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Tarke A, Zhang Y, Methot N, Narowski TM, Phillips E, Mallal S, Frazier A, Filaci G, Weiskopf D, Dan JM, Premkumar L, Scheuermann RH, Sette A, Grifoni A. Targets and cross-reactivity of human T cell recognition of Common Cold Coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522794. [PMID: 36656777 PMCID: PMC9844015 DOI: 10.1101/2023.01.04.522794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Coronavirus (CoV) family includes a variety of viruses able to infect humans. Endemic CoVs that can cause common cold belong to the alphaCoV and betaCoV genera, with the betaCoV genus also containing subgenera with zoonotic and pandemic concern, including sarbecoCoV (SARS-CoV and SARS-CoV-2) and merbecoCoV (MERS-CoV). It is therefore warranted to explore pan-CoV vaccine concepts, to provide adaptive immune protection against new potential CoV outbreaks, particularly in the context of betaCoV sub lineages. To explore the feasibility of eliciting CD4 + T cell responses widely cross-recognizing different CoVs, we utilized samples collected pre-pandemic to systematically analyze T cell reactivity against representative alpha (NL63) and beta (OC43) common cold CoVs (CCC). Similar to previous findings on SARS-CoV-2, the S, N, M, and nsp3 antigens were immunodominant for both viruses while nsp2 and nsp12 were immunodominant for NL63 and OC43, respectively. We next performed a comprehensive T cell epitope screen, identifying 78 OC43 and 87 NL63-specific epitopes. For a selected subset of 18 epitopes, we experimentally assessed the T cell capability to cross-recognize sequences from representative viruses belonging to alphaCoV, sarbecoCoV, and beta-non-sarbecoCoV groups. We found general conservation within the alpha and beta groups, with cross-reactivity experimentally detected in 89% of the instances associated with sequence conservation of >67%. However, despite sequence conservation, limited cross-reactivity was observed in the case of sarbecoCoV (50% of instances), indicating that previous CoV exposure to viruses phylogenetically closer to this subgenera is a contributing factor in determining cross-reactivity. Overall, these results provided critical insights in the development of future pan-CoV vaccines.
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Affiliation(s)
- Alison Tarke
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA,Department of Experimental Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, 16132, Italy
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Nils Methot
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Tara M. Narowski
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Gilberto Filaci
- Center of Excellence for Biomedical Research, Department of Internal Medicine, University of Genoa, Genoa 16132, Italy;,Biotherapy Unit, IRCCS Ospedale Policlinico San Martino, Genoa 16132, Italy
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jennifer M. Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA,Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, CA 92037, USA,Department of Pathology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA,These authors contributed equally
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA,Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA,These authors contributed equally
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA,These authors contributed equally,Lead Contact
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Naidu SAG, Tripathi YB, Shree P, Clemens RA, Naidu AS. Phytonutrient Inhibitors of SARS-CoV-2/NSP5-Encoded Main Protease (M pro) Autocleavage Enzyme Critical for COVID-19 Pathogenesis. J Diet Suppl 2023; 20:284-311. [PMID: 34821532 DOI: 10.1080/19390211.2021.2006388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The genomic reshuffling, mutagenicity, and high transmission rate of the SARS-CoV-2 pathogen highlights an urgent need for effective antiviral interventions for COVID-19 control. Targeting the highly conserved viral genes and/or gene-encoded viral proteins such as main proteinase (Mpro), RNA-dependent RNA polymerase (RdRp) and helicases are plausible antiviral approaches to prevent replication and propagation of the SARS-CoV-2 infection. Coronaviruses (CoVs) are prone to extensive mutagenesis; however, any genetic alteration to its highly conserved Mpro enzyme is often detrimental to the viral pathogen. Therefore, inhibitors that target the Mpro enzyme could reduce the risk of mutation-mediated drug resistance and provide effective antiviral protection. Several existing antiviral drugs and dietary bioactives are currently repurposed to treat COVID-19. Dietary bioactives from three ayurvedic medicinal herbs, 18 β-glycyrrhetinic acid (ΔG = 8.86 kcal/mol), Solanocapsine (ΔG = 8.59 kcal/mol), and Vasicoline (ΔG = 7.34 kcal/mol), showed high-affinity binding to Mpro enzyme than the native N3 inhibitor (ΔG = 5.41 kcal/mol). Flavonoids strongly inhibited SARS-CoV-2 Mpro with comparable or higher potency than the antiviral drug, remdesivir. Several tannin hydrolysates avidly bound to the receptor-binding domain and catalytic dyad (His41 and Cys145) of SARS-CoV-2 Mpro through H-bonding forces. Quercetin binding to Mpro altered the thermostability of the viral protein through redox-based mechanism and inhibited the viral enzymatic activity. Interaction of quercetin-derivatives with the Mpro seem to be influenced by the 7-OH group and the acetoxylation of sugar moiety on the ligand molecule. Based on pharmacokinetic and ADMET profiles, several phytonutrients could serve as a promising redox nutraceutical for COVID-19 management.
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Affiliation(s)
- Sreus A G Naidu
- N-terminus Research Laboratory, Yorba Linda, California, USA
| | - Yamini B Tripathi
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Priya Shree
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Roger A Clemens
- Department of International Regulatory Science, University of Southern California School of Pharmacy, Los Angeles, California, USA
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103
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Väisänen E, Jiang M, Laine L, Waris M, Julkunen I, Österlund P. Infectious viruses from transfected SARS-CoV-2 genomic RNA. Front Bioeng Biotechnol 2023; 11:1129111. [PMID: 37064222 PMCID: PMC10098207 DOI: 10.3389/fbioe.2023.1129111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
SARS-CoV-2 emerged at the end of 2019, and like other novel pathogens causing severe symptoms, WHO recommended heightened biosafety measures for laboratories working with the virus. The positive-stranded genomic RNA of coronaviruses has been known to be infectious since the 1970s, and overall, all experiments with the possibility of SARS-CoV-2 propagation are carried out in higher containment level laboratories. However, as SARS-CoV-2 RNA has been routinely handled in BSL-2 laboratories, the question of the true nature of RNA infectiousness has risen along with discussion of appropriate biosafety measures. Here, we studied the ability of native SARS-CoV-2 genomic RNA to produce infectious viruses when transfected into permissive cells and discussed the biosafety control measures related to these assays. In transfection assays large quantities of genomic vRNA of SARS-CoV-2 was required for a successful production of infectious viruses. However, the quantity of vRNA alone was not the only factor, and especially when the transfected RNA was derived from infected cells, even small amounts of genomic vRNA was enough for an infection. Virus replication was found to start rapidly after transfection, and infectious viruses were detected in the cell culture media at 24 h post-transfection. In addition, silica membrane-based kits were shown to be as good as traditional TRI-reagent based methods in extracting high-quality, 30 kb-long genomic vRNA. Taken together, our data indicates that all transfection experiments with samples containing genomic SARS-CoV-2 RNA should be categorized as a propagative work and the work should be conducted only in a higher containment BSL-3 laboratory.
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Affiliation(s)
- Elina Väisänen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
- *Correspondence: Elina Väisänen,
| | - Miao Jiang
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Larissa Laine
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Matti Waris
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ilkka Julkunen
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Pamela Österlund
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
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104
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Kim JA, Kim SH, Seo JS, Noh H, Jeong H, Kim J, Jeon D, Kim JJ, On D, Yoon S, Lee SG, Lee YW, Jang HJ, Park IH, Oh J, Seok SH, Lee YJ, Hong SM, An SH, Bae JY, Choi JA, Kim SY, Kim YB, Hwang JY, Lee HJ, Kim HB, Jeong DG, Song D, Song M, Park MS, Choi KS, Park JW, Yun JW, Shin JS, Lee HY, Seo JY, Nam KT, Gee HY, Seong JK. Temporal Transcriptome Analysis of SARS-CoV-2-Infected Lung and Spleen in Human ACE2-Transgenic Mice. Mol Cells 2022; 45:896-910. [PMID: 36324270 PMCID: PMC9794551 DOI: 10.14348/molcells.2022.0089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/19/2022] [Accepted: 08/05/2022] [Indexed: 11/06/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and potentially fatal virus. So far, most comprehensive analyses encompassing clinical and transcriptional manifestation have concentrated on the lungs. Here, we confirmed evident signs of viral infection in the lungs and spleen of SARS-CoV-2-infected K18-hACE2 mice, which replicate the phenotype and infection symptoms in hospitalized humans. Seven days post viral detection in organs, infected mice showed decreased vital signs, leading to death. Bronchopneumonia due to infiltration of leukocytes in the lungs and reduction in the spleen lymphocyte region were observed. Transcriptome profiling implicated the meticulous regulation of distress and recovery from cytokine-mediated immunity by distinct immune cell types in a time-dependent manner. In lungs, the chemokine-driven response to viral invasion was highly elevated at 2 days post infection (dpi). In late infection, diseased lungs, post the innate immune process, showed recovery signs. The spleen established an even more immediate line of defense than the lungs, and the cytokine expression profile dropped at 7 dpi. At 5 dpi, spleen samples diverged into two distinct groups with different transcriptome profile and pathophysiology. Inhibition of consecutive host cell viral entry and massive immunoglobulin production and proteolysis inhibition seemed that one group endeavored to survive, while the other group struggled with developmental regeneration against consistent viral intrusion through the replication cycle. Our results may contribute to improved understanding of the longitudinal response to viral infection and development of potential therapeutics for hospitalized patients affected by SARS-CoV-2.
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Affiliation(s)
- Jung Ah Kim
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sung-Hee Kim
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jung Seon Seo
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hyuna Noh
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Korea
| | - Haengdueng Jeong
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jiseon Kim
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Donghun Jeon
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jeong Jin Kim
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Dain On
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Korea
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Suhyeon Yoon
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Korea
| | - Sang Gyu Lee
- Interdisciplinary Program for Bioinformatics, Seoul National University, Seoul 08826, Korea
| | - Youn Woo Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Hui Jeong Jang
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - In Ho Park
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
- Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jooyeon Oh
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sang-Hyuk Seok
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea
| | - Yu Jin Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea
| | - Seung-Min Hong
- Laboratory of Avian Diseases, BK21 PLUS Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Se-Hee An
- Laboratory of Avian Diseases, BK21 PLUS Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, Biosafety Center, Korea University College of Medicine, Seoul 02841, Korea
| | - Jung-ah Choi
- Science Unit, International Vaccine Institute, Seoul 08826, Korea
| | - Seo Yeon Kim
- Preclinical Research Center, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Young Been Kim
- Preclinical Research Center, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Ji-Yeon Hwang
- Preclinical Research Center, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Hyo-Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam 13620, Korea
| | - Dae Gwin Jeong
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Daesub Song
- Department of Veterinary Medicine Virology Laboratory, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea
| | - Manki Song
- Science Unit, International Vaccine Institute, Seoul 08826, Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Biosafety Center, Korea University College of Medicine, Seoul 02841, Korea
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, BK21 PLUS Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Jun Won Park
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea
| | - Jun-Won Yun
- Laboratory of Veterinary Toxicology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Jeon-Soo Shin
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
- Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
- Department of Microbiology, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ho-Young Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jun-Young Seo
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ki Taek Nam
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Heon Yung Gee
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Korea
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
- Interdisciplinary Program for Bioinformatics, Seoul National University, Seoul 08826, Korea
- BIO-MAX Institute, Seoul National University, Seoul 08826, Korea
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105
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Carvalho PPD, Alves NA. Featuring ACE2 binding SARS-CoV and SARS-CoV-2 through a conserved evolutionary pattern of amino acid residues. J Biomol Struct Dyn 2022; 40:11719-11728. [PMID: 34486937 PMCID: PMC8425439 DOI: 10.1080/07391102.2021.1965028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Spike (S) glycoproteins mediate the coronavirus entry into the host cell. The S1 subunit of S-proteins contains the receptor-binding domain (RBD) that is able to recognize different host receptors, highlighting its remarkable capacity to adapt to their hosts along the viral evolution. While RBD in spike proteins is determinant for the virus-receptor interaction, the active residues lie at the receptor-binding motif (RBM), a region located in RBD that plays a fundamental role binding the outer surface of their receptors. Here, we address the hypothesis that SARS-CoV and SARS-CoV-2 strains able to use angiotensin-converting enzyme 2 (ACE2) proteins have adapted their RBM along the viral evolution to explore specific conformational topology driven by the residues YGF to infect host cells. We also speculate that this YGF-based mechanism can act as a protein signature located at the RBM to distinguish coronaviruses able to use ACE2 as a cell entry receptor.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Patrícia P. D. Carvalho
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,CONTACT Patrícia P. D. Carvalho ;
| | - Nelson A. Alves
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,Nelson Alves
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106
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Li M, Guo L, Feng L. Interplay between swine enteric coronaviruses and host innate immune. Front Vet Sci 2022; 9:1083605. [PMID: 36619958 PMCID: PMC9814124 DOI: 10.3389/fvets.2022.1083605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Swine enteric coronavirus (SeCoV) causes acute diarrhea, vomiting, dehydration, and high mortality in neonatal piglets, causing severe losses worldwide. SeCoV includes the following four members: transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), porcine delta coronavirus (PDCoV), and swine acute diarrhea syndrome coronavirus (SADS-CoV). Clinically, mixed infections with several SeCoVs, which are more common in global farms, cause widespread infections. It is worth noting that PDCoV has a broader host range, suggesting the risk of PDCoV transmission across species, posing a serious threat to public health and global security. Studies have begun to focus on investigating the interaction between SeCoV and its host. Here, we summarize the effects of viral proteins on apoptosis, autophagy, and innate immunity induced by SeCoV, providing a theoretical basis for an in-depth understanding of the pathogenic mechanism of coronavirus.
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107
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Sangwan J, Tripathi S, Yadav N, Kumar Y, Sangwan N. Comparative sequence analysis of SARS nCoV and SARS CoV genomes for variation in structural proteins. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [PMCID: PMC9765352 DOI: 10.1007/s43538-022-00140-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-nCoV was identified as corona virus had spread worldwide very quickly and affected more than million people worldwide. To halt this acceleration and for efficient control the knowledge on genomic information is of utmost importance. We attempted to determine the nature of variation i.e., insertion, deletion, substitution, among structural sequences required to code for membrane, spike, nucleocapsid, envelope protein and glycosylation variation between SARS CoV and SARS nCoV spike glycoproteins, respectively. Comparative sequence analysis was performed by using retrieved sequences from the NCBI database. The analyzed sequences revealed, that the sequences coding for envelope protein show minor substituting amino acids. SARS CoV showed 94.74 percent amino acid identities with SARS nCoV amino acid sequences coding for envelope protein. In comparison to SARS nCoV, distinct amino acid residues vary in SARS CoV sequences coding for membrane, nucleocapsid, and spike proteins, respectively. S protein coding sequences of SARS CoV exhibited one deletion, six insertion and six hundred three substitutions in SARS nCoV sequence. Insertion of valine was found in receptor binding domain of SARS nCoV at position 487, and NSPR amino acid residues at position 683–686. Deletions and substitutions were also found in nucleotide sequences of strain B.1.617.2 of SARS nCoV. Additionally, binding interaction pattern of ACE2 receptor protein with original wild-type SARS-CoV-2 strain with the recently evolved Omicron variant was also evaluated. The docking results substantiated that the specific variation in binding residues is likely to impact virulence pattern of both variants.
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Affiliation(s)
- Jyoti Sangwan
- Department of Biochemistry, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, India
| | | | - Nisha Yadav
- Department of Biochemistry, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, India
| | - Yogesh Kumar
- Department of General, Visceral and Thoracic Surgery, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Neelam Sangwan
- Department of Biochemistry, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, India
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108
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Bello M, Hasan MK. Elucidation of the inhibitory activity of plant-derived SARS-CoV inhibitors and their potential as SARS-CoV-2 inhibitors. J Biomol Struct Dyn 2022; 40:9992-10004. [PMID: 34121618 DOI: 10.1080/07391102.2021.1938234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Several drugs are now being tested as possible therapies due to the necessity of treating SARS-CoV-2 infection. Although approved vaccines bring much hope, a vaccination program covering the entire global population will take a very long time, making the development of effective antiviral drugs an effective solution for the immediate treatment of this dangerous infection. Previous studies found that three natural compounds, namely, tannic acid, 3-isotheaflavin-3-gallate and theaflavin-3,3-digallate, are effective proteinase (3CLpro) inhibitors of SARS-CoV (IC50 <10 µM). Based on this information and due to the high sequence identity between SARS-CoV and SARS-CoV-2 3CLpro, these three compounds could be candidate inhibitors of SARS-CoV-2 3CLpro. This paper explores the structural and energetic features that guided the molecular recognition of these three compounds for dimeric SARS-CoV-2 and SARS-CoV 3CLpro, the functional state of this enzyme, using docking and MD simulations with the molecular mechanics-generalized-born surface area (MMGBSA) approach. Energetic analysis demonstrated that the three compounds reached good affinities in both systems in the following order: tannic acid > 3-isotheaflavin-3-gallate > theaflavin-3,3-digallate. This tendency is in line with that experimentally reported between these ligands and SARS-CoV 3CLpro. Therefore, tannic acid may have clinical usefulness against COVID-19 by acting as a potent inhibitor of SARS-CoV-2 3CLpro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, México
| | - Md Kamrul Hasan
- Department of Biochemistry and Molecular Biology, Tejgaon College, National University, Gazipur, Bangladesh
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109
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Krivić H, Himbert S, Rheinstädter MC. Perspective on the Application of Erythrocyte Liposome-Based Drug Delivery for Infectious Diseases. MEMBRANES 2022; 12:1226. [PMID: 36557133 PMCID: PMC9785899 DOI: 10.3390/membranes12121226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Nanoparticles are explored as drug carriers with the promise for the treatment of diseases to increase the efficacy and also reduce side effects sometimes seen with conventional drugs. To accomplish this goal, drugs are encapsulated in or conjugated to the nanocarriers and selectively delivered to their targets. Potential applications include immunization, the delivery of anti-cancer drugs to tumours, antibiotics to infections, targeting resistant bacteria, and delivery of therapeutic agents to the brain. Despite this great promise and potential, drug delivery systems have yet to be established, mainly due to their limitations in physical instability and rapid clearance by the host's immune response. Recent interest has been taken in using red blood cells (RBC) as drug carriers due to their naturally long circulation time, flexible structure, and direct access to many target sites. This includes coating of nanoparticles with the membrane of red blood cells, and the fabrication and manipulation of liposomes made of the red blood cells' cytoplasmic membrane. The properties of these erythrocyte liposomes, such as charge and elastic properties, can be tuned through the incorporation of synthetic lipids to optimize physical properties and the loading efficiency and retention of different drugs. Specificity can be established through the anchorage of antigens and antibodies in the liposomal membrane to achieve targeted delivery. Although still at an early stage, this erythrocyte-based platform shows first promising results in vitro and in animal studies. However, their full potential in terms of increased efficacy and side effect minimization still needs to be explored in vivo.
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Affiliation(s)
- Hannah Krivić
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Sebastian Himbert
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Maikel C. Rheinstädter
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
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Antibody-Dependent Enhancement (ADE) and the role of complement system in disease pathogenesis. Mol Immunol 2022; 152:172-182. [PMCID: PMC9647202 DOI: 10.1016/j.molimm.2022.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022]
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111
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Zheng Q, Lin R, Chen Y, Lv Q, Zhang J, Zhai J, Xu W, Wang W. SARS-CoV-2 induces "cytokine storm" hyperinflammatory responses in RA patients through pyroptosis. Front Immunol 2022; 13:1058884. [PMID: 36532040 PMCID: PMC9751040 DOI: 10.3389/fimmu.2022.1058884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/15/2022] [Indexed: 12/04/2022] Open
Abstract
Background The coronavirus disease (COVID-19) is a pandemic disease that threatens worldwide public health, and rheumatoid arthritis (RA) is the most common autoimmune disease. COVID-19 and RA are each strong risk factors for the other, but their molecular mechanisms are unclear. This study aims to investigate the biomarkers between COVID-19 and RA from the mechanism of pyroptosis and find effective disease-targeting drugs. Methods We obtained the common gene shared by COVID-19, RA (GSE55235), and pyroptosis using bioinformatics analysis and then did the principal component analysis(PCA). The Co-genes were evaluated by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and ClueGO for functional enrichment, the protein-protein interaction (PPI) network was built by STRING, and the k-means machine learning algorithm was employed for cluster analysis. Modular analysis utilizing Cytoscape to identify hub genes, functional enrichment analysis with Metascape and GeneMANIA, and NetworkAnalyst for gene-drug prediction. Network pharmacology analysis was performed to identify target drug-related genes intersecting with COVID-19, RA, and pyroptosis to acquire Co-hub genes and construct transcription factor (TF)-hub genes and miRNA-hub genes networks by NetworkAnalyst. The Co-hub genes were validated using GSE55457 and GSE93272 to acquire the Key gene, and their efficacy was assessed using receiver operating curves (ROC); SPEED2 was then used to determine the upstream pathway. Immune cell infiltration was analyzed using CIBERSORT and validated by the HPA database. Molecular docking, molecular dynamics simulation, and molecular mechanics-generalized born surface area (MM-GBSA) were used to explore and validate drug-gene relationships through computer-aided drug design. Results COVID-19, RA, and pyroptosis-related genes were enriched in pyroptosis and pro-inflammatory pathways(the NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome complex, death-inducing signaling complex, regulation of interleukin production), natural immune pathways (Network map of SARS-CoV-2 signaling pathway, activation of NLRP3 inflammasome by SARS-CoV-2) and COVID-19-and RA-related cytokine storm pathways (IL, nuclear factor-kappa B (NF-κB), TNF signaling pathway and regulation of cytokine-mediated signaling). Of these, CASP1 is the most involved pathway and is closely related to minocycline. YY1, hsa-mir-429, and hsa-mir-34a-5p play an important role in the expression of CASP1. Monocytes are high-caspase-1-expressing sentinel cells. Minocycline can generate a highly stable state for biochemical activity by docking closely with the active region of caspase-1. Conclusions Caspase-1 is a common biomarker for COVID-19, RA, and pyroptosis, and it may be an important mediator of the excessive inflammatory response induced by SARS-CoV-2 in RA patients through pyroptosis. Minocycline may counteract cytokine storm inflammation in patients with COVID-19 combined with RA by inhibiting caspase-1 expression.
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Affiliation(s)
- Qingcong Zheng
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Rongjie Lin
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Yuchao Chen
- Department of Paediatrics, Fujian Provincial Hospital South Branch, Fuzhou, China
| | - Qi Lv
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Jin Zhang
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Jingbo Zhai
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Medical College, Inner Mongolia Minzu University, Tongliao, China
| | - Weihong Xu
- Department of Orthopedics, First Affiliated Hospital of Fujian Medical University, Fuzhou, China,*Correspondence: Weihong Xu, ; Wanming Wang,
| | - Wanming Wang
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China,*Correspondence: Weihong Xu, ; Wanming Wang,
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Abstract
Purpose: COVID-19, a novel infection, presented with several complications, including socioeconomical and reproductive health challenges such as erectile dysfunction (ED). The present review summarizes the available shreds of evidence on the impact of COVID-19 on ED.Materials and methods: All published peer-reviewed articles from the onset of the COVID-19 outbreak to date, relating to ED, were reviewed. Results: Available pieces of evidence that ED is a consequence of COVID-19 are convincing. COVID-19 and ED share common risk factors such as disruption of vascular integrity, cardiovascular disease (CVD), cytokine storm, diabetes, obesity, and chronic kidney disease (CKD). COVID-19 also induces impaired pulmonary haemodynamics, increased ang II, testicular damage and low serum testosterone, and reduced arginine-dependent NO bioavailability that promotes reactive oxygen species (ROS) generation and endothelial dysfunction, resulting in ED. In addition, COVID-19 triggers psychological/mental stress and suppresses testosterone-dependent dopamine concentration, which contributes to incident ED.Conclusions: In conclusion, COVID-19 exerts a detrimental effect on male reproductive function, including erectile function. This involves a cascade of events from multiple pathways. As the pandemic dwindles, identifying the long-term effects of COVID-19-induced ED, and proffering adequate and effective measures in militating against COVID-19-induced ED remains pertinent.
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Affiliation(s)
- D H Adeyemi
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Osun State University, Nigeria
| | - A F Odetayo
- Department of Physiology, University of Ilorin, Ilorin, Nigeria
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
| | - M A Hamed
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
- The Brainwill Laboratories, Osogbo, Nigeria
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Afe Babalola University, Ado-Ekiti, Nigeria
| | - R E Akhigbe
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
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Zhao L, Hall M, de Cesare M, MacIntyre-Cockett G, Lythgoe K, Fraser C, Bonsall D, Golubchik T, Ferretti L. The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA. Proc Biol Sci 2022; 289:20221747. [PMID: 36382519 PMCID: PMC9667359 DOI: 10.1098/rspb.2022.1747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The raw material for viral evolution is provided by intra-host mutations occurring during replication, transcription or post-transcription. Replication and transcription of Coronaviridae proceed through the synthesis of negative-sense 'antigenomes' acting as templates for positive-sense genomic and subgenomic RNA. Hence, mutations in the genomes of SARS-CoV-2 and other coronaviruses can occur during (and after) the synthesis of either negative-sense or positive-sense RNA, with potentially distinct patterns and consequences. We explored for the first time the mutational spectrum of SARS-CoV-2 (sub)genomic and anti(sub)genomic RNA. We use a high-quality deep sequencing dataset produced using a quantitative strand-aware sequencing method, controlled for artefacts and sequencing errors, and scrutinized for accurate detection of within-host diversity. The nucleotide differences between negative- and positive-sense strand consensus vary between patients and do not show dependence on age or sex. Similarities and differences in mutational patterns between within-host minor variants on the two RNA strands suggested strand-specific mutations or editing by host deaminases and oxidative damage. We observe generally neutral and slight negative selection on the negative strand, contrasting with purifying selection in ORF1a, ORF1b and S genes of the positive strand of the genome.
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Affiliation(s)
- Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | | | | | - Katrina Lythgoe
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK,Sydney Infectious Diseases Institute (Sydney ID), Faculty of Medicine and Health, University of Sydney, Sydney NSW 2006, Australia
| | | | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
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Bianchini F, Crivelli V, Abernathy ME, Guerra C, Palus M, Muri J, Marcotte H, Piralla A, Pedotti M, De Gasparo R, Simonelli L, Matkovic M, Toscano C, Biggiogero M, Calvaruso V, Svoboda P, Rincón TC, Fava T, Podešvová L, Shanbhag AA, Celoria A, Sgrignani J, Stefanik M, Hönig V, Pranclova V, Michalcikova T, Prochazka J, Guerrini G, Mehn D, Ciabattini A, Abolhassani H, Jarrossay D, Uguccioni M, Medaglini D, Pan-Hammarström Q, Calzolai L, Fernandez D, Baldanti F, Franzetti-Pellanda A, Garzoni C, Sedlacek R, Ruzek D, Varani L, Cavalli A, Barnes CO, Robbiani DF. Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.11.24.515932. [PMID: 36482967 PMCID: PMC9727766 DOI: 10.1101/2022.11.24.515932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Emergence of SARS-CoV-2 variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera , including the nine human coronaviruses, through recognition of a conserved motif that includes the S2' site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization and, like fp.006 and hr2.016, protects mice when present as bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae , including SARS-CoV-2 variants. One sentence summary Broadly cross-reactive antibodies that protect from SARS-CoV-2 variants are revealed by virus coldspot-driven discovery.
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Affiliation(s)
- Filippo Bianchini
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Virginia Crivelli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | | | - Concetta Guerra
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
| | - Jonathan Muri
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Harold Marcotte
- Department of Biosciences and Nutrition, Karolinska Institutet; Huddinge, Sweden
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo; Pavia, Italy
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Raoul De Gasparo
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Milos Matkovic
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Chiara Toscano
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Maira Biggiogero
- Clinical Research Unit, Clinica Luganese Moncucco; Lugano, Switzerland
| | | | - Pavel Svoboda
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University; Brno, Czech Republic
- Department of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary Sciences; Brno, Czech Republic
| | - Tomás Cervantes Rincón
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Tommaso Fava
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Lucie Podešvová
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Akanksha A. Shanbhag
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Andrea Celoria
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Michal Stefanik
- Veterinary Research Institute; Brno, Czech Republic
- Department of Chemistry and Biochemistry, Mendel University in Brno; Brno, Czech Republic
| | - Vaclav Hönig
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
| | - Veronika Pranclova
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia; Ceske Budejovice, Czech Republic
| | - Tereza Michalcikova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences; Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences; Vestec, Czech Republic
| | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC); Ispra, Italy
| | - Annalisa Ciabattini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies; University of Siena, Siena, Italy
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institutet; Huddinge, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences; Tehran, Iran
| | - David Jarrossay
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies; University of Siena, Siena, Italy
| | | | - Luigi Calzolai
- European Commission, Joint Research Centre (JRC); Ispra, Italy
| | - Daniel Fernandez
- Sarafan ChEM-H Macromolecular Structure Knowledge Center, Stanford University; Stanford, USA
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo; Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia; Pavia, Italy
| | | | - Christian Garzoni
- Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco; Lugano, Switzerland
| | - Radislav Sedlacek
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences; Vestec, Czech Republic
| | - Daniel Ruzek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University; Brno, Czech Republic
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
- Swiss Institute of Bioinformatics; Lausanne, Switzerland
| | - Christopher O. Barnes
- Department of Biology, Stanford University; Stanford, USA
- Chan Zuckerberg Biohub; San Francisco, USA
| | - Davide F. Robbiani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
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Identifying MicroRNA Markers That Predict COVID-19 Severity Using Machine Learning Methods. LIFE (BASEL, SWITZERLAND) 2022; 12:life12121964. [PMID: 36556329 PMCID: PMC9784129 DOI: 10.3390/life12121964] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
Individuals with the SARS-CoV-2 infection may experience a wide range of symptoms, from being asymptomatic to having a mild fever and cough to a severe respiratory impairment that results in death. MicroRNA (miRNA), which plays a role in the antiviral effects of SARS-CoV-2 infection, has the potential to be used as a novel marker to distinguish between patients who have various COVID-19 clinical severities. In the current study, the existing blood expression profiles reported in two previous studies were combined for deep analyses. The final profiles contained 1444 miRNAs in 375 patients from six categories, which were as follows: 30 patients with mild COVID-19 symptoms, 81 patients with moderate COVID-19 symptoms, 30 non-COVID-19 patients with mild symptoms, 137 patients with severe COVID-19 symptoms, 31 non-COVID-19 patients with severe symptoms, and 66 healthy controls. An efficient computational framework containing four feature selection methods (LASSO, LightGBM, MCFS, and mRMR) and four classification algorithms (DT, KNN, RF, and SVM) was designed to screen clinical miRNA markers, and a high-precision RF model with a 0.780 weighted F1 was constructed. Some miRNAs, including miR-24-3p, whose differential expression was discovered in patients with acute lung injury complications brought on by severe COVID-19, and miR-148a-3p, differentially expressed against SARS-CoV-2 structural proteins, were identified, thereby suggesting the effectiveness and accuracy of our framework. Meanwhile, we extracted classification rules based on the DT model for the quantitative representation of the role of miRNA expression in differentiating COVID-19 patients with different severities. The search for novel biomarkers that could predict the severity of the disease could aid in the clinical diagnosis of COVID-19 and in exploring the specific mechanisms of the complications caused by SARS-CoV-2 infection. Moreover, new therapeutic targets for the disease may be found.
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116
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Lobato TB, Gennari-Felipe M, Pauferro JRB, Correa IS, Santos BF, Dias BB, de Oliveira Borges JC, dos Santos CS, de Sousa Santos ES, de Araújo MJL, Ferreira LA, Pereira SA, Serdan TDA, Levada-Pires AC, Hatanaka E, Borges L, Cury-Boaventura MF, Vinolo MAR, Pithon-Curi TC, Masi LN, Curi R, Hirabara SM, Gorjão R. Leukocyte metabolism in obese type 2 diabetic individuals associated with COVID-19 severity. Front Microbiol 2022; 13:1037469. [PMID: 36406408 PMCID: PMC9670542 DOI: 10.3389/fmicb.2022.1037469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/12/2022] [Indexed: 03/27/2024] Open
Abstract
Recent studies show that the metabolic characteristics of different leukocytes, such as, lymphocytes, neutrophils, and macrophages, undergo changes both in the face of infection with SARS-CoV-2 and in obesity and type 2 diabetes mellitus (DM2) condition. Thus, the objective of this review is to establish a correlation between the metabolic changes caused in leukocytes in DM2 and obesity that may favor a worse prognosis during SARS-Cov-2 infection. Chronic inflammation and hyperglycemia, specific and usual characteristics of obesity and DM2, contributes for the SARS-CoV-2 replication and metabolic disturbances in different leukocytes, favoring the proinflammatory response of these cells. Thus, obesity and DM2 are important risk factors for pro-inflammatory response and metabolic dysregulation that can favor the occurrence of the cytokine storm, implicated in the severity and high mortality risk of the COVID-19 in these patients.
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Affiliation(s)
- Tiago Bertola Lobato
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Matheus Gennari-Felipe
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | | | - Ilana Souza Correa
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Beatriz Ferreira Santos
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Beatriz Belmiro Dias
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - João Carlos de Oliveira Borges
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Camila Soares dos Santos
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | | | - Maria Janaína Leite de Araújo
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Liliane Araújo Ferreira
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Sara Araujo Pereira
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | | | - Adriana Cristina Levada-Pires
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Elaine Hatanaka
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Leandro Borges
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Maria Fernanda Cury-Boaventura
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Marco Aurélio Ramirez Vinolo
- Laboratory of Immunoinflammation, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Tania Cristina Pithon-Curi
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Laureane Nunes Masi
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Rui Curi
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
- Immunobiological Production Section, Bioindustrial Center, Butantan Institute, São Paulo, Brazil
| | - Sandro Massao Hirabara
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
| | - Renata Gorjão
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brasil
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Jose AM. Analyzing the Impermeable Structure and Myriad of Antiviral Therapies for SARS-CoV-2. JOURNAL OF THE ASSOCIATION OF PHYSICIANS OF INDIA 2022. [DOI: 10.5005/japi-11001-0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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118
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Carlson CR, Adly AN, Bi M, Howard CJ, Frost A, Cheng Y, Morgan DO. Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation. J Biol Chem 2022; 298:102560. [PMID: 36202211 PMCID: PMC9529352 DOI: 10.1016/j.jbc.2022.102560] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 is responsible for compaction of the ∼30-kb RNA genome in the ∼90-nm virion. Previous studies suggest that each virion contains 35 to 40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined in vitro with short fragments of the viral genome, forms 15-nm particles similar to the vRNP structures observed within virions. These vRNPs depend on regions of N protein that promote protein-RNA and protein-protein interactions. Phosphorylation of N protein in its disordered serine/arginine region weakens these interactions to generate less compact vRNPs. We propose that unmodified N protein binds structurally diverse regions in genomic RNA to form compact vRNPs within the nucleocapsid, while phosphorylation alters vRNP structure to support other N protein functions in viral transcription.
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Affiliation(s)
| | - Armin N Adly
- Department of Physiology, University of California, San Francisco, California, USA
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Conor J Howard
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Adam Frost
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, California, USA.
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Banerjee S, Baidya SK, Adhikari N, Ghosh B, Jha T. Glycyrrhizin as a promising kryptonite against SARS-CoV-2: Clinical, experimental, and theoretical evidences. J Mol Struct 2022; 1275:134642. [DOI: 10.1016/j.molstruc.2022.134642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/24/2022] [Accepted: 11/24/2022] [Indexed: 11/27/2022]
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Plant Molecular Pharming and Plant-Derived Compounds towards Generation of Vaccines and Therapeutics against Coronaviruses. Vaccines (Basel) 2022; 10:vaccines10111805. [DOI: 10.3390/vaccines10111805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
The current century has witnessed infections of pandemic proportions caused by Coronaviruses (CoV) including severe acute respiratory syndrome-related CoV (SARS-CoV), Middle East respiratory syndrome-related CoV (MERS-CoV) and the recently identified SARS-CoV2. Significantly, the SARS-CoV2 outbreak, declared a pandemic in early 2020, has wreaked devastation and imposed intense pressure on medical establishments world-wide in a short time period by spreading at a rapid pace, resulting in high morbidity and mortality. Therefore, there is a compelling need to combat and contain the CoV infections. The current review addresses the unique features of the molecular virology of major Coronaviruses that may be tractable towards antiviral targeting and design of novel preventative and therapeutic intervention strategies. Plant-derived vaccines, in particular oral vaccines, afford safer, effectual and low-cost avenues to develop antivirals and fast response vaccines, requiring minimal infrastructure and trained personnel for vaccine administration in developing countries. This review article discusses recent developments in the generation of plant-based vaccines, therapeutic/drug molecules, monoclonal antibodies and phytochemicals to preclude and combat infections caused by SARS-CoV, MERS-CoV and SARS-CoV-2 viruses. Efficacious plant-derived antivirals could contribute significantly to combating emerging and re-emerging pathogenic CoV infections and help stem the tide of any future pandemics.
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Dhorne-Pollet S, Fitzpatrick C, Da Costa B, Bourgon C, Eléouët JF, Meunier N, Burzio VA, Delmas B, Barrey E. Antisense oligonucleotides targeting ORF1b block replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Front Microbiol 2022; 13:915202. [PMID: 36386681 PMCID: PMC9644129 DOI: 10.3389/fmicb.2022.915202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/29/2022] [Indexed: 10/15/2023] Open
Abstract
The ongoing COVID-19 pandemic continues to pose a need for new and efficient therapeutic strategies. We explored antisense therapy using oligonucleotides targeting the severe acute respiratory syndrome coronavirus (SARS-CoV-2) genome. We predicted in silico four antisense oligonucleotides (ASO gapmers with 100% PTO linkages and LNA modifications at their 5' and 3'ends) targeting viral regions ORF1a, ORF1b, N and the 5'UTR of the SARS-CoV-2 genome. Efficiency of ASOs was tested by transfection in human ACE2-expressing HEK-293T cells and monkey VeroE6/TMPRSS2 cells infected with SARS-CoV-2. The ORF1b-targeting ASO was the most efficient, with a 71% reduction in the number of viral genome copies. N- and 5'UTR-targeting ASOs also significantly reduced viral replication by 55 and 63%, respectively, compared to non-related control ASO (ASO-C). Viral titration revealed a significant decrease in SARS-CoV-2 multiplication both in culture media and in cells. These results show that anti-ORF1b ASO can specifically reduce SARS-CoV-2 genome replication in vitro in two different cell infection models. The present study presents proof-of concept of antisense oligonucleotide technology as a promising therapeutic strategy for COVID-19.
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Affiliation(s)
| | - Christopher Fitzpatrick
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
- Universidad Andrés Bello, Santiago, Chile
| | - Bruno Da Costa
- INRAE, UMR VIM, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clara Bourgon
- INRAE, UMR VIM, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Nicolas Meunier
- INRAE, UMR VIM, Université Paris-Saclay, Jouy-en-Josas, France
| | - Verónica A. Burzio
- Universidad Andrés Bello, Santiago, Chile
- Centro Científico y Tecnológico de Excelencia Ciencia, Vida/Andes Biotechnologies SpA, Santiago, Chile
| | - Bernard Delmas
- INRAE, UMR VIM, Université Paris-Saclay, Jouy-en-Josas, France
| | - Eric Barrey
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
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122
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Dolan KA, Dutta M, Kern DM, Kotecha A, Voth GA, Brohawn SG. Structure of SARS-CoV-2 M protein in lipid nanodiscs. eLife 2022; 11:e81702. [PMID: 36264056 PMCID: PMC9642992 DOI: 10.7554/elife.81702] [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: 07/08/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 encodes four structural proteins incorporated into virions, spike (S), envelope (E), nucleocapsid (N), and membrane (M). M plays an essential role in viral assembly by organizing other structural proteins through physical interactions and directing them to sites of viral budding. As the most abundant protein in the viral envelope and a target of patient antibodies, M is a compelling target for vaccines and therapeutics. Still, the structure of M and molecular basis for its role in virion formation are unknown. Here, we present the cryo-EM structure of SARS-CoV-2 M in lipid nanodiscs to 3.5 Å resolution. M forms a 50 kDa homodimer that is structurally related to the SARS-CoV-2 ORF3a viroporin, suggesting a shared ancestral origin. Structural comparisons reveal how intersubunit gaps create a small, enclosed pocket in M and large open cavity in ORF3a, consistent with a structural role and ion channel activity, respectively. M displays a strikingly electropositive cytosolic surface that may be important for interactions with N, S, and viral RNA. Molecular dynamics simulations show a high degree of structural rigidity in a simple lipid bilayer and support a role for M homodimers in scaffolding viral assembly. Together, these results provide insight into roles for M in coronavirus assembly and structure.
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Affiliation(s)
- Kimberly A Dolan
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, and California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Mandira Dutta
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of ChicagoChicagoUnited States
| | - David M Kern
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, and California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Abhay Kotecha
- Materials and Structural Analysis Division, Thermo Fisher ScientificEindhovenNetherlands
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of ChicagoChicagoUnited States
| | - Stephen G Brohawn
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, and California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
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Ma S, Damfo S, Lou J, Pinotsis N, Bowler MW, Haider S, Kozielski F. Two Ligand-Binding Sites on SARS-CoV-2 Non-Structural Protein 1 Revealed by Fragment-Based X-ray Screening. Int J Mol Sci 2022; 23:ijms232012448. [PMID: 36293303 PMCID: PMC9604401 DOI: 10.3390/ijms232012448] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
The regular reappearance of coronavirus (CoV) outbreaks over the past 20 years has caused significant health consequences and financial burdens worldwide. The most recent and still ongoing novel CoV pandemic, caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) has brought a range of devastating consequences. Due to the exceptionally fast development of vaccines, the mortality rate of the virus has been curbed to a significant extent. However, the limitations of vaccination efficiency and applicability, coupled with the still high infection rate, emphasise the urgent need for discovering safe and effective antivirals against SARS-CoV-2 by suppressing its replication or attenuating its virulence. Non-structural protein 1 (nsp1), a unique viral and conserved leader protein, is a crucial virulence factor for causing host mRNA degradation, suppressing interferon (IFN) expression and host antiviral signalling pathways. In view of the essential role of nsp1 in the CoV life cycle, it is regarded as an exploitable target for antiviral drug discovery. Here, we report a variety of fragment hits against the N-terminal domain of SARS-CoV-2 nsp1 identified by fragment-based screening via X-ray crystallography. We also determined the structure of nsp1 at atomic resolution (0.99 Å). Binding affinities of hits against nsp1 and potential stabilisation were determined by orthogonal biophysical assays such as microscale thermophoresis and thermal shift assays. We identified two ligand-binding sites on nsp1, one deep and one shallow pocket, which are not conserved between the three medically relevant SARS, SARS-CoV-2 and MERS coronaviruses. Our study provides an excellent starting point for the development of more potent nsp1-targeting inhibitors and functional studies on SARS-CoV-2 nsp1.
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Affiliation(s)
- Shumeng Ma
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Shymaa Damfo
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Jiaqi Lou
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | | | - Shozeb Haider
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
- UCL Centre for Advanced Research Computing, University College London, London WC1H 9RN, UK
| | - Frank Kozielski
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
- Correspondence:
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Fanelli M, Petrone V, Buonifacio M, Delibato E, Balestrieri E, Grelli S, Minutolo A, Matteucci C. Multidistrict Host-Pathogen Interaction during COVID-19 and the Development Post-Infection Chronic Inflammation. Pathogens 2022; 11:1198. [PMID: 36297256 PMCID: PMC9607297 DOI: 10.3390/pathogens11101198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 12/15/2022] Open
Abstract
Due to the presence of the ACE2 receptor in different tissues (nasopharynx, lung, nervous tissue, intestine, liver), the COVID-19 disease involves several organs in our bodies. SARS-CoV-2 is able to infect different cell types, spreading to different districts. In the host, an uncontrolled and altered immunological response is triggered, leading to cytokine storm, lymphopenia, and cellular exhaustion. Hence, respiratory distress syndrome (ARDS) and systemic multi-organ dysfunction syndrome (MODS) are established. This scenario is also reflected in the composition of the microbiota, the balance of which is regulated by the interaction with the immune system. A change in microbial diversity has been demonstrated in COVID-19 patients compared with healthy donors, with an increase in potentially pathogenic microbial genera. In addition to other symptoms, particularly neurological, the occurrence of dysbiosis persists after the SARS-CoV-2 infection, characterizing the post-acute COVID syndrome. This review will describe and contextualize the role of the immune system in unbalance and dysbiosis during SARS-CoV-2 infection, from the acute phase to the post-COVID-19 phase. Considering the tight relationship between the immune system and the gut-brain axis, the analysis of new, multidistrict parameters should be aimed at understanding and addressing chronic multisystem dysfunction related to COVID-19.
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Affiliation(s)
- Marialaura Fanelli
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Vita Petrone
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Margherita Buonifacio
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Elisabetta Delibato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Emanuela Balestrieri
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Sandro Grelli
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
- Virology Unit, Tor Vergata University Hospital, 00133 Rome, Italy
| | - Antonella Minutolo
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Claudia Matteucci
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
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125
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Buhr TL, Borgers-Klonkowski E, Gutting BW, Hammer EE, Hamilton SM, Huhman BM, Jackson SL, Kennihan NL, Lilly SD, Little JD, Luck BB, Matuczinski EA, Miller CT, Sides RE, Yates VL, Young AA. Ultraviolet dosage and decontamination efficacy were widely variable across 14 UV devices after testing a dried enveloped ribonucleic acid virus surrogate for SARS-CoV-2. Front Bioeng Biotechnol 2022; 10:875817. [PMID: 36267449 PMCID: PMC9578676 DOI: 10.3389/fbioe.2022.875817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Aims: The dosages and efficacy of 14 ultraviolet (UV) decontamination technologies were measured against a SARS-CoV-2 surrogate virus that was dried onto different materials for laboratory and field testing. Methods and results: A live enveloped, ribonucleic acid (RNA) virus surrogate for SARS-CoV-2 was dried on stainless steel 304 (SS304), Navy Top Coat-painted SS304 (NTC), cardboard, polyurethane, polymethyl methacrylate (PMMA), and acrylonitrile butadiene styrene (ABS) materials at > 8.0 log10 plaque-forming units (PFU) per test coupon. The coupons were then exposed to UV radiation during both laboratory and field testing. Commercial and prototype UV-emitting devices were measured for efficacy: four handheld devices, three room/surface-disinfecting machines, five air disinfection devices, and two larger custom-made machines. UV device dosages ranged from 0.01 to 729 mJ cm−2. The antiviral efficacy among the different UV devices ranged from no decontamination up to nearly achieving sterilization. Importantly, cardboard required far greater dosage than SS304. Conclusion: Enormous variability in dosage and efficacy was measured among the different UV devices. Porous materials limit the utility of UV decontamination. Significance and impact of the study: UV devices have wide variability in dosages, efficacy, hazards, and UV output over time, indicating that each UV device needs independent technical measurement and assessment for product development prior to and during use.
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Affiliation(s)
- Tony L. Buhr
- Naval Surface Warfare Center-Dahlgren Division, Concepts and Experimentation Branch (B64), Dahlgren, VA, United States
- *Correspondence: Tony L. Buhr,
| | - Erica Borgers-Klonkowski
- Naval Surface Warfare Center-Dahlgren Division, Concepts and Experimentation Branch (B64), Dahlgren, VA, United States
| | - Bradford W. Gutting
- Naval Surface Warfare Center-Dahlgren Division, Concepts and Experimentation Branch (B64), Dahlgren, VA, United States
| | - Emlyn E. Hammer
- Naval Surface Warfare Center-Dahlgren Division, Concepts and Experimentation Branch (B64), Dahlgren, VA, United States
| | - Shelia M. Hamilton
- Naval Surface Warfare Center-Dahlgren Division, Concepts and Experimentation Branch (B64), Dahlgren, VA, United States
| | - Brett M. Huhman
- Naval Research Laboratory (Plasma Physics Division), Washington, DC, United States
| | - Stuart L. Jackson
- Naval Research Laboratory (Plasma Physics Division), Washington, DC, United States
| | - Neil L. Kennihan
- Naval Surface Warfare Center-Dahlgren Division, Concepts and Experimentation Branch (B64), Dahlgren, VA, United States
| | - Samuel D. Lilly
- Naval Surface Warfare Center-Dahlgren Division, Concepts and Experimentation Branch (B64), Dahlgren, VA, United States
| | - John D. Little
- Naval Research Laboratory (Plasma Physics Division), Washington, DC, United States
| | - Brooke B. Luck
- Naval Surface Warfare Center-Dahlgren Division, Concepts and Experimentation Branch (B64), Dahlgren, VA, United States
| | - Emily A. Matuczinski
- Naval Surface Warfare Center-Dahlgren Division, Concepts and Experimentation Branch (B64), Dahlgren, VA, United States
| | - Charles T. Miller
- Naval Surface Warfare Center-Dahlgren Division, Concepts and Experimentation Branch (B64), Dahlgren, VA, United States
| | - Rachel E. Sides
- Naval Surface Warfare Center-Dahlgren Division, Concepts and Experimentation Branch (B64), Dahlgren, VA, United States
| | - Vanessa L. Yates
- Naval Surface Warfare Center-Dahlgren Division, Concepts and Experimentation Branch (B64), Dahlgren, VA, United States
| | - Alice A. Young
- Naval Surface Warfare Center-Dahlgren Division, Concepts and Experimentation Branch (B64), Dahlgren, VA, United States
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Muacevic A, Adler JR. Emerging and Re-Emerging Viral Infections: An Indian Perspective. Cureus 2022; 14:e30062. [PMID: 36381846 PMCID: PMC9637451 DOI: 10.7759/cureus.30062] [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: 09/17/2022] [Accepted: 10/08/2022] [Indexed: 01/25/2023] Open
Abstract
Emerging and re-emerging viral infections pose a constant threat, especially in healthcare settings. Viral infections can be thought of as an ecological system, like a forest or a pond, with different species competing for resources. Pandemics tend to occur when there is a disruption to this ecosystem, such as introducing a strain of virus into humans or animals that they have no immunity against. Around 60% of human infectious diseases and 75% of emerging infections are zoonotic, with two-thirds originating in wildlife. There is an ongoing risk of viral diseases as the human population continues to grow and the rate of urbanization increases. The emergence and re-emergence of viral diseases are influenced by a variety of virologic and environmental factors. These factors can be roughly categorized as affecting humans, the environment and/or ecology, and viruses. The spread of zoonotic diseases among humans can be prevented by reducing the transmission risk associated with wildlife and exotic pets through education, legislation, and behavioral change programs that target individuals at risk for exposure.
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127
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Kulesza J, Kulesza E, Koziński P, Karpik W, Broncel M, Fol M. BCG and SARS-CoV-2-What Have We Learned? Vaccines (Basel) 2022; 10:vaccines10101641. [PMID: 36298506 PMCID: PMC9610589 DOI: 10.3390/vaccines10101641] [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: 07/11/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/19/2022] Open
Abstract
Despite controversy over the protective effect of the BCG (Bacille Calmette-Guérin) vaccine in preventing pulmonary tuberculosis (TB) in adults, it has been used worldwide since 1921. Although the first reports in the 1930s had noted a remarkable decrease in child mortality after BCG immunization, this could not be explained solely by a decrease in mortality from TB. These observations gave rise to the suggestion of nonspecific beneficial effects of BCG vaccination, beyond the desired protection against M. tuberculosis. The existence of an innate immunity-training mechanism based on epigenetic changes was demonstrated several years ago. The emergence of the pandemic caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in 2019 revived the debate about whether the BCG vaccine can affect the immune response against the virus or other unrelated pathogens. Due to the mortality of the coronavirus disease (COVID-19), it is important to verify each factor that may have a potential protective value against the severe course of COVID-19, complications, and death. This paper reviews the results of numerous retrospective studies and prospective trials which shed light on the potential of a century-old vaccine to mitigate the pandemic impact of the new virus. It should be noted, however, that although there are numerous studies intending to verify the hypothesis that the BCG vaccine may have a beneficial effect on COVID-19, there is no definitive evidence on the efficacy of the BCG vaccine against SARS-CoV-2.
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Affiliation(s)
- Jakub Kulesza
- Department of Internal Diseases and Clinical Pharmacology, Medical University of Lodz, Kniaziewicza 1/5, 91-347 Lodz, Poland
| | - Ewelina Kulesza
- Department of Rheumatology and Internal Diseases, Medical University of Lodz, Żeromskiego 113, 90-549 Lodz, Poland
| | - Piotr Koziński
- Tuberculosis and Lung Diseases Outpatient Clinic, Health Facility Unit in Łęczyca, Zachodnia 6, 99-100 Łęczyca, Poland
| | - Wojciech Karpik
- Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Marlena Broncel
- Department of Internal Diseases and Clinical Pharmacology, Medical University of Lodz, Kniaziewicza 1/5, 91-347 Lodz, Poland
| | - Marek Fol
- Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
- Correspondence: ; Tel.: +48-42-635-44-72
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128
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Khodaei A, Shams P, Sharifi H, Mozaffari-Tazehkand B. Identification and classification of coronavirus genomic signals based on linear predictive coding and machine learning methods. Biomed Signal Process Control 2022; 80:104192. [PMID: 36168586 PMCID: PMC9500098 DOI: 10.1016/j.bspc.2022.104192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/12/2022] [Accepted: 09/10/2022] [Indexed: 11/30/2022]
Abstract
Corona disease has become one of the problems and challenges of humankind over the past two years. One of the problems that existed from the first days of this epidemic was clinical symptoms similar to other infectious viruses such as colds and influenza. Therefore, diagnosis of this disease and its coping and treatment approaches is also been difficult. In this study, Attempts has been made to investigate the origin of this disease and the genetic structure of the virus leading to it. For this purpose, signal processing and linear predictive coding approaches were used which are widely used in data compression. A pattern recognition model was presented for the detection and separation of covid samples from the influenza virus case studies. This model, which was based on support vector machine classifier, was tested successfully on several datasets collected from different countries. The obtained results performed on all datasets by more than 98% accuracy. The proposed model, in addition to its good performance accuracy, can be a step forward in quantifying and digitizing medical big data information.
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Affiliation(s)
- Amin Khodaei
- Faculty of Electrical & Computer Engineering of University of Tabriz, 29 Bahman Blvd, Tabriz, Iran
| | - Parvaneh Shams
- Computer Engineering Department, Istanbul Aydin University, Turkey
| | - Hadi Sharifi
- Faculty of Electrical & Computer Engineering of University of Tabriz, 29 Bahman Blvd, Tabriz, Iran
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129
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Jaron M, Lehky M, Zarà M, Zaydowicz CN, Lak A, Ballmann R, Heine PA, Wenzel EV, Schneider KT, Bertoglio F, Kempter S, Köster RW, Barbieri SS, van den Heuvel J, Hust M, Dübel S, Schubert M. Baculovirus-Free SARS-CoV-2 Virus-like Particle Production in Insect Cells for Rapid Neutralization Assessment. Viruses 2022. [PMID: 36298643 DOI: 10.3390/v14102087/s1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Virus-like particles (VLPs) resemble authentic virus while not containing any genomic information. Here, we present a fast and powerful method for the production of SARS-CoV-2 VLP in insect cells and the application of these VLPs to evaluate the inhibition capacity of monoclonal antibodies and sera of vaccinated donors. Our method avoids the baculovirus-based approaches commonly used in insect cells by employing direct plasmid transfection to co-express SARS-CoV-2 envelope, membrane, and spike protein that self-assemble into VLPs. After optimization of the expression plasmids and vector ratios, VLPs with an ~145 nm diameter and the typical "Corona" aura were obtained, as confirmed by nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM). Fusion of the membrane protein to GFP allowed direct quantification of binding inhibition to angiotensin II-converting enzyme 2 (ACE2) on cells by therapeutic antibody candidates or sera from vaccinated individuals. Neither VLP purification nor fluorescent labeling by secondary antibodies are required to perform these flow cytometric assays.
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Affiliation(s)
- Marcel Jaron
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Michael Lehky
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Marta Zarà
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Chris Nicole Zaydowicz
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Aidin Lak
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering, Technische Universität Braunschweig, Hans-Sommer-Straße 66, 38106 Braunschweig, Germany
| | - Rico Ballmann
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Philip Alexander Heine
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | | | - Kai-Thomas Schneider
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Federico Bertoglio
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Susanne Kempter
- Department of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Reinhard Wolfgang Köster
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Silvia Stella Barbieri
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Joop van den Heuvel
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Stefan Dübel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Maren Schubert
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
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130
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Jaron M, Lehky M, Zarà M, Zaydowicz CN, Lak A, Ballmann R, Heine PA, Wenzel EV, Schneider KT, Bertoglio F, Kempter S, Köster RW, Barbieri SS, van den Heuvel J, Hust M, Dübel S, Schubert M. Baculovirus-Free SARS-CoV-2 Virus-like Particle Production in Insect Cells for Rapid Neutralization Assessment. Viruses 2022; 14:v14102087. [PMID: 36298643 PMCID: PMC9606917 DOI: 10.3390/v14102087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/16/2022] Open
Abstract
Virus-like particles (VLPs) resemble authentic virus while not containing any genomic information. Here, we present a fast and powerful method for the production of SARS-CoV-2 VLP in insect cells and the application of these VLPs to evaluate the inhibition capacity of monoclonal antibodies and sera of vaccinated donors. Our method avoids the baculovirus-based approaches commonly used in insect cells by employing direct plasmid transfection to co-express SARS-CoV-2 envelope, membrane, and spike protein that self-assemble into VLPs. After optimization of the expression plasmids and vector ratios, VLPs with an ~145 nm diameter and the typical “Corona” aura were obtained, as confirmed by nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM). Fusion of the membrane protein to GFP allowed direct quantification of binding inhibition to angiotensin II-converting enzyme 2 (ACE2) on cells by therapeutic antibody candidates or sera from vaccinated individuals. Neither VLP purification nor fluorescent labeling by secondary antibodies are required to perform these flow cytometric assays.
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Affiliation(s)
- Marcel Jaron
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Michael Lehky
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Marta Zarà
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Chris Nicole Zaydowicz
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Aidin Lak
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering, Technische Universität Braunschweig, Hans-Sommer-Straße 66, 38106 Braunschweig, Germany
| | - Rico Ballmann
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Philip Alexander Heine
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | | | - Kai-Thomas Schneider
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Federico Bertoglio
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Susanne Kempter
- Department of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Reinhard Wolfgang Köster
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Silvia Stella Barbieri
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Joop van den Heuvel
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Stefan Dübel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Maren Schubert
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
- Correspondence:
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131
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Luo Q, Zhang C, Chen Y, Chen H, Yang Y. Alpiniae oxyphyllae fructus polysaccharide 3 inhibits porcine epidemic diarrhea virus entry into IPEC-J2 cells. Res Vet Sci 2022; 152:434-441. [PMID: 36126510 DOI: 10.1016/j.rvsc.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/30/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) is deadly for suckling piglets and is a significant threat to most pig farms. Alpiniae oxyphyllae fructus polysaccharide 3 (AOFP3) shows antiviral activity against PEDV. However, the anti-PEDV mechanism of AOFP3 is unknown. Entering the host cell is important for viral infection, and many drugs play antiviral roles by inhibiting this process. To understand the antiviral mechanism of AOFP3 against PEDV, the effect of AOFP3 on PEDV entering IPEC-J2 cells was investigated in the present study. Real-time PCR and immunofluorescence were used to study the effect of AOFP3 on PEDV binding and penetrating IPEC-J2 cells. The effect of PEDV on AOFP3 attachment to IPEC-J2 cells was also investigated. Afterward, the effect of AOFP3 on PEDV spike (S) protein binding to porcine aminopeptidase was tested by using coimmunoprecipitation, and the effect of AOFP3 on the cholesterol level of IPEC-J2 cells was detected. The results showed that AOFP3 competitively inhibited PEDV adsorption on IPEC-J2 cells by blocking PEDV S protein binding to porcine aminopeptidase in IPEC-J2 cells. Furthermore, AOFP3 decreased PEDV penetration into host cells by decreasing the cholesterol level in IPEC-J2 cells.
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Affiliation(s)
- Qiyuan Luo
- Institute of Traditional South Chinese Veterinary Pharmacology, College of Animal Science and Technology, Hainan University, Haikou 570228, PR China
| | - Chenglong Zhang
- Institute of Traditional South Chinese Veterinary Pharmacology, College of Animal Science and Technology, Hainan University, Haikou 570228, PR China
| | - Yun Chen
- Institute of Traditional South Chinese Veterinary Pharmacology, College of Animal Science and Technology, Hainan University, Haikou 570228, PR China.
| | - Huricha Chen
- Institute of Traditional South Chinese Veterinary Pharmacology, College of Animal Science and Technology, Hainan University, Haikou 570228, PR China
| | - Yuhui Yang
- Institute of Traditional South Chinese Veterinary Pharmacology, College of Animal Science and Technology, Hainan University, Haikou 570228, PR China
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132
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Zheng Q, Wang D, Lin R, Lv Q, Wang W. IFI44 is an immune evasion biomarker for SARS-CoV-2 and Staphylococcus aureus infection in patients with RA. Front Immunol 2022; 13:1013322. [PMID: 36189314 PMCID: PMC9520788 DOI: 10.3389/fimmu.2022.1013322] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 08/29/2022] [Indexed: 12/04/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global pandemic of severe coronavirus disease 2019 (COVID-19). Staphylococcus aureus is one of the most common pathogenic bacteria in humans, rheumatoid arthritis (RA) is among the most prevalent autoimmune conditions. RA is a significant risk factor for SARS-CoV-2 and S. aureus infections, although the mechanism of RA and SARS-CoV-2 infection in conjunction with S. aureus infection has not been elucidated. The purpose of this study is to investigate the biomarkers and disease targets between RA and SARS-CoV-2 and S. aureus infections using bioinformatics analysis, to search for the molecular mechanisms of SARS-CoV-2 and S. aureus immune escape and potential drug targets in the RA population, and to provide new directions for further analysis and targeted development of clinical treatments. Methods The RA dataset (GSE93272) and the S. aureus bacteremia (SAB) dataset (GSE33341) were used to obtain differentially expressed gene sets, respectively, and the common differentially expressed genes (DEGs) were determined through the intersection. Functional enrichment analysis utilizing GO, KEGG, and ClueGO methods. The PPI network was created utilizing the STRING database, and the top 10 hub genes were identified and further examined for functional enrichment using Metascape and GeneMANIA. The top 10 hub genes were intersected with the SARS-CoV-2 gene pool to identify five hub genes shared by RA, COVID-19, and SAB, and functional enrichment analysis was conducted using Metascape and GeneMANIA. Using the NetworkAnalyst platform, TF-hub gene and miRNA-hub gene networks were built for these five hub genes. The hub gene was verified utilizing GSE17755, GSE55235, and GSE13670, and its effectiveness was assessed utilizing ROC curves. CIBERSORT was applied to examine immune cell infiltration and the link between the hub gene and immune cells. Results A total of 199 DEGs were extracted from the GSE93272 and GSE33341 datasets. KEGG analysis of enrichment pathways were NLR signaling pathway, cell membrane DNA sensing pathway, oxidative phosphorylation, and viral infection. Positive/negative regulation of the immune system, regulation of the interferon-I (IFN-I; IFN-α/β) pathway, and associated pathways of the immunological response to viruses were enriched in GO and ClueGO analyses. PPI network and Cytoscape platform identified the top 10 hub genes: RSAD2, IFIT3, GBP1, RTP4, IFI44, OAS1, IFI44L, ISG15, HERC5, and IFIT5. The pathways are mainly enriched in response to viral and bacterial infection, IFN signaling, and 1,25-dihydroxy vitamin D3. IFI44, OAS1, IFI44L, ISG15, and HERC5 are the five hub genes shared by RA, COVID-19, and SAB. The pathways are primarily enriched for response to viral and bacterial infections. The TF-hub gene network and miRNA-hub gene network identified YY1 as a key TF and hsa-mir-1-3p and hsa-mir-146a-5p as two important miRNAs related to IFI44. IFI44 was identified as a hub gene by validating GSE17755, GSE55235, and GSE13670. Immune cell infiltration analysis showed a strong positive correlation between activated dendritic cells and IFI44 expression. Conclusions IFI144 was discovered as a shared biomarker and disease target for RA, COVID-19, and SAB by this study. IFI44 negatively regulates the IFN signaling pathway to promote viral replication and bacterial proliferation and is an important molecular target for SARS-CoV-2 and S. aureus immune escape in RA. Dendritic cells play an important role in this process. 1,25-Dihydroxy vitamin D3 may be an important therapeutic agent in treating RA with SARS-CoV-2 and S. aureus infections.
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Affiliation(s)
- Qingcong Zheng
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Du Wang
- Arthritis Clinical and Research Center, Peking University People’s Hospital, Beijing, China
| | - Rongjie Lin
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Qi Lv
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Wanming Wang
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
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In Silico Evaluation of Hexamethylene Amiloride Derivatives as Potential Luminal Inhibitors of SARS-CoV-2 E Protein. Int J Mol Sci 2022; 23:ijms231810647. [PMID: 36142556 PMCID: PMC9503309 DOI: 10.3390/ijms231810647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
The coronavirus E proteins are small membrane proteins found in the virus envelope of alpha and beta coronaviruses that have a high degree of overlap in their biochemical and functional properties despite minor sequence variations. The SARS-CoV-2 E is a 75-amino acid transmembrane protein capable of acting as an ion channel when assembled in a pentameric fashion. Various studies have found that hexamethylene amiloride (HMA) can inhibit the ion channel activity of the E protein in bilayers and also inhibit viral replication in cultured cells. Here, we use the available structural data in conjunction with homology modelling to build a comprehensive model of the E protein to assess potential binding sites and molecular interactions of HMA derivatives. Furthermore, we employed an iterative cycle of molecular modelling, extensive docking simulations, molecular dynamics and leveraging steered molecular dynamics to better understand the pore characteristics and quantify the affinity of the bound ligands. Results from this work highlight the potential of acylguanidines as blockers of the E protein and guide the development of subsequent small molecule inhibitors.
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134
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Nelli RK, Roth JA, Gimenez-Lirola LG. Distribution of Coronavirus Receptors in the Swine Respiratory and Intestinal Tract. Vet Sci 2022; 9:vetsci9090500. [PMID: 36136717 PMCID: PMC9504008 DOI: 10.3390/vetsci9090500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/06/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Coronaviruses use a broad range of host receptors for binding and cell entry, essential steps in establishing viral infections. This pilot study evaluated the overall distribution of angiotensin-converting enzyme 2 (ACE2), aminopeptidase N (APN), carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), and dipeptidyl peptidase 4 (DPP4) receptors in the pig respiratory and intestinal tract. All the receptors evaluated in this study were expressed and differentially distributed through the respiratory and intestinal tract. The presence and expression levels of these receptors could determine susceptibility to coronavirus infections. This study may have important implications for the development of research models and the assessment of the potential risk and introduction of novel coronaviruses into the swine population.
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135
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Sharma N, Kulkarni GT, Bhatt AN, Satija S, Singh L, Sharma A, Dua K, Karwasra R, Khan AA, Ahmad N, Raza K. Therapeutic Options for the SARS-CoV-2 Virus: Is There a Key in Herbal Medicine? Nat Prod Commun 2022. [DOI: 10.1177/1934578x221126303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
SARS-CoV-2 has been responsible for over 500 million cumulative cases all over the world since December 2019 and has marked the third introduction of a highly pathogenic virus after SARS-CoV and MERS-CoV. This virus is in a winning situation because scientists are still racing to explore effective therapeutics, vaccines, and event treatment regimens. In view of progress in current disease management, until now none of the preventive/treatment measures can be considered entirely effective to treat SARS-CoV-2 infection. Therefore, it is required to look up substitute ways for the management of this disease. In this context, herbal medicines could be a good choice. This article emphasizes the antiviral potential of some herbal constituents which further can be a drug of choice in SARS-CoV-2 treatment. This article may be a ready reference for discovering natural lead compounds and targets in SARS-CoV-2 associated works.
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Affiliation(s)
- Nitin Sharma
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
| | | | - Anant Narayan Bhatt
- Department of Nuclear Medicine, Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Delhi, India
| | - Saurabh Satija
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, Australia
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Lubhan Singh
- Department of Pharmacology, KharvelSubharti College of Pharmacy, Swami Vivekanand Subharti University, Meerut, India
| | - Anjana Sharma
- Department of Pharmaceutical Technology, Meerut Institute of Engineering and Technology, Meerut, UP, India
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, Australia
| | - Ritu Karwasra
- Central Council for Research in Unani Medicine (CCRUM), Ministry of AYUSH, Govt of India, New Delhi, India
| | - Asim Ali Khan
- Central Council for Research in Unani Medicine (CCRUM), Ministry of AYUSH, Govt of India, New Delhi, India
| | - Nadeem Ahmad
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
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136
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Beeraka NM, Sukocheva OA, Lukina E, Liu J, Fan R. Development of antibody resistance in emerging mutant strains of SARS CoV-2: Impediment for COVID-19 vaccines. Rev Med Virol 2022; 32:e2346. [PMID: 35416390 PMCID: PMC9111059 DOI: 10.1002/rmv.2346] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/28/2022] [Accepted: 03/06/2022] [Indexed: 02/05/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a highly infectious agent associated with unprecedented morbidity and mortality. A failure to stop growth of COVID-19-linked morbidity rates is caused by SARS-CoV-2 mutations and the emergence of new highly virulent SARS-CoV-2 strains. Several acquired SARS-CoV-2 mutations reflect viral adaptations to host immune defence. Mutations in the virus Spike-protein were associated with the lowered effectiveness of current preventive therapies, including vaccines. Recent in vitro studies detected diminished neutralisation capacity of vaccine-induced antibodies, which are targeted to bind Spike receptor-binding and N-terminal domains in the emerging strains. Lower than expected inhibitory activity of antibodies was reported against viruses with E484K Spike mutation, including B.1.1.7 (UK), P.1 (Brazil), B.1.351 (South African), and new Omicron variant (B.1.1.529) with E484A mutation. The vaccine effectiveness is yet to be examined against new mutant strains of SARS-CoV-2 originating in Europe, Nigeria, Brazil, South Africa, and India. To prevent the loss of anti-viral protection in vivo, often defined as antibody resistance, it is required to target highly conserved viral sequences (including Spike protein) and enhance the potency of antibody cocktails. In this review, we assess the reported mutation-acquiring potential of coronaviruses and compare efficacies of current COVID-19 vaccines against 'parent' and 'mutant' strains of SARS-CoV-2 (Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529)).
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Affiliation(s)
- Narasimha M. Beeraka
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
- Department of Human AnatomyI.M. Sechenov First Moscow State Medical University (Sechenov University)MoscowRussian Federation
| | - Olga A. Sukocheva
- Discipline of Health SciencesCollege of Nursing and Health SciencesFlinders University of South AustraliaBedford ParkAustralia
| | - Elena Lukina
- Discipline of BiologyCollege of SciencesFlinders University of South AustraliaBedford ParkAustralia
| | - Junqi Liu
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
| | - Ruitai Fan
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
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Samrat SK, Xu J, Xie X, Gianti E, Chen H, Zou J, Pattis JG, Elokely K, Lee H, Li Z, Klein ML, Shi PY, Zhou J, Li H. Allosteric inhibitors of the main protease of SARS-CoV-2. Antiviral Res 2022; 205:105381. [PMID: 35835291 PMCID: PMC9272661 DOI: 10.1016/j.antiviral.2022.105381] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 12/19/2022]
Abstract
SARS-CoV-2 has raised the alarm to search for effective therapy for this virus. To date several vaccines have been approved but few available drugs reported recently still need approval from FDA. Remdesivir was approved for emergency use only. In this report, the SARS-CoV-2 3CLpro was expressed and purified. By using a FRET-based enzymatic assay, we have screened a library consisting of more than 300 different niclosamide derivatives and identified three molecules JMX0286, JMX0301, and JMX0941 as potent allosteric inhibitors against SARS-CoV-2 3CLpro, with IC50 values similar to that of known covalent inhibitor boceprevir. In a cell-based antiviral assay, these inhibitors can inhibit the virus growth with EC50 in the range of 2-3 μM. The mechanism of action of JMX0286, JMX0301, and JMX0941 were characterized by enzyme kinetics, affinity binding and protein-based substrate digestion. Molecular docking, molecular dynamics (MD) simulations and hydration studies suggested that JMX0286, JMX0301, JMX0941 bind specifically to an allosteric pocket of the SARS-CoV-2 3CL protease. This study provides three potent compounds for further studies.
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Affiliation(s)
- Subodh Kumar Samrat
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ, 85721-0207, USA.
| | - Jimin Xu
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Eleonora Gianti
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jason G Pattis
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Khaled Elokely
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Hyun Lee
- Department of Pharmaceutical Sciences at College of Pharmacy and Biophysics Core at Research Resources Center, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Zhong Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ, 85721-0207, USA
| | - Michael L Klein
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, 77555, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ, 85721-0207, USA; BIO5 Institute, The University of Arizona, Tucson, Tucson, AZ, 85721, USA.
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Chen S, Guan F, Candotti F, Benlagha K, Camara NOS, Herrada AA, James LK, Lei J, Miller H, Kubo M, Ning Q, Liu C. The role of B cells in COVID-19 infection and vaccination. Front Immunol 2022; 13:988536. [PMID: 36110861 PMCID: PMC9468879 DOI: 10.3389/fimmu.2022.988536] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/26/2022] [Indexed: 12/23/2022] Open
Abstract
B cells secrete antibodies and mediate the humoral immune response, making them extremely important in protective immunity against SARS-CoV-2, which caused the coronavirus disease 2019 (COVID-19) pandemic. In this review, we summarize the positive function and pathological response of B cells in SARS-CoV-2 infection and re-infection. Then, we structure the immunity responses that B cells mediated in peripheral tissues. Furthermore, we discuss the role of B cells during vaccination including the effectiveness of antibodies and memory B cells, viral evolution mechanisms, and future vaccine development. This review might help medical workers and researchers to have a better understanding of the interaction between B cells and SARS-CoV-2 and broaden their vision for future investigations.
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Affiliation(s)
- Shiru Chen
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, China
- Department of Internal Medicine, The Division of Gastroenterology and Hepatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Guan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, China
| | - Fabio Candotti
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Kamel Benlagha
- Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Niels Olsen Saraiva Camara
- Laboratory of Human Immunology, Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Andres A. Herrada
- Lymphatic and Inflammation Research Laboratory, Facultad de Ciencias de la Salud, Instituto de Ciencias Biomedicas, Universidad Autonoma de Chile, Talca, Chile
| | - Louisa K. James
- Centre for Immunobiology, Bizard Institute, Queen Mary University of London, London, United Kingdom
| | - Jiahui Lei
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, China
| | - Heather Miller
- Cytek Biosciences, R&D Clinical Reagents, Fremont, CA, United States
| | - Masato Kubo
- Laboratory for Cytokine Regulation, Center for Integrative Medical Science (IMS), Rikagaku Kenkyusho, Institute of Physical and Chemical Research (RIKEN) Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Qin Ning
- Department of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, China
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139
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Ávila-Gálvez MÁ, Rafael-Pita C, Fernández N, Baixinho J, Anastácio JD, Cankar K, Bosch D, Nunes Dos Santos C. Targeting proteases involved in the viral replication of SARS-CoV-2 by sesquiterpene lactones from chicory ( Cichorium intybus L.). Food Funct 2022; 13:8977-8988. [PMID: 35938740 DOI: 10.1039/d2fo00933a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SARS-CoV-2 is a highly transmissible and pathogenic coronavirus causing a respiratory disease that emerged in 2019, leading to a public health emergency situation which continues to date. The treatment options are still very limited and vaccines available are less effective against new variants. SARS-CoV-2 enzymes, namely main protease (Mpro) and papain-like protease (PLpro), play a pivotal role in the viral life cycle, making them a putative drug target. Here, we described for the first time the potential inhibitory activity of chicory extract against both proteases. Besides, we have identified that the four most abundant sesquiterpene lactones in chicory inhibited these proteases, showing an effective binding in the active sites of Mpro and PLpro. This paper provides new insight for further drug development or food-based strategies for the prevention of SARS-CoV-2 by targeting viral proteases.
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Affiliation(s)
- María Ángeles Ávila-Gálvez
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Carlos Rafael-Pita
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Naiara Fernández
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
| | - João Baixinho
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - José D Anastácio
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Katarina Cankar
- Wageningen University and Research, Wageningen Plant Research, BU Bioscience, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Dirk Bosch
- Wageningen University and Research, Wageningen Plant Research, BU Bioscience, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Cláudia Nunes Dos Santos
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal.
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140
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Gourdelier M, Swain J, Arone C, Mouttou A, Bracquemond D, Merida P, Saffarian S, Lyonnais S, Favard C, Muriaux D. Optimized production and fluorescent labeling of SARS-CoV-2 virus-like particles. Sci Rep 2022; 12:14651. [PMID: 36030323 PMCID: PMC9419636 DOI: 10.1038/s41598-022-18681-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 is an RNA enveloped virus responsible for the COVID-19 pandemic that conducted in 6 million deaths worldwide so far. SARS-CoV-2 particles are mainly composed of the 4 main structural proteins M, N, E and S to form 100 nm diameter viral particles. Based on productive assays, we propose an optimal transfected plasmid ratio mimicking the viral RNA ratio in infected cells. This allows SARS-CoV-2 Virus-Like Particle (VLPs) formation composed of the viral structural proteins M, N, E and mature S. Furthermore, fluorescent or photoconvertible VLPs were generated by adding a fluorescent protein tag on N or M mixing with unlabeled viral proteins and characterized by western blots, atomic force microscopy coupled to fluorescence and immuno-spotting. Thanks to live fluorescence and super-resolution microscopies, we quantified VLPs size and concentration. SARS-CoV-2 VLPs present a diameter of 110 and 140 nm respectively for MNE-VLPs and MNES-VLPs with a concentration of 10e12 VLP/ml. In this condition, we were able to establish the incorporation of the Spike in the fluorescent VLPs. Finally, the Spike functionality was assessed by monitoring fluorescent MNES-VLPs docking and internalization in human pulmonary cells expressing or not the receptor hACE2. Results show a preferential maturation of S on N(GFP) labeled VLPs and an hACE2-dependent VLP internalization and a potential fusion in host cells. This work provides new insights on the use of non-fluorescent and fluorescent VLPs to study and visualize the SARS-CoV-2 viral life cycle in a safe environment (BSL-2 instead of BSL-3). Moreover, optimized SARS-CoV-2 VLP production can be further adapted to vaccine design strategies.
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Affiliation(s)
- Manon Gourdelier
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR9004, Montpellier, France
| | - Jitendriya Swain
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR9004, Montpellier, France
| | - Coline Arone
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR9004, Montpellier, France
| | - Anita Mouttou
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR9004, Montpellier, France
| | - David Bracquemond
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR9004, Montpellier, France
| | - Peggy Merida
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR9004, Montpellier, France
| | - Saveez Saffarian
- Department of Physics and Astronomy, Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
| | | | - Cyril Favard
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR9004, Montpellier, France
| | - Delphine Muriaux
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR9004, Montpellier, France.
- CEMIPAI, Université de Montpellier, CNRS UAR3725, Montpellier, France.
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141
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Tao S, Wang X, Yang X, Liu Y, Fu Z, Zhang L, Wang Z, Ni J, Shuai Z, Pan H. COVID-19 and inflammatory bowel disease crosstalk: From emerging association to clinical proposal. J Med Virol 2022; 94:5640-5652. [PMID: 35971954 PMCID: PMC9538900 DOI: 10.1002/jmv.28067] [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: 06/16/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can cause coronavirus disease 2019 (COVID-19), an acute respiratory inflammation that has emerged worldwide since December 2019, and it quickly became a global epidemic. Inflammatory bowel disease (IBD) is a group of chronic nonspecific intestinal inflammatory diseases whose etiology has not been elucidated. The two have many overlapping symptoms in clinical presentation, such as abdominal pain, diarrhea, pneumonia, etc. Imbalance of the autoimmune system in IBD patients and long-term use of immunosuppressive drugs may increase the risk of infection; and systemic symptoms caused by COVID-19 may also induce or exacerbate intestinal inflammation. It has been found that the SARS-CoV-2 receptor angiotensin converting enzyme 2, which is highly expressed in the lung and intestine, is an inflammatory protective factor, and is downregulated and upregulated in COVID-19 and IBD, respectively, suggesting that there may be a coregulatory pathway. In addition, the immune activation pattern of COVID-19 and the cytokine storm in the inflammatory response have similar roles in IBD, indicating that the two diseases may influence each other. Therefore, this review aimed to address the following research questions: whether SARS-CoV-2 infection leads to the progression of IBD; whether IBD increases the risk of COVID-19 infection and poor prognosis; possible common mechanisms and genetic cross-linking between the two diseases; new treatment and care strategies for IBD patients, and the feasibility and risk of vaccination in the context of the COVID-19 epidemic.
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Affiliation(s)
- Sha‐Sha Tao
- Department of Epidemiology and Biostatistics, School of Public HealthAnhui Medical UniversityHefeiAnhuiChina
| | - Xin‐Yi Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Anhui Medical University, First Clinical Medical CollegeAnhui Medical UniversityHefeiAnhuiChina
| | - Xiao‐Ke Yang
- Department of Rheumatology and ImmunologyThe First Affiliated Hospital of Anhui Medical UniversityHefeiAnhuiChina
| | - Yu‐Chen Liu
- Department of Otolaryngology, Head, and Neck SurgeryThe First Affiliated Hospital of Anhui Medical UniversityHefeiAnhuiChina
| | - Zi‐Yue Fu
- Department of Clinical Medicine, The Second School of Clinical MedicineAnhui Medical UniversityHefeiAnhuiChina
| | - Li‐Zhi Zhang
- Department of Clinical Medicine, The First School of Clinical MedicineAnhui Medical UniversityHefeiAnhuiChina
| | - Zhi‐Xin Wang
- Department of Rheumatology and ImmunologyThe First Affiliated Hospital of Anhui Medical UniversityHefeiAnhuiChina
| | - Jing Ni
- Department of Epidemiology and Biostatistics, School of Public HealthAnhui Medical UniversityHefeiAnhuiChina
| | - Zong‐Wen Shuai
- Department of Rheumatology and ImmunologyThe First Affiliated Hospital of Anhui Medical UniversityHefeiAnhuiChina
| | - Hai‐Feng Pan
- Department of Epidemiology and Biostatistics, School of Public HealthAnhui Medical UniversityHefeiAnhuiChina
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142
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Ning L, Liu M, Gou Y, Yang Y, He B, Huang J. Development and application of ribonucleic acid therapy strategies against COVID-19. Int J Biol Sci 2022; 18:5070-5085. [PMID: 35982905 PMCID: PMC9379410 DOI: 10.7150/ijbs.72706] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/16/2022] [Indexed: 11/17/2022] Open
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome 2 coronavirus (SARS-CoV-2), remaining a global health crisis since its outbreak until now. Advanced biotechnology and research findings have revealed many suitable viral and host targets for a wide range of therapeutic strategies. The emerging ribonucleic acid therapy can modulate gene expression by post-transcriptional gene silencing (PTGS) based on Watson-Crick base pairing. RNA therapies, including antisense oligonucleotides (ASO), ribozymes, RNA interference (RNAi), aptamers, etc., were used to treat SARS-CoV whose genome is similar to SARV-CoV-2, and the past experience also applies for the treatment of COVID-19. Several studies against SARS-CoV-2 based on RNA therapeutic strategy have been reported, and a dozen of relevant preclinical or clinical trials are in process globally. RNA therapy has been a very active and important part of COVID-19 treatment. In this review, we focus on the progress of ribonucleic acid therapeutic strategies development and application, discuss corresponding problems and challenges, and suggest new strategies and solutions.
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Affiliation(s)
- Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Sichuan, China.,School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
| | - Mujiexin Liu
- Ineye Hospital of Chengdu University of TCM, Sichuan, China
| | - Yushu Gou
- School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
| | - Yue Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
| | - Bifang He
- Medical College, Guizhou University, Guizhou, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
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143
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Mahgoub MA, Alnaem A, Fadlelmola M, Abo-Idris M, Makki AA, Abdelgadir AA, Alzain AA. Discovery of novel potential inhibitors of TMPRSS2 and Mpro of SARS-CoV-2 using E-pharmacophore and docking-based virtual screening combined with molecular dynamic and quantum mechanics. J Biomol Struct Dyn 2022:1-14. [PMID: 35997154 DOI: 10.1080/07391102.2022.2112080] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The pandemic of coronavirus disease is caused by the SARS-CoV-2 which is considered a global health issue. The main protease of COVID 19 (Mpro) has an important role in viral multiplication in the host cell. Inhibiting Mpro is a novel approach to drug discovery and development. Also, transmembrane serine proteases (TMPSS2) facilitate viral activation by cleavage S glycoproteins, thus considered one of the essential host factors for COVID-19 pathogenicity. Computational tools were widely used to reduce time and costs in search of effective inhibitors. A chemical library that contains over two million molecules was virtually screened against TMPRSS2. Also, XP docking for the top hits was screened against (Mpro) to identify dual-target inhibitors. Furthermore, MM-GBSA and predictive ADMET were performed. The top hits were further studied through density functional theory (DFT) calculation and showed good binding to the active sites. Moreover, molecular dynamics (MD) for the top hits were performed which gave information about the stability of the protein-ligand complex during the simulation period. This study has led to the discovery of potential dual-target inhibitors Z751959696, Z751954014, and Z56784282 for COVID-19 with acceptable pharmacokinetic properties. The outcome of this study can participate in the development of novel inhibitors to defeat SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohanad A Mahgoub
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Ahmed Alnaem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Mohammed Fadlelmola
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Mazin Abo-Idris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Alaa A Makki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | | | - Abdulrahim A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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144
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Hu R, Hotta M, Maruyama T, Fujisawa M, Sou K, Takeoka S. Temperature-Responsive Liposome-Linked Immunosorbent Assay for the Rapid Detection of SARS-CoV-2 Using Immunoliposomes. ACS OMEGA 2022; 7:26936-26944. [PMID: 35915635 PMCID: PMC9328125 DOI: 10.1021/acsomega.2c03597] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/07/2022] [Indexed: 05/02/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the etiological agent of coronavirus disease 2019 (COVID-19), has infected more than 340 million people since the outbreak of the pandemic in 2019, resulting in approximately 55 million deaths. The rapid and effective diagnosis of COVID-19 patients is vital to prevent the spread of the disease. In a previous study, we reported a novel temperature-responsive liposome-linked immunosorbent assay (TLip-LISA) using biotinylated-TLip that exhibited high detection sensitivity for the prostate-specific antigen. Herein, we used immunoglobulin-TLip (IgG-TLip), in which the antibodies were directly conjugated to the liposomal surface to simplify pretreatment procedures and reduce the detection time for SARS-CoV-2. The results indicated that TLip-LISA could detect the recombinant nucleocapsid protein and the nucleocapsid protein in inactivated virus with 20 min incubation time in total, and the limit of detection was calculated to be 2.2 and 1.0 pg/mL, respectively. Therefore, TLip-LISA has high potential to be used in clinic for rapid diagnosis and disease control.
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Affiliation(s)
- Runkai Hu
- Department
of Life Science and Medical Bioscience, Graduate School of Advanced
Science and Engineering, Waseda University, Tokyo 162-8480, Japan
| | - Morihiro Hotta
- Department
of Life Science and Medical Bioscience, Graduate School of Advanced
Science and Engineering, Waseda University, Tokyo 162-8480, Japan
| | - Taro Maruyama
- Department
of Life Science and Medical Bioscience, Graduate School of Advanced
Science and Engineering, Waseda University, Tokyo 162-8480, Japan
| | - Mizuki Fujisawa
- Department
of Life Science and Medical Bioscience, Graduate School of Advanced
Science and Engineering, Waseda University, Tokyo 162-8480, Japan
| | - Keitaro Sou
- Waseda
Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Shinji Takeoka
- Department
of Life Science and Medical Bioscience, Graduate School of Advanced
Science and Engineering, Waseda University, Tokyo 162-8480, Japan
- Institute
for Advanced Research of Biosystem Dynamics, Waseda Research Institute
for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
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145
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Feng X, Zhang X, Jiang S, Tang Y, Cheng C, Krishna PA, Wang X, Dai J, Zhao D, Xia T, Zeng J. A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis. Comput Struct Biotechnol J 2022; 20:5193-5202. [PMID: 36059866 PMCID: PMC9424123 DOI: 10.1016/j.csbj.2022.08.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/02/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022] Open
Abstract
The coronavirus disease-2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has seriously affected public health around the world. In-depth studies on the pathogenic mechanisms of SARS-CoV-2 is urgently necessary for pandemic prevention. However, most laboratory studies on SARS-CoV-2 have to be carried out in bio-safety level 3 (BSL-3) laboratories, greatly restricting the progress of relevant experiments. In this study, we used a bacterial artificial chromosome (BAC) method to assemble a SARS-CoV-2 replication and transcription system in Vero E6 cells without virion envelope formation, thus avoiding the risk of coronavirus exposure. Furthermore, an improved real-time quantitative reverse transcription PCR (RT-qPCR) approach was used to distinguish the replication of full-length replicon RNAs and transcription of subgenomic RNAs (sgRNAs). Using the SARS-CoV-2 replicon, we demonstrated that the nucleocapsid (N) protein of SARS-CoV-2 facilitates the transcription of sgRNAs in the discontinuous synthesis process. Moreover, two high-frequency mutants of N protein, R203K and S194L, can obviously enhance the transcription level of the replicon, hinting that these mutations likely allow SARS-CoV-2 to spread and reproduce more quickly. In addition, remdesivir and chloroquine, two well-known drugs demonstrated to be effective against coronavirus in previous studies, also inhibited the transcription of our replicon, indicating the potential applications of this system in antiviral drug discovery. Overall, we developed a bio-safe and valuable replicon system of SARS-CoV-2 that is useful to study the mechanisms of viral RNA synthesis and has potential in novel antiviral drug screening.
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146
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Shah S, Chaple D, Arora S, Yende S, Mehta C, Nayak U. Prospecting for Cressa cretica to treat COVID-19 via in silico molecular docking models of the SARS-CoV-2. J Biomol Struct Dyn 2022; 40:5643-5652. [PMID: 33446077 PMCID: PMC7814567 DOI: 10.1080/07391102.2021.1872419] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 01/02/2021] [Indexed: 12/12/2022]
Abstract
The severe acute respiratory syndrome COVID-19 declared as a global pandemic by the World Health Organization has become the present wellbeing worry to the whole world. There is an emergent need to search for possible medications. Cressa cretica is reported to show antitubercular, antibacterial and expectorant property. In this research, we aim to prospect the COVID-19 main protease crystal structure (Mpro; PDB ID: 6LU7) and the active chemical constituents from Cressa cretica in order to understand the structural basis of their interactions. We examined the binding potential of active constituents of Cressa cretica plant to immensely conserved protein Mpro of SARS-CoV-2 followed by exploration of the vast conformational space of protein-ligand complexes by molecular dynamics (MD) simulations. The results suggest the effectiveness of 3,5-Dicaffeoylquinic acid and Quercetin against standard drug Remdesivir. The active chemical constituents exhibited good docking scores, and interacts with binding site residues of Mpro by forming hydrogen bond and hydrophobic interactions. 3,5-Dicaffeoylquinic acid showed the best affinity towards Mpro receptor which is one of the target enzymes required by SARS CoV-2 virus for replication suggesting it to be a novel research molecule. The potential of the active chemical constituents from Cressa cretica against the SARS-CoV-2 virus has best been highlighted through this study. Therefore, these chemical entities can be further scrutinized and provides direction for further consideration for in-vivo and in-vitro validations for the treatment of covid-19. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sapan Shah
- Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Nagpur, Maharashtra, India
| | - Dinesh Chaple
- Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Nagpur, Maharashtra, India
| | - Sumit Arora
- Pharmacognosy and Phytochemistry Division, Gurunanak College of Pharmacy, Nagpur, Maharashtra, India
| | - Subhash Yende
- Pharmacology Dvision, Gurunanak College of Pharmacy, Nagpur, Mahrashtra, India
| | - Chetan Mehta
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences (MCOPS), MAHE, Manipal, Karnataka, India
| | - Usha Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences (MCOPS), MAHE, Manipal, Karnataka, India
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147
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Zamani Rarani F, Zamani Rarani M, Hamblin MR, Rashidi B, Hashemian SMR, Mirzaei H. Comprehensive overview of COVID-19-related respiratory failure: focus on cellular interactions. Cell Mol Biol Lett 2022; 27:63. [PMID: 35907817 PMCID: PMC9338538 DOI: 10.1186/s11658-022-00363-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/06/2022] [Indexed: 01/08/2023] Open
Abstract
The pandemic outbreak of coronavirus disease 2019 (COVID-19) has created health challenges in all parts of the world. Understanding the entry mechanism of this virus into host cells is essential for effective treatment of COVID-19 disease. This virus can bind to various cell surface molecules or receptors, such as angiotensin-converting enzyme 2 (ACE2), to gain cell entry. Respiratory failure and pulmonary edema are the most important causes of mortality from COVID-19 infections. Cytokines, especially proinflammatory cytokines, are the main mediators of these complications. For normal respiratory function, a healthy air-blood barrier and sufficient blood flow to the lungs are required. In this review, we first discuss airway epithelial cells, airway stem cells, and the expression of COVID-19 receptors in the airway epithelium. Then, we discuss the suggested molecular mechanisms of endothelial dysfunction and blood vessel damage in COVID-19. Coagulopathy can be caused by platelet activation leading to clots, which restrict blood flow to the lungs and lead to respiratory failure. Finally, we present an overview of the effects of immune and non-immune cells and cytokines in COVID-19-related respiratory failure.
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Affiliation(s)
- Fahimeh Zamani Rarani
- Department of Anatomical Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Zamani Rarani
- Department of Anatomical Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028 South Africa
| | - Bahman Rashidi
- Department of Anatomical Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Mohammad Reza Hashemian
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamed Mirzaei
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, IR Iran
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148
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Inchingolo AD, Malcangi G, Ceci S, Patano A, Corriero A, Vimercati L, Azzollini D, Marinelli G, Coloccia G, Piras F, Barile G, Settanni V, Mancini A, De Leonardis N, Garofoli G, Palmieri G, Isacco CG, Rapone B, Scardapane A, Curatoli L, Quaranta N, Ribezzi M, Massaro M, Jones M, Bordea IR, Tartaglia GM, Scarano A, Lorusso F, Macchia L, Larocca AMV, Aityan SK, Tafuri S, Stefanizzi P, Migliore G, Brienza N, Dipalma G, Favia G, Inchingolo F. Effectiveness of SARS-CoV-2 Vaccines for Short- and Long-Term Immunity: A General Overview for the Pandemic Contrast. Int J Mol Sci 2022; 23:ijms23158485. [PMID: 35955621 PMCID: PMC9369331 DOI: 10.3390/ijms23158485] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 11/22/2022] Open
Abstract
Background: The recent COVID-19 pandemic produced a significant increase in cases and an emergency state was induced worldwide. The current knowledge about the COVID-19 disease concerning diagnoses, patient tracking, the treatment protocol, and vaccines provides a consistent contribution for the primary prevention of the viral infection and decreasing the severity of the SARS-CoV-2 disease. The aim of the present investigation was to produce a general overview about the current findings for the COVID-19 disease, SARS-CoV-2 interaction mechanisms with the host, therapies and vaccines’ immunization findings. Methods: A literature overview was produced in order to evaluate the state-of-art in SARS-CoV-2 diagnoses, prognoses, therapies, and prevention. Results: Concerning to the interaction mechanisms with the host, the virus binds to target with its Spike proteins on its surface and uses it as an anchor. The Spike protein targets the ACE2 cell receptor and enters into the cells by using a special enzyme (TMPRSS2). Once the virion is quietly accommodated, it releases its RNA. Proteins and RNA are used in the Golgi apparatus to produce more viruses that are released. Concerning the therapies, different protocols have been developed in observance of the disease severity and comorbidity with a consistent reduction in the mortality rate. Currently, different vaccines are currently in phase IV but a remarkable difference in efficiency has been detected concerning the more recent SARS-CoV-2 variants. Conclusions: Among the many questions in this pandemic state, the one that recurs most is knowing why some people become more seriously ill than others who instead contract the infection as if it was a trivial flu. More studies are necessary to investigate the efficiency of the treatment protocols and vaccines for the more recent detected SARS-CoV-2 variant.
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Affiliation(s)
- Alessio Danilo Inchingolo
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Giuseppina Malcangi
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Sabino Ceci
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Assunta Patano
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Alberto Corriero
- Unit of Anesthesia and Resuscitation, Department of Emergencies and Organ Transplantations, Aldo Moro University, 70121 Bari, Italy; (A.C.); (M.R.); (N.B.)
| | - Luigi Vimercati
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Daniela Azzollini
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Grazia Marinelli
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Giovanni Coloccia
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Fabio Piras
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Giuseppe Barile
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Vito Settanni
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Antonio Mancini
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Nicole De Leonardis
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Grazia Garofoli
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Giulia Palmieri
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Ciro Gargiulo Isacco
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Biagio Rapone
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Arnaldo Scardapane
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Luigi Curatoli
- Department Neurosciences & Sensory Organs & Musculoskeletal System, University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Nicola Quaranta
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
- Department Neurosciences & Sensory Organs & Musculoskeletal System, University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Mario Ribezzi
- Unit of Anesthesia and Resuscitation, Department of Emergencies and Organ Transplantations, Aldo Moro University, 70121 Bari, Italy; (A.C.); (M.R.); (N.B.)
| | - Maria Massaro
- Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy;
| | - Megan Jones
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Ioana Roxana Bordea
- Department of Oral Rehabilitation, Faculty of Dentistry, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| | - Gianluca Martino Tartaglia
- UOC Maxillo-Facial Surgery and Dentistry, Department of Biomedical, Surgical and Dental Sciences, School of Dentistry, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, University of Milan, 20100 Milan, Italy;
| | - Antonio Scarano
- Department of Innovative Technologies in Medicine and Dentistry, University of Chieti-Pescara, 66100 Chieti, Italy;
| | - Felice Lorusso
- Department of Innovative Technologies in Medicine and Dentistry, University of Chieti-Pescara, 66100 Chieti, Italy;
- Correspondence: (F.L.); (F.I.); Tel.: +39-3282132586 (F.L.)
| | - Luigi Macchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari Aldo Moro, 70124 Bari, Italy;
| | - Angela Maria Vittoria Larocca
- Hygiene Complex Operating Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, Place Giulio Cesare 11 BARI CAP, 70124 Bari, Italy;
| | | | - Silvio Tafuri
- Department of Biomedical Science and Human Oncology, University of Bari, 70121 Bari, Italy;
| | - Pasquale Stefanizzi
- Interdisciplinary Department of Medicine, University Hospital of Bari, 70100 Bari, Italy; (P.S.); (G.M.)
| | - Giovanni Migliore
- Interdisciplinary Department of Medicine, University Hospital of Bari, 70100 Bari, Italy; (P.S.); (G.M.)
| | - Nicola Brienza
- Unit of Anesthesia and Resuscitation, Department of Emergencies and Organ Transplantations, Aldo Moro University, 70121 Bari, Italy; (A.C.); (M.R.); (N.B.)
| | - Gianna Dipalma
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Gianfranco Favia
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
| | - Francesco Inchingolo
- Department of Interdisciplinary Medicine, Section of Dental Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.M.); (S.C.); (A.P.); (L.V.); (D.A.); (G.M.); (G.C.); (F.P.); (G.B.); (V.S.); (A.M.); (N.D.L.); (G.G.); (G.P.); (C.G.I.); (B.R.); (A.S.); (N.Q.); (M.J.); (G.D.); (G.F.)
- Correspondence: (F.L.); (F.I.); Tel.: +39-3282132586 (F.L.)
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Ebeyer-Masotta M, Eichhorn T, Weiss R, Lauková L, Weber V. Activated Platelets and Platelet-Derived Extracellular Vesicles Mediate COVID-19-Associated Immunothrombosis. Front Cell Dev Biol 2022; 10:914891. [PMID: 35874830 PMCID: PMC9299085 DOI: 10.3389/fcell.2022.914891] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/08/2022] [Indexed: 12/12/2022] Open
Abstract
Activated platelets and platelet-derived extracellular vesicles (EVs) have emerged as central players in thromboembolic complications associated with severe coronavirus disease 2019 (COVID-19). Platelets bridge hemostatic, inflammatory, and immune responses by their ability to sense pathogens via various pattern recognition receptors, and they respond to infection through a diverse repertoire of mechanisms. Dysregulated platelet activation, however, can lead to immunothrombosis, a simultaneous overactivation of blood coagulation and the innate immune response. Mediators released by activated platelets in response to infection, such as antimicrobial peptides, high mobility group box 1 protein, platelet factor 4 (PF4), and PF4+ extracellular vesicles promote neutrophil activation, resulting in the release of neutrophil extracellular traps and histones. Many of the factors released during platelet and neutrophil activation are positively charged and interact with endogenous heparan sulfate or exogenously administered heparin via electrostatic interactions or via specific binding sites. Here, we review the current state of knowledge regarding the involvement of platelets and platelet-derived EVs in the pathogenesis of immunothrombosis, and we discuss the potential of extracorporeal therapies using adsorbents functionalized with heparin to deplete platelet-derived and neutrophil-derived mediators of immunothrombosis.
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Affiliation(s)
- Marie Ebeyer-Masotta
- Center for Biomedical Technology, Department for Biomedical Research, University for Continuing Education Krems, Krems, Austria
| | - Tanja Eichhorn
- Center for Biomedical Technology, Department for Biomedical Research, University for Continuing Education Krems, Krems, Austria
| | - René Weiss
- Center for Biomedical Technology, Department for Biomedical Research, University for Continuing Education Krems, Krems, Austria
| | - Lucia Lauková
- Center for Biomedical Technology, Department for Biomedical Research, University for Continuing Education Krems, Krems, Austria
| | - Viktoria Weber
- Center for Biomedical Technology, Department for Biomedical Research, University for Continuing Education Krems, Krems, Austria
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150
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Bhargava A, Dahiya P. COVID-19 Pandemic: Assessment of Current Strategies and Socio-economic Impact. JOURNAL OF HEALTH MANAGEMENT 2022. [DOI: 10.1177/09720634221109295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The coronavirus disease is a respiratory tract disorder which causes pneumonia-like symptoms in severe patients and mild flu-like symptoms in mild symptomatic cases first noticed in Wuhan, China. DNA sequencing and further analysis shows it to be 79% like the 2002 SARS-CoV and 50% like the 2012 MERS-CoV. It was also observed that the novel coronavirus’s spike protein was larger and very different from its previously known strains. For diagnosis, multiple strategies were developed and real time reverse-transcriptase-polymerase chain reaction (RT-PCR) technique was determined to be the best technique. The CT scan was also found effective majorly for the continuous assessment of the disease. Treatment strategies used in previous outbreaks were looked into and put to trial like convalescent plasma therapy. Vaccine development using various genetic engineering strategies are going on across the world. To contain the spread of the disease, countries with positive cases were put under lockdown to break the chain of spread. These lockdowns forced industries, offices, schools, religious places, stadiums, travel, and many more to close which impacted the economies of all the major countries. Lesser human interaction and more use of social media has impacted the social aspects of human life. Cases of domestic violence and mental stress increased among households. Economic stimulus package was announced by various countries to curb the socio-economic impact of the COVID-19 pandemic.
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Affiliation(s)
- Anushka Bhargava
- Centre for Biotechnology and Biochemical Engineering, Amity Institute of Biotechnology, Amity University Uttar Pradesh (AUUP), Noida, Uttar Pradesh, India
| | - Praveen Dahiya
- Centre for Biotechnology and Biochemical Engineering, Amity Institute of Biotechnology, Amity University Uttar Pradesh (AUUP), Noida, Uttar Pradesh, India
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