboratoryZhuhaiGuangdong519000China
| | - Siyi Tan
- Center for Infection and ImmunityGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdong519000China
- Southern Marine Science and Engineering Guangdong LaboratoryZhuhaiGuangdong519000China
| | - Qunying Hu
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of EducationXizang Minzu UniversityXianyangShaanxi712082China
| | - Ben Zhong Tang
- Department of ChemistryThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong Kong999077China
| | - Xi Huang
- Center for Infection and ImmunityGuangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdong519000China
- Southern Marine Science and Engineering Guangdong LaboratoryZhuhaiGuangdong519000China
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Sivaraman V, Parker D, Zhang R, Jones MM, Onyenwoke RU. Vaping Exacerbates Coronavirus-Related Pulmonary Infection in a Murine Model. Front Physiol 2021; 12:634839. [PMID: 34040540 PMCID: PMC8143436 DOI: 10.3389/fphys.2021.634839] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/31/2021] [Indexed: 12/21/2022] Open
Abstract
Though the current preponderance of evidence indicates the toxicity associated with the smoking of tobacco products through conventional means, less is known about the role of "vaping" in respiratory disease. "Vaping" is described as the use of electronic cigarettes (E-Cigarettes or E-Cigs), which has only more recently been available to the public (∼10 years) but has quickly emerged as a popular means of tobacco consumption worldwide. The World Health Organization (WHO) declared the SARS-CoV-2 outbreak as a global pandemic in March 2020. SARS-CoV-2 can easily be transmitted between people in close proximity through direct contact or respiratory droplets to develop coronavirus infectious disease 2019 (COVID-19). Symptoms of COVID-19 range from a mild flu-like illness with high fever to severe respiratory distress syndrome and death. The risk factors for increased disease severity remain unclear. Herein, we utilize a murine-tropic coronavirus (beta coronavirus) MHV-A59 along with a mouse model and measures of pathology (lung weight/dry ratios and histopathology) and inflammation (ELISAs and cytokine array panels) to examine whether vaping may exacerbate the pulmonary disease severity of coronavirus disease. While vaping alone did result in some noted pathology, mice exposed with intranasal vaped e-liquid suffered more severe mortality due to pulmonary inflammation than controls when exposed to coronavirus infection. Our data suggest a role for vaping in increased coronavirus pulmonary disease in a mouse model. Furthermore, our data indicate that disease exacerbation may involve calcium (Ca2+) dysregulation, identifying a potential therapeutic intervention.
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Affiliation(s)
- Vijay Sivaraman
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, United States
| | - De’Jana Parker
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, United States
| | - Rui Zhang
- Department of Respiratory and Critical Care Medicine, General Hospital of Ningxia Medical University, Yinchuan, China
- Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, United States
| | - Myles M. Jones
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, United States
| | - Rob U. Onyenwoke
- Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, United States
- Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC, United States
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Mathur A, Raj S, Jha NK, Jha SK, Rathi B, Kumar D. Mutational heterogeneity in spike glycoproteins of severe acute respiratory syndrome coronavirus 2. 3 Biotech 2021; 11:236. [PMID: 33936927 PMCID: PMC8070983 DOI: 10.1007/s13205-021-02791-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/12/2021] [Indexed: 12/02/2022] Open
Abstract
The novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has led to a global crisis by infecting millions of people across the globe eventually causing multiple deaths. The prominent player of the virus has been known as the spike protein which enters the host system and leads to the infection. The S2 subunit is the most essential in this process of infection as it helps the SARS-CoV-2 to infect the host by binding to the human angiotensin converting enzyme 2 (hACE2), with the help of the receptor binding domain found at the S2 subunit of the virus. Studies also hypothesize that the S glycoproteins present in the virus interacts with different hosts in different ways which might be due to the mutations taking place in the genome of the virus over time. This work aims to decipher the similarities and differences in the sequences of spike proteins from samples of SARS-CoV-2 acquired from different infected individuals in different countries with the help of in silico methods such as multiple sequence alignment and phylogenetic analysis. It also aims to understand the differential infection rates among the infected countries by studying the amino acid composition and interactions of the virus with the host.
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Affiliation(s)
- Aanchal Mathur
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sec-125, Noida, 201313 India
| | - Sibi Raj
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sec-125, Noida, 201313 India
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, New Delhi, India
| | - Dhruv Kumar
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sec-125, Noida, 201313 India
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Luo R, Delaunay‐Moisan A, Timmis K, Danchin A. SARS-CoV-2 biology and variants: anticipation of viral evolution and what needs to be done. Environ Microbiol 2021; 23:2339-2363. [PMID: 33769683 PMCID: PMC8251359 DOI: 10.1111/1462-2920.15487] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022]
Abstract
The global propagation of SARS-CoV-2 and the detection of a large number of variants, some of which have replaced the original clade to become dominant, underscores the fact that the virus is actively exploring its evolutionary space. The longer high levels of viral multiplication occur - permitted by high levels of transmission -, the more the virus can adapt to the human host and find ways to success. The third wave of the COVID-19 pandemic is starting in different parts of the world, emphasizing that transmission containment measures that are being imposed are not adequate. Part of the consideration in determining containment measures is the rationale that vaccination will soon stop transmission and allow a return to normality. However, vaccines themselves represent a selection pressure for evolution of vaccine-resistant variants, so the coupling of a policy of permitting high levels of transmission/virus multiplication during vaccine roll-out with the expectation that vaccines will deal with the pandemic, is unrealistic. In the absence of effective antivirals, it is not improbable that SARS-CoV-2 infection prophylaxis will involve an annual vaccination campaign against 'dominant' viral variants, similar to influenza prophylaxis. Living with COVID-19 will be an issue of SARS-CoV-2 variants and evolution. It is therefore crucial to understand how SARS-CoV-2 evolves and what constrains its evolution, in order to anticipate the variants that will emerge. Thus far, the focus has been on the receptor-binding spike protein, but the virus is complex, encoding 26 proteins which interact with a large number of host factors, so the possibilities for evolution are manifold and not predictable a priori. However, if we are to mount the best defence against COVID-19, we must mount it against the variants, and to do this, we must have knowledge about the evolutionary possibilities of the virus. In addition to the generic cellular interactions of the virus, there are extensive polymorphisms in humans (e.g. Lewis, HLA, etc.), some distributed within most or all populations, some restricted to specific ethnic populations and these variations pose additional opportunities for/constraints on viral evolution. We now have the wherewithal - viral genome sequencing, protein structure determination/modelling, protein interaction analysis - to functionally characterize viral variants, but access to comprehensive genome data is extremely uneven. Yet, to develop an understanding of the impacts of such evolution on transmission and disease, we must link it to transmission (viral epidemiology) and disease data (patient clinical data), and the population granularities of these. In this editorial, we explore key facets of viral biology and the influence of relevant aspects of human polymorphisms, human behaviour, geography and climate and, based on this, derive a series of recommendations to monitor viral evolution and predict the types of variants that are likely to arise.
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Affiliation(s)
- Ruibang Luo
- Department of Computer ScienceThe University of Hong KongBonham RoadPokfulamHong Kong
| | - Agnès Delaunay‐Moisan
- Université Paris‐Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Gif‐sur‐Yvette91198France
| | - Kenneth Timmis
- Institute of MicrobiologyTechnical University of BraunschweigBraunschweigGermany
| | - Antoine Danchin
- Kodikos Labs, Institut Cochin, 24 rue du Faubourg Saint‐JacquesParis75014France
- School of Biomedical Sciences, Li Kashing Faculty of MedicineUniversity of Hong Kong21 Sassoon RoadHong Kong
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49
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Weissenberger G, Henderikx RJM, Peters PJ. Understanding the invisible hands of sample preparation for cryo-EM. Nat Methods 2021; 18:463-471. [PMID: 33963356 DOI: 10.1038/s41592-021-01130-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/30/2021] [Indexed: 02/03/2023]
Abstract
Cryo-electron microscopy (cryo-EM) is rapidly becoming an attractive method in the field of structural biology. With the exploding popularity of cryo-EM, sample preparation must evolve to prevent congestion in the workflow. The dire need for improved microscopy samples has led to a diversification of methods. This Review aims to categorize and explain the principles behind various techniques in the preparation of vitrified samples for the electron microscope. Various aspects and challenges in the workflow are discussed, from sample optimization and carriers to deposition and vitrification. Reliable and versatile specimen preparation remains a challenge, and we hope to give guidelines and posit future directions for improvement.
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Affiliation(s)
- Giulia Weissenberger
- CryoSol-World, Maastricht, the Netherlands.,Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands
| | - Rene J M Henderikx
- CryoSol-World, Maastricht, the Netherlands.,Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands.
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50
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Noy-Porat T, Mechaly A, Levy Y, Makdasi E, Alcalay R, Gur D, Aftalion M, Falach R, Leviatan Ben-Arye S, Lazar S, Zauberman A, Epstein E, Chitlaru T, Weiss S, Achdout H, Edgeworth JD, Kikkeri R, Yu H, Chen X, Yitzhaki S, Shapira SC, Padler-Karavani V, Mazor O, Rosenfeld R. Therapeutic antibodies, targeting the SARS-CoV-2 spike N-terminal domain, protect lethally infected K18-hACE2 mice. iScience 2021; 24:102479. [PMID: 33937725 PMCID: PMC8074524 DOI: 10.1016/j.isci.2021.102479] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/24/2021] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
Neutralizing antibodies represent a valuable therapeutic approach to countermeasure the current COVID-19 pandemic. Emergence of SARS-CoV-2 variants emphasizes the notion that antibody treatments need to rely on highly neutralizing monoclonal antibodies (mAbs), targeting several distinct epitopes for circumventing therapy escape mutants. Previously, we reported efficient human therapeutic mAbs recognizing epitopes on the spike receptor-binding domain (RBD) of SARS-CoV-2. Here we report the isolation, characterization, and recombinant production of 12 neutralizing human mAbs, targeting three distinct epitopes on the spike N-terminal domain of the virus. Neutralization mechanism of these antibodies involves receptors other than the canonical hACE2 on target cells, relying both on amino acid and N-glycan epitope recognition, suggesting alternative viral cellular portals. Two selected mAbs demonstrated full protection of K18-hACE2 transgenic mice when administered at low doses and late post-exposure, demonstrating the high potential of the mAbs for therapy of SARS-CoV-2 infection. Isolation of potent neutralizing antibodies, targeting the NTD of SARS-CoV-2 Involvement of both protein and glycan moieties in antibody binding was suggested Post-exposure protection of lethally infected K18-hACE2 mice by BLN12 and BLN14
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Affiliation(s)
- Tal Noy-Porat
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Adva Mechaly
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Yinon Levy
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Efi Makdasi
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ron Alcalay
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | - David Gur
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Moshe Aftalion
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Reut Falach
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Shani Leviatan Ben-Arye
- Department of Cell Research and Immunology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shirley Lazar
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | | | - Eyal Epstein
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | | | - Shay Weiss
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Hagit Achdout
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Jonathan D. Edgeworth
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Raghavendra Kikkeri
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| | - Hai Yu
- Department of Chemistry, University of California-Davis, Davis, CA, USA
| | - Xi Chen
- Department of Chemistry, University of California-Davis, Davis, CA, USA
| | - Shmuel Yitzhaki
- Israel Institute for Biological Research, Ness-Ziona, Israel
| | | | - Vered Padler-Karavani
- Department of Cell Research and Immunology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ohad Mazor
- Israel Institute for Biological Research, Ness-Ziona, Israel
- Corresponding author
| | - Ronit Rosenfeld
- Israel Institute for Biological Research, Ness-Ziona, Israel
- Corresponding author
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