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Cheng S, Feng Y, Li W, Liu T, Lv X, Tong X, Xi G, Ye X, Li X. Development of novel antivrial agents that induce the degradation of the main protease of human-infecting coronaviruses. Eur J Med Chem 2024; 275:116629. [PMID: 38941718 DOI: 10.1016/j.ejmech.2024.116629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 06/30/2024]
Abstract
The family of human-infecting coronaviruses (HCoVs) poses a serious threat to global health and includes several highly pathogenic strains that cause severe respiratory illnesses. It is essential that we develop effective broad-spectrum anti-HCoV agents to prepare for future outbreaks. In this study, we used PROteolysis TArgeting Chimera (PROTAC) technology focused on degradation of the HCoV main protease (Mpro), a conserved enzyme essential for viral replication and pathogenicity. By adapting the Mpro inhibitor GC376, we produced two novel PROTACs, P2 and P3, which showed relatively broad-spectrum activity against the human-infecting CoVs HCoV-229E, HCoV-OC43, and SARS-CoV-2. The concentrations of these PROTACs that reduced virus replication by 50 % ranged from 0.71 to 4.6 μM, and neither showed cytotoxicity at 100 μM. Furthermore, mechanistic binding studies demonstrated that P2 and P3 effectively targeted HCoV-229E, HCoV-OC43, and SARS-CoV-2 by degrading Mpro within cells in vitro. This study highlights the potential of PROTAC technology in the development of broad-spectrum anti-HCoVs agents, presenting a novel approach for dealing with future viral outbreaks, particularly those stemming from CoVs.
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Affiliation(s)
- Shuihong Cheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China.
| | - Yong Feng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Wei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| | - Tong Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China
| | - Xun Lv
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China
| | - Xiaomei Tong
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Gan Xi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China
| | - Xin Ye
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Xuebing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China.
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Wang R, Stevaert A, Truong TN, Li Q, Krasniqi B, Van Loy B, Voet A, Naesens L, Dehaen W. Exploration of 1,2,3-triazolo fused triterpenoids as inhibitors of human coronavirus 229E targeting the viral nsp15 protein. Arch Pharm (Weinheim) 2024; 357:e2300442. [PMID: 37840345 DOI: 10.1002/ardp.202300442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
The coronavirus disease-19 (COVID-19) pandemic has raised major interest in innovative drug concepts to suppress human coronavirus (HCoV) infections. We previously reported on a class of 1,2,3-triazolo fused betulonic acid derivatives causing strong inhibition of HCoV-229E replication via the viral nsp15 protein, which is proposedly related to compound binding at an intermonomer interface in hexameric nsp15. In the present study, we further explored the structure-activity relationship (SAR), by varying the substituent at the 1,2,3-triazolo ring as well as the triterpenoid skeleton. The 1,2,3-triazolo fused triterpenoids were synthesized by a multicomponent triazolization reaction, which has been developed in-house. Several analogs possessing a betulin, oleanolic acid, or ursolic acid core displayed favorable activity and selectivity (EC50 values for HCoV-229E: 1.6-3.5 μM), but neither of them proved as effective as the lead compound containing betulonic acid. The 18β-glycyrrhetinic acid-containing analogs had low selectivity. The antiviral findings were rationalized by in silico docking in the available structure of the HCoV-229E nsp15 protein. The new SAR insights will aid the further development of these 1,2,3-triazolo fused triterpenoid compounds as a unique type of coronavirus inhibitors.
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Affiliation(s)
- Rui Wang
- Department of Chemistry, Sustainable Chemistry for Metals and Molecules, KU Leuven, Leuven, Belgium
| | - Annelies Stevaert
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Tien Nguyen Truong
- Department of Chemistry, Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium
| | - Qifei Li
- Department of Chemistry, Sustainable Chemistry for Metals and Molecules, KU Leuven, Leuven, Belgium
| | - Besir Krasniqi
- Department of Chemistry, Sustainable Chemistry for Metals and Molecules, KU Leuven, Leuven, Belgium
| | - Benjamin Van Loy
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Arnout Voet
- Department of Chemistry, Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium
| | - Lieve Naesens
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Wim Dehaen
- Department of Chemistry, Sustainable Chemistry for Metals and Molecules, KU Leuven, Leuven, Belgium
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Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. Cell Rep 2023; 42:113478. [PMID: 37991919 PMCID: PMC10785701 DOI: 10.1016/j.celrep.2023.113478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/13/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) remains a significant public health threat due to the ability of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and Middle East respiratory syndrome (MERS)-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here, we use our recently developed integrative DNA And Protein Tagging methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.
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Affiliation(s)
- Jonathan D Lee
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA.
| | - Bridget L Menasche
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Maria Mavrikaki
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Madison M Uyemura
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Su Min Hong
- Department of Genetics, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Nina Kozlova
- Department of Genetics, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mia M Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Arne Müller
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Tanvi Saxena
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan R Posey
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Priscilla Cheung
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Taru Muranen
- Department of Genetics, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Yujing J Heng
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Frank J Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Department of Genetics, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
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Joseph JO, Ylade M, Daag JV, Aogo R, Crisostomo MV, Mpingabo P, Premkumar L, Deen J, Katzelnick L. High transmission of endemic human coronaviruses before and during the COVID-19 pandemic in adolescents in Cebu, Philippines. RESEARCH SQUARE 2023:rs.3.rs-3581033. [PMID: 38014070 PMCID: PMC10680936 DOI: 10.21203/rs.3.rs-3581033/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
BACKGROUND SARS-CoV-2, the causative agent of COVID-19, is a betacoronavirus belonging to the same genus as endemic human coronaviruses (hCoVs) OC43 and HKU1 and is distinct from alpha hCoVs 229E and NL63. In a study of adolescents in the Philippines, we evaluated the seroprevalence to hCoVs, whether pre-pandemic hCoV immunity modulated subsequent risk of SARS-CoV-2 infection, and if SARS-CoV-2 infection affected the transmission of the hCoVs. METHODS From 499 samples collected in 2021 and screened by SARS-CoV-2 receptor binding domain (RBD) enzyme-linked immunosorbent assay (ELISA), we randomly selected 59 SARS-CoV-2 negative and 61 positive individuals for further serological evaluation. We measured RBD and spike antibodies to the four hCoVs and SARS-CoV-2 by ELISA in samples from the same participants collected pre-pandemic (2018-2019) and mid-pandemic (2021), before COVID-19 vaccination. RESULTS We observed over 72% seropositivity to the four hCoVs pre-pandemic. Binding antibodies increased with age to 229E and OC43, suggesting endemic circulation, while immunity was flat across ages for HKU1 and NL63. During the COVID-19 pandemic, antibody level increased significantly to the RBDs of OC43, NL63, and 229E and spikes of all four hCoVs in both SARS-CoV-2 negative and positive adolescents. Those aged 12-15 years old in 2021 had higher antibodies to RBD and spike of OC43, NL63, and 229E than adolescents the same age in 2019, further demonstrating intense transmission of the hCoVs during the pandemic. CONCLUSIONS We observe a limited impact of the COVID-19 pandemic on endemic hCoV transmission. This study provides insight into co-circulation of hCoVs and SARS-CoV-2.
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Zhao MC, Wen C, Sun L, Duan SX, Zang KX, Wang L, Cui XW. Epidemiology and Clinical Characteristics of Seasonal Human Coronaviruses in Children Hospitalized in Hebei Province, China Before and During the COVID-19 Pandemic. Risk Manag Healthc Policy 2023; 16:1801-1807. [PMID: 37705991 PMCID: PMC10497059 DOI: 10.2147/rmhp.s423077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/19/2023] [Indexed: 09/15/2023] Open
Abstract
Background This study aimed to assess the impact of the COVID-19 pandemic on the prevalence and clinical characteristics of seasonal human coronavirus (HCoV) infections among children hospitalized in Hebei, China. Methods We examined nasopharyngeal aspirate (NPA) specimens for seasonal HCoVs from January 2018 to December 2021, at the Children's Hospital of Hebei Province. We used a GeXP-based multiplex reverse transcription PCR assay for the detection of 11 common respiratory viruses (including seasonal HCoVs), chlamydia, and Mycoplasma pneumoniae. The demographic and clinical characteristics of children who tested positive for seasonal HCoVs were recorded and analyzed. Results A total of 377 (1.96%) of the 19,248 specimens from 2018 to 2019 and 263 (1.96%) of the 13,426 specimens from 2020 to 2021 exhibited seasonal HCoVs. Compared to 2018 and 2019, the positive rate of seasonal HCoVs was lower from January to July of 2020 and increased beginning in August 2020, peaking in the autumn and winter. In 2020-2021, nasal blockage and swollen adenoids were detected more frequently in children who tested positive for seasonal HCoVs. During 2018-2019, however, the duration of fever was significantly longer, and cough and dyspnea were more prominent among children who had fallen ill. In addition, seasonal HCoV-positive patients in 2018-2019 were more likely to experience complications, had a higher risk of severe community-acquired pneumonia (CAP), and had a tendency to require a longer hospital stay than patients in 2020-2021. Conclusion According to our findings, there were significant changes in the epidemiology of seasonal HCoVs in Hebei, China during the COVID-19 pandemic, and children infected with seasonal HCoVs usually experienced milder clinical symptoms during the pandemic than before it.
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Affiliation(s)
- Meng-Chuan Zhao
- Department of Laborotory Medicine, Children’s Hospital of Hebei Province, Shijiazhuang, People’s Republic of China
| | - Chan Wen
- Department of Medical, Children’s Hospital of Hebei Province, Shijiazhuang, People’s Republic of China
| | - Ling Sun
- Department of Medical, Children’s Hospital of Hebei Province, Shijiazhuang, People’s Republic of China
| | - Su-xia Duan
- Department of Laborotory Medicine, Children’s Hospital of Hebei Province, Shijiazhuang, People’s Republic of China
| | - Ke-xin Zang
- Hebei Medical University, Shijiazhuang, People’s Republic of China
| | - Le Wang
- Department of Laborotory Medicine, Children’s Hospital of Hebei Province, Shijiazhuang, People’s Republic of China
| | - Xiao-Wei Cui
- Children’s Hospital of Hebei Province, Shijiazhuang, People’s Republic of China
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Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555625. [PMID: 37693555 PMCID: PMC10491142 DOI: 10.1101/2023.08.31.555625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
COVID-19 remains a significant public health threat due to the ability of SARS-CoV-2 variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and MERS-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here we used our recently developed integrative DNA And Protein Tagging (iDAPT) methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.
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Wang J, Zhang M, Ding Y, Lin Y, Xue Y, Wang X, Wang X. Coronaviral Main Protease Induces LPCAT3 Cleavage and Endoplasmic Reticulum (ER) Stress. Viruses 2023; 15:1696. [PMID: 37632038 PMCID: PMC10457833 DOI: 10.3390/v15081696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Zoonotic coronaviruses infect mammals and birds, causing pulmonary and gastrointestinal infections. Some animal coronaviruses, such as the porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus (TGEV), lead to severe diarrhea and animal deaths. Gastrointestinal symptoms were also found in COVID-19 and SARS patients. However, the pathogenesis of gastrointestinal symptoms in coronavirus diseases remains elusive. In this study, the main protease-induced LPCAT3 cleavage was monitored by exogenous gene expression and protease inhibitors, and the related regulation of gene expression was confirmed by qRT-PCR and gene knockdown. Interestingly, LPCAT3 plays an important role in lipid absorption in the intestines. The Mpro of coronaviruses causing diarrhea, such as PEDV and MERS-CoV, but not the Mpro of HCoV-OC43 and HCoV-HKU1, which could induce LPCAT3 cleavage. Mutagenesis analysis and inhibitor experiments indicated that LPCAT3 cleavage was independent of the catalytic activity of Mpro. Moreover, LPCAT3 cleavage in cells boosted CHOP and GRP78 expression, which were biomarkers of ER stress. Since LPCAT3 is critical for lipid absorption in the intestines and malabsorption may lead to diarrhea in coronavirus diseases, Mpro-induced LPCAT3 cleavage might trigger gastrointestinal symptoms during coronavirus infection.
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Affiliation(s)
- Jia Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (J.W.); (M.Z.); (Y.D.); (Y.L.)
| | - Meifang Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (J.W.); (M.Z.); (Y.D.); (Y.L.)
- Key Laboratory of Tropical Biological Resources of Ministry of Education and One Health Institute, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Yanli Ding
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (J.W.); (M.Z.); (Y.D.); (Y.L.)
| | - Yuxi Lin
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (J.W.); (M.Z.); (Y.D.); (Y.L.)
| | - Yan Xue
- Department of Physiology, School of Basic Medicine, Qingdao University, Qingdao 266071, China;
| | - Xiaohong Wang
- Shandong Foreign Trade Vocational College, Qingdao 266100, China;
| | - Xin Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (J.W.); (M.Z.); (Y.D.); (Y.L.)
- Key Laboratory of Tropical Biological Resources of Ministry of Education and One Health Institute, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- Song Li’ Academician Workstation, School of Pharmaceutical Sciences, Hainan University, Sanya 572000, China
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Gerencer M, McGuffin LJ. Are the integrin binding motifs within SARS CoV-2 spike protein and MHC class II alleles playing the key role in COVID-19? Front Immunol 2023; 14:1177691. [PMID: 37492575 PMCID: PMC10364474 DOI: 10.3389/fimmu.2023.1177691] [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: 03/01/2023] [Accepted: 05/22/2023] [Indexed: 07/27/2023] Open
Abstract
The previous studies on the RGD motif (aa403-405) within the SARS CoV-2 spike (S) protein receptor binding domain (RBD) suggest that the RGD motif binding integrin(s) may play an important role in infection of the host cells. We also discussed the possible role of two other integrin binding motifs that are present in S protein: LDI (aa585-587) and ECD (661-663), the motifs used by some other viruses in the course of infection. The MultiFOLD models for protein structure analysis have shown that the ECD motif is clearly accessible in the S protein, whereas the RGD and LDI motifs are partially accessible. Furthermore, the amino acids that are present in Epstein-Barr virus protein (EBV) gp42 playing very important role in binding to the HLA-DRB1 molecule and in the subsequent immune response evasion, are also present in the S protein heptad repeat-2. Our MultiFOLD model analyses have shown that these amino acids are clearly accessible on the surface in each S protein chain as monomers and in the homotrimer complex and bind to HLA-DRB1 β chain. Therefore, they may have the identical role in SARS CoV-2 immune evasion as in EBV infection. The prediction analyses of the MHC class II binding peptides within the S protein have shown that the RGD motif is present in the core 9-mer peptide IRGDEVRQI within the two HLA-DRB1*03:01 and HLA-DRB3*01.01 strong binding 15-mer peptides suggesting that RGD motif may be the potential immune epitope. Accordingly, infected HLA-DRB1*03:01 or HLA-DRB3*01.01 positive individuals may develop high affinity anti-RGD motif antibodies that react with the RGD motif in the host proteins, like fibrinogen, thrombin or von Willebrand factor, affecting haemostasis or participating in autoimmune disorders.
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Affiliation(s)
| | - Liam J. McGuffin
- School of Biological Sciences, University of Reading, Reading, United Kingdom
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Maity S, Santra A, Vardhan Hebbani A, Pulakuntla S, Chatterjee A, Rao Badri K, Damodara Reddy V. Targeting cytokine storm as the potential anti-viral therapy: Implications in regulating SARS-CoV-2 pathogenicity. Gene 2023:147612. [PMID: 37423400 DOI: 10.1016/j.gene.2023.147612] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/18/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
The latest global pandemic corona virus disease - 2019 (COVID-19) caused by the virus SARS-CoV-2 is still a matter of worrying concern both for the scientific communities and health care organizations. COVID-19 disease is proved to be a highly contagious disease transmitted through respiratory droplets and even close contact with affected individuals. COVID-19 disease is also understood to exhibit diverse symptoms of ranging severities i.e., from mild fatigue to death. Affected individuals' susceptibility to induce immunologic dysregulation phenomena termed 'cytokine storm' seems to be playing the damaging role of escalating the disease manifestation from mild to severe. Cytokine storm in patients with severe symptoms is understood to be characterized by enhanced serum levels of many cytokines including interleukin-1β, interleukin-6, IL-10, TNF, interferon-γ, MIP-1α, MIP-1β and VEGF. Since cytokine production in general is the most important antiviral defense response, understanding the COVID-19 associated cytokine storm in particular and differentiating it from the regular cytokine production response becomes crucial in developing an effective therapeutic strategy.This review focuses on the potential targeting of COVID-19 associated cytokine storm and its challenges.
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Affiliation(s)
- Subashish Maity
- Department of Biotechnology, REVA University, Bengaluru-560064, Karnataka, India
| | - Ayantika Santra
- Department of Biochemistry, Indian Academy Degree College, Bengaluru, 560 043, India
| | | | - Swetha Pulakuntla
- Department of Biotechnology, REVA University, Bengaluru-560064, Karnataka, India
| | - Ankita Chatterjee
- Department of Biotechnology, REVA University, Bengaluru-560064, Karnataka, India
| | - Kameswara Rao Badri
- Department of Pharmacology and Toxicology, Cardiovascular Research Institute, Morehouse School of Medicine, GA, Atlanta-30310, USA; Clinical Analytical Chemistry Laboratory, COVID-19 Testing Laboratory, Morehouse School of Medicine, GA, Atlanta-30310, USA.
| | - Vaddi Damodara Reddy
- Department of Biotechnology, REVA University, Bengaluru-560064, Karnataka, India.
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Doleman G, Coventry L, Towell-Barnard A, Ghosh M, Gent L, Saunders R, O'Connell B. Staff perceptions of the effectiveness of managerial communication during the COVID-19 pandemic: A cross-sectional study. Int J Nurs Pract 2023:e13149. [PMID: 36942620 DOI: 10.1111/ijn.13149] [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: 11/01/2021] [Revised: 02/23/2023] [Accepted: 03/04/2023] [Indexed: 03/23/2023]
Abstract
AIMS This work aims to explore staff perceptions of (1) the effectiveness of organizational communication during the COVID-19 pandemic and (2) the impact of organizational communication on staff well-being and ability to progress their work and patient care. BACKGROUND Effective coordination and communication are essential in a pandemic management response. However, the effectiveness of communication strategies used during the COVID-19 pandemic is not well understood. DESIGN An exploratory cross-sectional research design was used. A 33-item survey tool was created for the study. METHODS The study was conducted at a tertiary teaching hospital in Western Australia. Convenience sampling was used to recruit participants from nursing, medical, allied health services, administrative and clerical, and personal support services (N = 325). Data were collected between December 2020 and May 2021. RESULTS Overall, all occupational groups found working during the COVID-19 pandemic stressful, and all groups wanted accessible and accurate communication from management and new policies, procedures, and protocols for future outbreaks. CONCLUSIONS The use of occupational group-relevant strategies and COVID-19 protocols, as well as the on-going use of email, face-to-face meetings with debrief sessions, are needed to improve communication and support staff to fulfil their roles.
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Affiliation(s)
- Gemma Doleman
- School of Nursing and Midwifery, Edith Cowan University, Joondalup, Western Australia, Australia
- Centre for Nursing Research, Sir Charles Gardiner Hospital, Nedlands, Western Australia, Australia
| | - Linda Coventry
- School of Nursing and Midwifery, Edith Cowan University, Joondalup, Western Australia, Australia
- Centre for Nursing Research, Sir Charles Gardiner Hospital, Nedlands, Western Australia, Australia
- Centre for Research in Aged Care, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Amanda Towell-Barnard
- School of Nursing and Midwifery, Edith Cowan University, Joondalup, Western Australia, Australia
- Centre for Nursing Research, Sir Charles Gardiner Hospital, Nedlands, Western Australia, Australia
- Centre for Research in Aged Care, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Manonita Ghosh
- School of Nursing and Midwifery, Edith Cowan University, Joondalup, Western Australia, Australia
- Centre for Nursing Research, Sir Charles Gardiner Hospital, Nedlands, Western Australia, Australia
| | - Lucy Gent
- Centre for Nursing Research, Sir Charles Gardiner Hospital, Nedlands, Western Australia, Australia
| | - Rosemary Saunders
- School of Nursing and Midwifery, Edith Cowan University, Joondalup, Western Australia, Australia
- Centre for Research in Aged Care, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Beverly O'Connell
- School of Nursing and Midwifery, Edith Cowan University, Joondalup, Western Australia, Australia
- Centre for Nursing Research, Sir Charles Gardiner Hospital, Nedlands, Western Australia, Australia
- Centre for Research in Aged Care, Edith Cowan University, Joondalup, Western Australia, Australia
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11
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Zhou Y, Wang W, Zeng P, Feng J, Li D, Jing Y, Zhang J, Yin X, Li J, Ye H, Wang Q. Structural basis of main proteases of HCoV-229E bound to inhibitor PF-07304814 and PF-07321332. Biochem Biophys Res Commun 2023; 657:16-23. [PMID: 36965419 PMCID: PMC10020134 DOI: 10.1016/j.bbrc.2023.03.043] [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: 03/06/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023]
Abstract
PF-07321332 and PF-07304814, inhibitors against SARS-CoV-2 developed by Pfizer, exhibit broad-spectrum inhibitory activity against the main protease (Mpro) from various coronaviruses. Structures of PF-07321332 or PF-07304814 in complex with Mpros of various coronaviruses reveal their inhibitory mechanisms against different Mpros. However, the structural information on the lower pathogenic coronavirus Mpro with PF-07321332 or PF-07304814 is currently scarce, which hinders our comprehensive understanding of the inhibitory mechanisms of these two inhibitors. Meanwhile, given that some immunocompromised individuals are still affected by low pathogenic coronaviruses, we determined the structures of lower pathogenic coronavirus HCoV-229E Mpro with PF-07321332 and PF-07304814, respectively, and analyzed and defined in detail the structural basis for the inhibition of HCoV-229E Mpro by both inhibitors. Further, we compared the crystal structures of multiple coronavirus Mpro complexes with PF-07321332 or PF-07304814 to illustrate the differences in the interaction of Mpros, and found that the inhibition mechanism of lower pathogenic coronavirus Mpro was more similar to that of moderately pathogenic coronaviruses. Our structural studies provide new insights into drug development for low pathogenic coronavirus Mpro, and provide theoretical basis for further optimization of both inhibitors to contain potential future coronaviruses.
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Affiliation(s)
- Yanru Zhou
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Weiwei Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Pei Zeng
- Shenzhen Crystalo Biopharmaceutical Co, Ltd, Shenzhen, 518118, China; Jiangxi Jmerry Biopharmaceutical Co, Ltd, Ganzhou, 341000, China
| | - Jingwen Feng
- Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China
| | - Dongyang Li
- Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China
| | - Yue Jing
- Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China
| | - Jin Zhang
- Shenzhen Crystalo Biopharmaceutical Co, Ltd, Shenzhen, 518118, China
| | - Xiushan Yin
- Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Heyang Ye
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China.
| | - Qisheng Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China; Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.
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12
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Lim CP, Kok BH, Lim HT, Chuah C, Abdul Rahman B, Abdul Majeed AB, Wykes M, Leow CH, Leow CY. Recent trends in next generation immunoinformatics harnessed for universal coronavirus vaccine design. Pathog Glob Health 2023; 117:134-151. [PMID: 35550001 PMCID: PMC9970233 DOI: 10.1080/20477724.2022.2072456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally devastated public health, the economies of many countries and quality of life universally. The recent emergence of immune-escaped variants and scenario of vaccinated individuals being infected has raised the global concerns about the effectiveness of the current available vaccines in transmission control and disease prevention. Given the high rate mutation of SARS-CoV-2, an efficacious vaccine targeting against multiple variants that contains virus-specific epitopes is desperately needed. An immunoinformatics approach is gaining traction in vaccine design and development due to the significant reduction in time and cost of immunogenicity studies and increasing reliability of the generated results. It can underpin the development of novel therapeutic methods and accelerate the design and production of peptide vaccines for infectious diseases. Structural proteins, particularly spike protein (S), along with other proteins have been studied intensively as promising coronavirus vaccine targets. Numbers of promising online immunological databases, tools and web servers have widely been employed for the design and development of next generation COVID-19 vaccines. This review highlights the role of immunoinformatics in identifying immunogenic peptides as potential vaccine targets, involving databases, and prediction and characterization of epitopes which can be harnessed for designing future coronavirus vaccines.
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Affiliation(s)
- Chin Peng Lim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia.,Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Boon Hui Kok
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Hui Ting Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Candy Chuah
- Faculty of Health Sciences, Universiti Teknologi MARA, Penang, Malaysia
| | | | | | - Michelle Wykes
- Molecular Immunology Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia
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13
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Antiviral effects of Korean Red Ginseng on human coronavirus OC43. J Ginseng Res 2023; 47:329-336. [PMID: 36217314 PMCID: PMC9534539 DOI: 10.1016/j.jgr.2022.09.009] [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: 08/03/2022] [Revised: 09/15/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022] Open
Abstract
Background Panax ginseng Meyer is a medicinal plant well-known for its antiviral activities against various viruses, but its antiviral effect on coronavirus has not yet been studied thoroughly. The antiviral activity of Korean Red Ginseng (KRG) and ten ginsenosides against Human coronavirus OC43 (HCoV-OC43) was investigated in vitro. Methods The antiviral response and mechanism of action of KRG extract and ginsenoside Rc, Re, Rf, Rg1, Rg2-20 (R) and -20 (S), Rg3-20 (R) and -20 (S), and Rh2-20 (R) and -20 (S), against the human coronavirus strain OC43 were investigated by using plaque assay, time of addition assay, real-time PCR, and FACS analysis. Results Virus plaque formation was reduced in KRG extract-treated and HCoV-OC43-infected HCT-8 cells. KRG extract decreased the viral proteins (Nucleocapsid protein and Spike protein) and mRNA (N and M gene) expression, while increased the expression of interferon genes. Conclusion KRG extract exhibits antiviral activity by enhancing the expression of interferons and can be used in treating infections caused by HCoV-OC43.
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14
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Sayama Y, Okamoto M, Saito M, Saito-Obata M, Tamaki R, Joboco CD, Lupisan S, Oshitani H. Seroprevalence of four endemic human coronaviruses and, reactivity and neutralization capability against SARS-CoV-2 among children in the Philippines. Sci Rep 2023; 13:2310. [PMID: 36759702 PMCID: PMC9909632 DOI: 10.1038/s41598-023-29072-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Four endemic human coronaviruses (HCoV), HCoV-229E, HCoV-NL63, HCoV-HKU1, and HCoV-OC43, are closely related to SARS-CoV-2. These coronaviruses are known to infect humans living in temperate areas, including children under 5 years old; however, the seroprevalence of four HCoVs among children in tropical areas, including the Philippines, remains unclear. This study aimed to assess the prevalence of antibodies against four HCoVs and to determine the reactivity and neutralization of these antibodies against SARS-CoV-2 among children in the Philippines. A total of 315 serum samples collected from 2015 to 2018, before the emergence of SARS-CoV-2, in Biliran island, Philippines, were tested for the presence of antibodies against four HCoVs and SARS-CoV-2 using recombinant spike ectodomain proteins by IgG-enzyme-linked immunosorbent assay (ELISA). Reactivity to and neutralization of SARS-CoV-2 were also investigated. The seroprevalence of the four HCoVs was 63.8% for HCoV-229E, 71.4% for HCoV-NL63, 76.5% for HCoV-HKU1, and 83.5% for HCoV-OC43 by ELISA. Age group analysis indicated that seropositivity to all HCoVs reached 80% by 2-3 years of age. While 69/315 (21.9%) of the samples showed reactive to SARS-CoV-2, almost no neutralization against SARS-CoV-2 was detected using neutralization assay. Reactivity of antibodies against SARS-CoV-2 spike protein obtained by ELISA may not correlate with neutralization capability.
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Affiliation(s)
- Yusuke Sayama
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan.
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Mariko Saito-Obata
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Raita Tamaki
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | | | - Socorro Lupisan
- Research Institute for Tropical Medicine, Metro Manila, Philippines
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
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15
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Human Coronavirus Cell Receptors Provide Challenging Therapeutic Targets. Vaccines (Basel) 2023; 11:vaccines11010174. [PMID: 36680018 PMCID: PMC9862439 DOI: 10.3390/vaccines11010174] [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: 12/02/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Coronaviruses interact with protein or carbohydrate receptors through their spike proteins to infect cells. Even if the known protein receptors for these viruses have no evolutionary relationships, they do share ontological commonalities that the virus might leverage to exacerbate the pathophysiology. ANPEP/CD13, DPP IV/CD26, and ACE2 are the three protein receptors that are known to be exploited by several human coronaviruses. These receptors are moonlighting enzymes involved in several physiological processes such as digestion, metabolism, and blood pressure regulation; moreover, the three proteins are expressed in kidney, intestine, endothelium, and other tissues/cell types. Here, we spot the commonalities between the three enzymes, the physiological functions of the enzymes are outlined, and how blocking either enzyme results in systemic deregulations and multi-organ failures via viral infection or therapeutic interventions is addressed. It can be difficult to pinpoint any coronavirus as the target when creating a medication to fight them, due to the multiple processes that receptors are linked to and their extensive expression.
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16
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Li Q, Shah T, Wang B, Qu L, Wang R, Hou Y, Baloch Z, Xia X. Cross-species transmission, evolution and zoonotic potential of coronaviruses. Front Cell Infect Microbiol 2023; 12:1081370. [PMID: 36683695 PMCID: PMC9853062 DOI: 10.3389/fcimb.2022.1081370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
Coronaviruses (CoVs) continuously evolve, crossing species barriers and spreading across host ranges. Over the last two decades, several CoVs (HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2) have emerged in animals and mammals, causing significant economic and human life losses. Due to CoV cross-species transmission and the evolution of novel viruses, it is critical to identify their natural reservoiurs and the circumstances under which their transmission occurs. In this review, we use genetic and ecological data to disentangle the evolution of various CoVs in wildlife, humans, and domestic mammals. We thoroughly investigate several host species and outline the epidemiology of CoVs toward specific hosts. We also discuss the cross-species transmission of CoVs at the interface of wildlife, animals, and humans. Clarifying the epidemiology and diversity of species reservoirs will significantly impact our ability to respond to the future emergence of CoVs in humans and domestic animals.
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Affiliation(s)
- Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China,The First Affiliated Hospital & Clinical Medical College, Dali University, Dali, Yunnan, China
| | - Taif Shah
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Linyu Qu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Rui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China,*Correspondence: Xueshan Xia,
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17
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Kaushik NK, Bhartiya P, Kaushik N, Shin Y, Nguyen LN, Park JS, Kim D, Choi EH. Nitric-oxide enriched plasma-activated water inactivates 229E coronavirus and alters antiviral response genes in human lung host cells. Bioact Mater 2023; 19:569-580. [PMID: 35574062 PMCID: PMC9080223 DOI: 10.1016/j.bioactmat.2022.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/20/2022] [Accepted: 05/03/2022] [Indexed: 12/18/2022] Open
Abstract
The ongoing pandemic caused by the novel coronavirus, SARS-CoV-2, is influencing global health. Moreover, there is a major threat of future coronaviruses affecting the entire world in a similar, or even more dreadful, manner. Therefore, effective and biocompatible therapeutic options against coronaviruses are urgently needed. To address this challenge, medical specialists require a well-informed and safe approach to treating human coronaviruses (HCoVs). Herein, an environmental friendly approach for viral inactivation, based on plasma technology, was considered. A microwave plasma system was employed for the generation of the high amount of gaseous nitric oxide to prepare nitric oxide enriched plasma-activated water (NO-PAW), the effects of which on coronaviruses, have not been reported to date. To determine these effects, alpha-HCoV-229E was used in an experimental model. We found that NO-PAW treatment effectively inhibited coronavirus infection in host lung cells, visualized by evaluating the cytopathic effect and expression level of spike proteins. Interestingly, NO-PAW showed minimal toxicity towards lung host cells, suggesting its potential for therapeutic application. Moreover, this new approach resulted in viral inactivation and greatly improved the gene levels involved in host antiviral responses. Together, our findings provide evidence of an initiation point for further progress toward the clinical development of antiviral treatments, including such coronaviruses.
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Affiliation(s)
- Nagendra Kumar Kaushik
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Pradeep Bhartiya
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong-si, 18323, Republic of Korea
| | - Yungoh Shin
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Linh Nhat Nguyen
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Jang Sick Park
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Doyoung Kim
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Eun Ha Choi
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul, 01897, Republic of Korea
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18
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Pasquereau S, Galais M, Bellefroid M, Pachón Angona I, Morot-Bizot S, Ismaili L, Van Lint C, Herbein G. Ferulic acid derivatives block coronaviruses HCoV-229E and SARS-CoV-2 replication in vitro. Sci Rep 2022; 12:20309. [PMID: 36434137 PMCID: PMC9700709 DOI: 10.1038/s41598-022-24682-9] [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: 12/01/2021] [Accepted: 11/18/2022] [Indexed: 11/27/2022] Open
Abstract
A novel coronavirus, SARS-CoV-2, emerged in China at the end of 2019 causing a large global outbreak. As treatments are of the utmost importance, drugs with broad anti-coronavirus activity embody a rich and rapid drug discovery landscape, where candidate drug compounds could be identified and optimized. To this end, we tested ten small-molecules with chemical structures close to ferulic acid derivatives (FADs) (n = 8), caffeic acid derivatives (CAFDs) (n = 1) and carboxamide derivatives (CAMDs) (n = 1) for their ability to reduce HCoV-229E replication, another member of the coronavirus family. Among these ten drugs tested, five of them namely MBA112, MBA33, MBA27-1, OS4-1 and MBA108-1 were highly cytotoxic and did not warrant further testing. In contrast, we observed a moderate cytotoxicity for two of them, MBA152 and 5c. Three drugs, namely MBA140, LIJ2P40, and MBA28 showed lower cytotoxicity. These candidates were then tested for their antiviral propreties against HCoV-229E and SARS-CoV2 replication. We first observed encouraging results in HCoV-229E. We then measured a reduction of the viral SARS-CoV2 replication by 46% with MBA28 (EC50 > 200 µM), by 58% with MBA140 (EC50 = 176 µM), and by 82% with LIJ2P40 (EC50 = 66.5 µM). Overall, the FAD LIJ2P40 showed a reduction of the viral titer on SARS-CoV-2 up to two logs with moderate cytotoxicity which opens the door to further evaluation to fight Covid-19.
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Affiliation(s)
- Sébastien Pasquereau
- grid.7459.f0000 0001 2188 3779Pathogens and Inflammation/EPILAB Laboratory, EA 4266, Université de Franche-Comté, Université Bourgogne Franche-Comté (UBFC), Besançon, France
| | - Mathilde Galais
- grid.4989.c0000 0001 2348 0746Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Maxime Bellefroid
- grid.4989.c0000 0001 2348 0746Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Irene Pachón Angona
- grid.493090.70000 0004 4910 6615Neurosciences Intégratives et Cliniques EA 481, Pôle de Chimie Organique et Thérapeutique, Univ. Bourgogne Franche-Comté, UFR Santé, Besançon, France
| | | | - Lhassane Ismaili
- grid.493090.70000 0004 4910 6615Neurosciences Intégratives et Cliniques EA 481, Pôle de Chimie Organique et Thérapeutique, Univ. Bourgogne Franche-Comté, UFR Santé, Besançon, France
| | - Carine Van Lint
- grid.4989.c0000 0001 2348 0746Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Georges Herbein
- grid.7459.f0000 0001 2188 3779Pathogens and Inflammation/EPILAB Laboratory, EA 4266, Université de Franche-Comté, Université Bourgogne Franche-Comté (UBFC), Besançon, France ,grid.411158.80000 0004 0638 9213Department of Virology, CHU Besançon, Besançon, France
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19
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Wang X, Tang G, Liu Y, Zhang L, Chen B, Han Y, Fu Z, Wang L, Hu G, Ma Q, Sheng S, Wang J, Hu X, Shao S. The role of IL-6 in coronavirus, especially in COVID-19. Front Pharmacol 2022; 13:1033674. [PMID: 36506506 PMCID: PMC9727200 DOI: 10.3389/fphar.2022.1033674] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/02/2022] [Indexed: 11/25/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infects both people and animals and may cause significant respiratory problems, including lung illness: Corona Virus Disease 2019 (COVID-19). Swabs taken from the throat and nose of people who have the illness or are suspected of having it have shown this pathogenic virus. When SARS-CoV-2 infects the upper and lower respiratory tracts, it may induce moderate to severe respiratory symptoms, as well as the release of pro-inflammatory cytokines including interleukin 6 (IL-6). COVID-19-induced reduction of IL-6 in an inflammatory state may have a hitherto undiscovered therapeutic impact. Many inflammatory disorders, including viral infections, has been found to be regulated by IL-6. In individuals with COVID-19, one of the primary inflammatory agents that causes inflammatory storm is IL-6. It promotes the inflammatory response of virus infection, including the virus infection caused by SARS-CoV-2, and provides a new diagnostic and therapeutic strategy. In this review article, we highlighted the functions of IL-6 in the coronavirus, especially in COVID-19, showing that IL-6 activation plays an important function in the progression of coronavirus and is a rational therapeutic goal for inflammation aimed at coronavirus.
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Affiliation(s)
- Xinyi Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Guozheng Tang
- Department of Orthopaedics, Lu’an Hospital of Anhui Medical University, Lu’an, Anhui, China
| | - Yuchen Liu
- Department of Otolaryngology, Head and Neck Surgery, The First Affifiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Lizhi Zhang
- First Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Bangjie Chen
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yanxun Han
- Department of Otolaryngology, Head and Neck Surgery, The First Affifiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Ziyue Fu
- Second Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Liuning Wang
- First Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Guangzhi Hu
- First Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Qing Ma
- First Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Shuyan Sheng
- First Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Jianpeng Wang
- First Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Xinyang Hu
- First Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Song Shao
- Department of Orthopaedics, Lu’an Hospital of Anhui Medical University, Lu’an, Anhui, China,*Correspondence: Song Shao,
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20
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Bonenfant G, Deyoe JE, Wong T, Grijalva CG, Cui D, Talbot HK, Hassell N, Halasa N, Chappell J, Thornburg NJ, Rolfes MA, Wentworth DE, Zhou B. Surveillance and Correlation of Severe Acute Respiratory Syndrome Coronavirus 2 Viral RNA, Antigen, Virus Isolation, and Self-Reported Symptoms in a Longitudinal Study With Daily Sampling. Clin Infect Dis 2022; 75:1698-1705. [PMID: 35442437 PMCID: PMC9213875 DOI: 10.1093/cid/ciac282] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/04/2022] [Indexed: 11/14/2022] Open
Abstract
The novel coronavirus pandemic incited unprecedented demand for assays that detect viral nucleic acids, viral proteins, and corresponding antibodies. The 320 molecular diagnostics in receipt of US Food and Drug Administration emergency use authorization mainly focus on viral detection; however, no currently approved test can be used to infer infectiousness, that is, the presence of replicable virus. As the number of tests conducted increased, persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA positivity by reverse-transcription polymerase chain reaction (RT-PCR) in some individuals led to concerns over quarantine guidelines. To this end, we attempted to design an assay that reduces the frequency of positive test results from individuals who do not shed culturable virus. We describe multiplex quantitative RT-PCR assays that detect genomic RNA (gRNA) and subgenomic RNA (sgRNA) species of SARS-CoV-2, including spike, nucleocapsid, membrane, envelope, and ORF8. Viral RNA abundances calculated from these assays were compared with antigen presence, self-reported symptoms, and culture outcome (virus isolation) using samples from a 14-day longitudinal household transmission study. By characterizing the clinical and molecular dynamics of infection, we show that sgRNA detection has higher predictive value for culture outcome compared to detection of gRNA alone. Our findings suggest that sgRNA presence correlates with active infection and may help identify individuals shedding culturable virus.
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Affiliation(s)
- Gaston Bonenfant
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Jessica E. Deyoe
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Terianne Wong
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Dan Cui
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- General Dynamics Information Technology, Inc, Falls Church, Virginia, USA
| | - H. Keipp Talbot
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Norman Hassell
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Natasha Halasa
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James Chappell
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Natalie J. Thornburg
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melissa A. Rolfes
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - David E. Wentworth
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Bin Zhou
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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21
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Semple SL, Alkie TN, Jenik K, Warner BM, Tailor N, Kobasa D, DeWitte-Orr SJ. More tools for our toolkit: The application of HEL-299 cells and dsRNA-nanoparticles to study human coronaviruses in vitro. Virus Res 2022; 321:198925. [PMID: 36115551 PMCID: PMC9474404 DOI: 10.1016/j.virusres.2022.198925] [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: 05/12/2022] [Revised: 08/31/2022] [Accepted: 09/08/2022] [Indexed: 12/24/2022]
Abstract
Human coronaviruses (HCoVs) are important human pathogens, as exemplified by the current SARS-CoV-2 pandemic. While the ability of type I interferons (IFNs) to limit coronavirus replication has been established, the ability of double-stranded (ds)RNA, a potent IFN inducer, to inhibit coronavirus replication when conjugated to a nanoparticle is largely unexplored. Additionally, the number of IFN competent cell lines that can be used to study coronaviruses in vitro are limited. In the present study, we show that poly inosinic: poly cytidylic acid (pIC), when conjugated to a phytoglycogen nanoparticle (pIC+NDX) is able to protect IFN-competent human lung fibroblasts (HEL-299 cells) from infection with different HCoV species. HEL-299 was found to be permissive to HCoV-229E, -OC43 and MERS-CoV-GFP but not to HCoV-NL63 or SARS-CoV-2. Further investigation revealed that HEL-299 does not contain the required ACE2 receptor to enable propagation of both HCoV-NL63 and SARS-CoV-2. Following 24h exposure, pIC+NDX was observed to stimulate a significant, prolonged increase in antiviral gene expression (IFNβ, CXCL10 and ISG15) when compared to both NDX alone and pIC alone. This antiviral response translated into complete protection against virus production, for 4 days or 7 days post treatment with HCoV-229E or -OC43 when either pre-treated for 6h or 24h respectively. Moreover, the pIC+NDX combination also provided complete protection for 2d post infection when HEL-299 cells were infected with MERS-CoV-GFP following a 24h pretreatment with pIC+NDX. The significance of this study is two-fold. Firstly, it was revealed that HEL-299 cells can effectively be used as an IFN-competent model system for in vitro analysis of MERS-CoV. Secondly, pIC+NDX acts as a powerful inducer of type I IFNs in HEL-299, to levels that provide complete protection against coronavirus replication. This suggests an exciting and novel area of investigation for antiviral therapies that utilize innate immune stimulants. The results of this study will help to expand the range of available tools scientists have to investigate, and thus further understand, human coronaviruses.
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Affiliation(s)
- Shawna L Semple
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Tamiru N Alkie
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Kristof Jenik
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Bryce M Warner
- Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Nikesh Tailor
- Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Darwyn Kobasa
- Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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22
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Kumar S, Basu M, Ghosh P, Ansari A, Ghosh MK. COVID-19: Clinical status of vaccine development to date. Br J Clin Pharmacol 2022; 89:114-149. [PMID: 36184710 PMCID: PMC9538545 DOI: 10.1111/bcp.15552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 11/30/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-induced COVID-19 is a complicated disease. Clinicians are continuously facing difficulties to treat infected patients using the principle of repurposing of drugs as no specific drugs are available to treat COVID-19. To minimize the severity and mortality, global vaccination is the only hope as a potential preventive measure. After a year-long global research and clinical struggle, 165 vaccine candidates have been developed and some are currently still in the pipeline. A total of 28 candidate vaccines have been approved for use and the remainder are in different phases of clinical trials. In this comprehensive report, the authors aim to demonstrate, classify and provide up-to-date clinical trial status of all the vaccines discovered to date and specifically focus on the approved candidates. Finally, the authors specifically focused on the vaccination of different types of medically distinct populations.
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Affiliation(s)
- Sunny Kumar
- Cancer Biology and Inflammatory Disorder DivisionCouncil of Scientific and Industrial Research‐Indian Institute of Chemical Biology (CSIR‐IICB), TRUE CampusKolkataIndia
| | - Malini Basu
- Department of MicrobiologyDhruba Chand Halder CollegeIndia
| | - Pratyasha Ghosh
- Department of Economics, Bethune CollegeUniversity of CalcuttaKolkataIndia
| | - Aafreen Ansari
- Cancer Biology and Inflammatory Disorder DivisionCouncil of Scientific and Industrial Research‐Indian Institute of Chemical Biology (CSIR‐IICB), TRUE CampusKolkataIndia
| | - Mrinal K. Ghosh
- Cancer Biology and Inflammatory Disorder DivisionCouncil of Scientific and Industrial Research‐Indian Institute of Chemical Biology (CSIR‐IICB), TRUE CampusKolkataIndia
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23
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Kumar V, Kumar S, Sharma PC. Recent advances in the vaccine development for the prophylaxis of SARS Covid-19. Int Immunopharmacol 2022; 111:109175. [PMID: 35994853 PMCID: PMC9381430 DOI: 10.1016/j.intimp.2022.109175] [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: 06/08/2022] [Revised: 08/08/2022] [Accepted: 08/14/2022] [Indexed: 12/14/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused Coronavirus Disease 2019 (COVID-19) is currently a global pandemic that has wreaked havoc on public health, lives, and the global economy. The present COVID-19 outbreak has put pressure on the scientific community to develop medications and vaccinations to combat COVID-19. However, according to highly optimistic forecasts, we could not have a COVID-19 vaccine until September 2020. This is due to the fact that a successful COVID-19 vaccine will necessitate a careful validation of effectiveness and adverse reactivity given that the target vaccine population includes high-risk people over 60, particularly those with severe co-morbid conditions, frontline healthcare professionals, and those involved in essential industrial sectors. For passive immunization, which is being considered for Covid-19, there are several platforms for vaccine development, each with its own advantages and disadvantages. The COVID-19 pandemic, which is arguably the deadliest in the last 100 years after the Spanish flu, necessitates a swift assessment of the various approaches for their ability to incite protective immunity and safety to prevent unintended immune potentiation, which is crucial to the pathogenesis of this virus. Considering the pandemic's high fatality rate and rapid spread, an efficient vaccination is critical for its management. As a result, academia, industry, and government are collaborating in unprecedented ways to create and test a wide range of vaccinations. In this review, we summarize the Covid-19 vaccine development initiatives, recent trends, difficulties, comparison between traditional vaccines development and Covid-19 vaccines development also listed the approved/authorized, phase-3 and pre-clinical trials Covid-19 vaccines in different countries.
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Affiliation(s)
- Vipul Kumar
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India
| | - Sahil Kumar
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India.
| | - Prabodh Chander Sharma
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India
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24
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Fielding BC. Editorial: Human coronavirus research: 20 years since the SARS-CoV outbreak. Front Microbiol 2022; 13:1035267. [PMID: 36212826 PMCID: PMC9540226 DOI: 10.3389/fmicb.2022.1035267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
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25
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Negru PA, Miculas DC, Behl T, Bungau AF, Marin RC, Bungau SG. Virtual screening of substances used in the treatment of SARS-CoV-2 infection and analysis of compounds with known action on structurally similar proteins from other viruses. Biomed Pharmacother 2022; 153:113432. [PMID: 36076487 PMCID: PMC9289048 DOI: 10.1016/j.biopha.2022.113432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/07/2022] [Accepted: 07/15/2022] [Indexed: 12/12/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is considered the etiological agent of the disease that caused the COVID-19 pandemic, and for which there is currently no effective treatment. This pandemic has shown that the rapid identification of therapeutic compounds is critical (when a new virus with high transmissibility occurs) to prevent or reduce as much as possible the loss of human lives. To meet the urgent need for drugs, many strategies were applied for the discovery, respectively the identification of potential therapies / drugs for SARS-CoV-2. Molecular docking and virtual screening are two of the in silico tools/techniques that provided the identification of few SARS-CoV-2 inhibitors, removing ineffective or less effective drugs and thus preventing the loss of resources such as time and additional costs. The main target of this review is to provide a comprehensive overview of how in-silico tools have been used in the crisis management of anti-SARS-CoV-2 drugs, especially in virtual screening of substances used in the treatment of SARS-CoV-2 infection and analysis of compounds with known action on structurally similar proteins from other viruses; also, completions were added to the way in which these methods came to meet the requirements of biomedical research in the field. Moreover, the importance and impact of the topic approached for researchers was highlighted by conducting an extensive bibliometric analysis.
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26
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Kiseleva I, Musaeva T, Ksenafontov A. SARS-CoV-2 Invasion: What Happens to Other Respiratory Viruses? Open Microbiol J 2022. [DOI: 10.2174/18742858-v16-e2206100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This letter briefly presents the relationships between respiratory viruses in the years prior to and during the COVID-19 pandemic. Viral common colds are self-limiting infections that typically resolve within a few days. However, when well-established epidemiological relationships are disrupted during a pandemic, they behave differently. For instance, during the 2009 influenza pandemic, while the majority of seasonal respiratory viruses lost ground under the pressure of a new pandemic strain, some others (for instance, human rhinoviruses) continued to circulate along with the pandemic pathogen and in some cases, even delayed its spread. With the arrival of the COVID-19 pandemic, the degree of circulation of many respiratory viruses has changed dramatically. Along with a significant reduction in the circulation of many seasonal respiratory pathogens, rhinoviruses, respiratory syncytial virus and non-COVID-19 coronaviruses—being the most frequently identified respiratory pathogens—have shown their unique capability to compete with SARS-CoV-2.
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27
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Rebendenne A, Roy P, Bonaventure B, Chaves Valadão AL, Desmarets L, Arnaud-Arnould M, Rouillé Y, Tauziet M, Giovannini D, Touhami J, Lee Y, DeWeirdt P, Hegde M, Urbach S, Koulali KE, de Gracia FG, McKellar J, Dubuisson J, Wencker M, Belouzard S, Moncorgé O, Doench JG, Goujon C. Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs. Nat Genet 2022; 54:1090-1102. [PMID: 35879413 DOI: 10.1038/s41588-022-01110-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 05/26/2022] [Indexed: 12/23/2022]
Abstract
CRISPR knockout (KO) screens have identified host factors regulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. Here, we conducted a meta-analysis of these screens, which showed a high level of cell-type specificity of the identified hits, highlighting the necessity of additional models to uncover the full landscape of host factors. Thus, we performed genome-wide KO and activation screens in Calu-3 lung cells and KO screens in Caco-2 colorectal cells, followed by secondary screens in four human cell lines. This revealed host-dependency factors, including AP1G1 adaptin and ATP8B1 flippase, as well as inhibitors, including mucins. Interestingly, some of the identified genes also modulate Middle East respiratory syndrome coronavirus (MERS-CoV) and seasonal human coronavirus (HCoV) (HCoV-NL63 and HCoV-229E) replication. Moreover, most genes had an impact on viral entry, with AP1G1 likely regulating TMPRSS2 activity at the plasma membrane. These results demonstrate the value of multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential targets for therapeutic interventions.
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Affiliation(s)
| | - Priyanka Roy
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Lowiese Desmarets
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - Yves Rouillé
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - Donatella Giovannini
- IGMM, CNRS, Montpellier University, Montpellier, France.,Metafora Biosystems, Paris, France
| | - Jawida Touhami
- IGMM, CNRS, Montpellier University, Montpellier, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Yenarae Lee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mudra Hegde
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Serge Urbach
- IGF, Montpellier University, CNRS, INSERM, Montpellier, France
| | | | | | - Joe McKellar
- IRIM, CNRS, Montpellier University, Montpellier, France
| | - Jean Dubuisson
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - Sandrine Belouzard
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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28
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Mahmood RA, Hasan A, Rahmatullah M, Paul AK, Jahan R, Jannat K, Bondhon TA, Mahboob T, Nissapatorn V, de Lourdes Pereira M, Paul TK, Rumi OH, Wiart C, Wilairatana P. Solanaceae Family Phytochemicals as Inhibitors of 3C-Like Protease of SARS-CoV-2: An In Silico Analysis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154739. [PMID: 35897915 PMCID: PMC9331421 DOI: 10.3390/molecules27154739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 11/24/2022]
Abstract
COVID-19, caused by the coronavirus SARS-CoV-2, emerged in late December 2019 in Wuhan, China. As of 8 April 2022, the virus has caused a global pandemic, resulting in 494,587,638 infections leading to 6,170,283 deaths around the world. Although several vaccines have received emergency authorization from USA and UK drug authorities and two more in Russia and China, it is too early to comment on the prolonged effectiveness of the vaccines, their availability, and affordability for the developing countries of the world, and the daunting task to vaccinate 7 billion people of the world with two doses of the vaccine with additional booster doses. As a result, it is still worthwhile to search for drugs and several promising leads have been found, mainly through in silico studies. In this study, we have examined the binding energies of several alkaloids and anthocyanin derivatives from the Solanaceae family, a family which contains common consumable vegetables and fruit items such as eggplant, pepper, and tomatoes. Our study demonstrates that Solanaceae family alkaloids such as incanumine and solaradixine, as well as anthocyanins and anthocyanidins, have very high predicted binding energies for the 3C-like protease of SARS-CoV-2 (also known as Mpro). Since Mpro is vital for SARS-CoV-2 replication, the compounds merit potential for further antiviral research towards the objective of obtaining affordable drugs.
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Affiliation(s)
- Raisul Awal Mahmood
- Department of Chemistry, Bangladesh University of Engineering & Technology, Dhaka 1000, Bangladesh;
| | - Anamul Hasan
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
| | - Mohammed Rahmatullah
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
- Correspondence: (M.R.); (M.d.L.P.)
| | - Alok K. Paul
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart, TAS 7001, Australia
| | - Rownak Jahan
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
| | - Khoshnur Jannat
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
| | - Tohmina Afroze Bondhon
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
| | - Tooba Mahboob
- School of Allied Health Sciences and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat 80160, Thailand; (T.M.); (V.N.)
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat 80160, Thailand; (T.M.); (V.N.)
| | - Maria de Lourdes Pereira
- Department of Medical Sciences, CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
- Correspondence: (M.R.); (M.d.L.P.)
| | - Tridib K. Paul
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
| | - Ommay Hany Rumi
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka 1207, Bangladesh; (A.H.); (A.K.P.); (R.J.); (K.J.); (T.A.B.); (T.K.P.); (O.H.R.)
| | - Christophe Wiart
- Institute for Tropical Biology and Conservation, Universiti Malaysia, Kota Kinabalu 88400, Sabah, Malaysia;
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
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29
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Xia S, Xia Y, Xiang C, Wang H, Wang C, He J, Shi G, Gu L. A virus–target host proteins recognition method based on integrated complexes data and seed extension. BMC Bioinformatics 2022; 23:256. [PMID: 35764916 PMCID: PMC9238269 DOI: 10.1186/s12859-022-04792-x] [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: 10/18/2021] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Target drugs play an important role in the clinical treatment of virus diseases. Virus-encoded proteins are widely used as targets for target drugs. However, they cannot cope with the drug resistance caused by a mutated virus and ignore the importance of host proteins for virus replication. Some methods use interactions between viruses and their host proteins to predict potential virus–target host proteins, which are less susceptible to mutated viruses. However, these methods only consider the network topology between the virus and the host proteins, ignoring the influences of protein complexes. Therefore, we introduce protein complexes that are less susceptible to drug resistance of mutated viruses, which helps recognize the unknown virus–target host proteins and reduce the cost of disease treatment.
Results
Since protein complexes contain virus–target host proteins, it is reasonable to predict virus–target human proteins from the perspective of the protein complexes. We propose a coverage clustering-core-subsidiary protein complex recognition method named CCA-SE that integrates the known virus–target host proteins, the human protein–protein interaction network, and the known human protein complexes. The proposed method aims to obtain the potential unknown virus–target human host proteins. We list part of the targets after proving our results effectively in enrichment experiments.
Conclusions
Our proposed CCA-SE method consists of two parts: one is CCA, which is to recognize protein complexes, and the other is SE, which is to select seed nodes as the core of protein complexes by using seed expansion. The experimental results validate that CCA-SE achieves efficient recognition of the virus–target host proteins.
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30
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The Cellular Characterization of SARS-CoV-2 Spike Protein in Virus-Infected Cells Using the Receptor Binding Domain Binding Specific Human Monoclonal Antibodies. J Virol 2022; 96:e0045522. [PMID: 35727030 PMCID: PMC9278116 DOI: 10.1128/jvi.00455-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A human monoclonal antibody panel (PD4, PD5, PD7, SC23, and SC29) was isolated from the B cells of convalescent patients and used to examine the S protein in SARS-CoV-2-infected cells. While all five antibodies bound conformational-specific epitopes within SARS-CoV-2 spike (S) protein, only PD5, PD7, and SC23 were able to bind to the receptor binding domain (RBD). Immunofluorescence microscopy was used to examine the S protein RBD in cells infected with the Singapore isolates SARS-CoV-2/0334 and SARS-CoV-2/1302. The RBD-binders exhibited a distinct cytoplasmic staining pattern that was primarily localized within the Golgi complex and was distinct from the diffuse cytoplasmic staining pattern exhibited by the non-RBD-binders (PD4 and SC29). These data indicated that the S protein adopted a conformation in the Golgi complex that enabled the RBD recognition by the RBD-binders. The RBD-binders also recognized the uncleaved S protein, indicating that S protein cleavage was not required for RBD recognition. Electron microscopy indicated high levels of cell-associated virus particles, and multiple cycle virus infection using RBD-binder staining provided evidence for direct cell-to-cell transmission for both isolates. Although similar levels of RBD-binder staining were demonstrated for each isolate, SARS-CoV-2/1302 exhibited slower rates of cell-to-cell transmission. These data suggest that a conformational change in the S protein occurs during its transit through the Golgi complex that enables RBD recognition by the RBD-binders and suggests that these antibodies can be used to monitor S protein RBD formation during the early stages of infection. IMPORTANCE The SARS-CoV-2 spike (S) protein receptor binding domain (RBD) mediates the attachment of SARS-CoV-2 to the host cell. This interaction plays an essential role in initiating virus infection, and the S protein RBD is therefore a focus of therapeutic and vaccine interventions. However, new virus variants have emerged with altered biological properties in the RBD that can potentially negate these interventions. Therefore, an improved understanding of the biological properties of the RBD in virus-infected cells may offer future therapeutic strategies to mitigate SARS- CoV-2 infection. We used physiologically relevant antibodies that were isolated from the B cells of convalescent COVID-19 patients to monitor the RBD in cells infected with SARS-CoV-2 clinical isolates. These immunological reagents specifically recognize the correctly folded RBD and were used to monitor the appearance of the RBD in SARS-CoV-2-infected cells and identified the site where the RBD first appears.
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31
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Ma M, Yang Y, Wu L, Zhou L, Shi Y, Han J, Xu Z, Zhu W. Conserved protein targets for developing pan-coronavirus drugs based on sequence and 3D structure similarity analyses. Comput Biol Med 2022; 145:105455. [PMID: 35364304 PMCID: PMC8957316 DOI: 10.1016/j.compbiomed.2022.105455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 11/23/2022]
Abstract
There are 7 known human pathogenic coronaviruses, which are HCoV-229E, HCoV-OC43, HCoV-NL63, HCoV-HKU1, MERS-CoV, SARS-CoV and SARS-CoV-2. While SARS-CoV-2 is currently caused a severe epidemic, experts believe that new pathogenic coronavirus would emerge in the future. Therefore, developing broad-spectrum anti-coronavirus drugs is of great significance. In this study, we performed protein sequence and three-dimensional structure analyses for all the 20 virus-encoded proteins across all the 7 coronaviruses, with the purpose to identify highly conserved proteins and binding sites for developing pan-coronavirus drugs. We found that nsp5, nsp10, nsp12, nsp13, nsp14, and nsp16 are highly conserved both in protein sequences (with average identity percentage higher than 52%, average amino acid conservation scores higher than 5.2) and binding pockets (with average amino acid conservation scores higher than 5.8). We also performed the similarity comparison between these 6 proteins and all the human proteins, and found that all the 6 proteins have similarity less than 25%, indicating that the drugs targeting the 6 proteins should have little interference of human protein function. Accordingly, we suggest that nsp5, nsp10, nsp12, nsp13, nsp14, and nsp16 are potential targets for pan-coronavirus drug development.
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Affiliation(s)
- Minfei Ma
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanqing Yang
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leyun Wu
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Zhou
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yulong Shi
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaxin Han
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210046, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Stake Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China.
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Eslami N, Aghbash PS, Shamekh A, Entezari-Maleki T, Nahand JS, Sales AJ, Baghi HB. SARS-CoV-2: Receptor and Co-receptor Tropism Probability. Curr Microbiol 2022; 79:133. [PMID: 35292865 PMCID: PMC8923825 DOI: 10.1007/s00284-022-02807-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 02/09/2022] [Indexed: 02/07/2023]
Abstract
The recent pandemic which arose from China, is caused by a pathogenic virus named "severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2)". Its rapid global expansion has inflicted an extreme public health concern. The attachment of receptor-binding domains (RBD) of the spike proteins (S) to the host cell's membrane, with or without the help of other cellular components such as proteases and especially co-receptors, is required for the first stage of its pathogenesis. In addition to humans, angiotensin-converting enzyme 2 (ACE2) is found on a wide range of vertebrate host's cellular surface. SARS-CoV-2 has a broad spectrum of tropism; thus, it can infect a vast range of tissues, organs, and hosts; even though the surface amino acids of the spike protein conflict in the receptor-binding region. Due to the heterogeneous ACE2 distribution and the presence of different domains on the SARS-CoV-2 spike protein for binding, the virus entry into diverse host cell types may depend on the host cells' receptor presentation with or without co-receptors. This review investigates multiple current types of receptor and co-receptor tropisms, with other molecular factors alongside their respective mechanisms, which facilitate the binding and entry of SARS-CoV-2 into the cells, extending the severity of the coronavirus disease 2019 (COVID-19). Understanding the pathogenesis of COVID-19 from this perspective can effectively help prevent this disease and provide more potent treatment strategies, particularly in vulnerable people with various cellular-level susceptibilities.
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Affiliation(s)
- Narges Eslami
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, 5166/15731, Tabriz, Iran
| | - Parisa Shiri Aghbash
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Shamekh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Taher Entezari-Maleki
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Sadri Nahand
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Jafari Sales
- Department of Microbiology School of Basic Sciences, Islamic Azad University, Kazerun BranchKazerun, Iran
| | - Hossein Bannazadeh Baghi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, 5166/15731, Tabriz, Iran.
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Tian S, Zheng N, Zu X, Wu G, Zhong J, Zhang J, Sheng L, Liu W, Wang C, Ge G, Han J, Zhao J, Li H, Zhang W. Integrated hepatic single-cell RNA sequencing and untargeted metabolomics reveals the immune and metabolic modulation of Qing-Fei-Pai-Du decoction in mice with coronavirus-induced pneumonia. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 97:153922. [PMID: 35032732 PMCID: PMC8720382 DOI: 10.1016/j.phymed.2021.153922] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/24/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Although Qing-Fei-Pai-Du decoction (QFPDD) is extensively used clinically to treat COVID-19 patients, the mechanism by which it modulates the immunological and metabolic functions of liver tissue remains unknown. PURPOSE The purpose of this study is to investigate the mechanism of action of QFPDD in the treatment of mice with coronavirus-induced pneumonia by combining integrated hepatic single-cell RNA sequencing and untargeted metabolomics. METHODS We developed a human coronavirus pneumonia model in BALB/c mice by infecting them with human coronavirus HCoV-229E with stimulating them with cold-damp environment. We initially assessed the status of inflammation and immunity in model mice treated with or without QFPDD by detecting peripheral blood lymphocytes and inflammatory cytokines. Then, single-cell RNA sequencing and untargeted metabolomics were performed on mouse liver tissue. RESULTS HCoV-229E infection in combination with exposure to a cold-damp environment significantly decreased the percentage of peripheral blood lymphocytes (CD4+ and CD8+ T cells, B cells) in mice, which was enhanced by QFPDD therapy. Meanwhile, the levels of inflammatory cytokines such as IL-6, TNF-α, and IFN-γ were significantly increased in mouse models but significantly decreased by QFPDD treatment. Single-cell RNA sequencing analysis showed that QFPDD could attenuate disease-associated alterations in gene expression, core transcriptional regulatory networks, and cell-type composition. Computational predictions indicated that QFPDD rectified the observed aberrant patterns of cell-cell communication. Additionally, the metabolic profiles of liver tissue in the Model group were distinct from mice in the Control group, and QFPDD significantly regulated hepatic purine metabolism. CONCLUSION To the best of our knowledge, this study is the first to integrate hepatic single-cell RNA sequencing and untargeted metabolomics into a TCM formula and these valuable findings indicate that QFPDD can improve immune function and reduce liver injury and inflammation.
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Affiliation(s)
- Saisai Tian
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Ningning Zheng
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xianpeng Zu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Gaosong Wu
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jing Zhong
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Huzhou 313000, China
| | - Jinbo Zhang
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China; Department of Pharmacy, Tianjin Rehabilitation and Recuperation Center, Joint Logistics Support Force, Tianjin, China
| | - Lili Sheng
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wei Liu
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Chaoran Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guangbo Ge
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jingyan Han
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Jing Zhao
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Houkai Li
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Weidong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China; The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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Liu M, Littler DR, Rossjohn J, Quinn RJ. Binding Studies of the Prodrug HAO472 to SARS-Cov-2 Nsp9 and Variants. ACS OMEGA 2022; 7:7327-7332. [PMID: 35224406 PMCID: PMC8862745 DOI: 10.1021/acsomega.1c07186] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2 (COVID-19) has infected over 219 million people and caused the death of over 4.55 million worldwide. In a previous screen of a natural product library against purified SARS-CoV-2 Nsp9 using a native mass spectrometry-based approach, we identified an ent-kaurane natural product, oridonin (1), with micromolar affinities. In this work, we have found that the prodrug HAO472 (2) directly binds to Nsp9, establishing replacement of the labile ester with a bioisostere as a candidate drug strategy. We further tested 1 and its clinical analogue 2 against two Nsp9 variants from human coronavirus 229E (HCoV-229E) and ferret systemic coronavirus F56 (FSCoV-F56). Both compounds showed significant binding selectivity to COVID-19 and HCoV-229E Nsp9 over FSCoV-F56 Nsp9, confirming the covalent bond with Cys73.
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Affiliation(s)
- Miaomiao Liu
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
| | - Dene R. Littler
- Infection
and Immunity Program & Department of Biochemistry and Molecular
Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Jamie Rossjohn
- Infection
and Immunity Program & Department of Biochemistry and Molecular
Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
- Institute
of Infection and Immunity, Cardiff University
School of Medicine, Heath
Park, Cardiff CF14 4XN, United Kingdom
| | - Ronald J Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
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Lohrasbi-Nejad A. Detection of homologous recombination events in SARS-CoV-2. Biotechnol Lett 2022; 44:399-414. [PMID: 35037234 PMCID: PMC8761517 DOI: 10.1007/s10529-021-03218-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 12/07/2021] [Indexed: 12/11/2022]
Abstract
PURPOSE The COVID-19 disease with acute respiratory symptoms emerged in 2019. The causal agent of the disease, the SARS-CoV-2 virus, is classified into the Betacoronaviruses family. Coronaviruses (CoVs) are a huge family of viruses. Therefore, homologous recombination studies can help recognize the phylogenetic relationships among these viruses. METHODS In order to detect possible recombination events in SASRS-CoV-2, the genome sequences of Betacoronaviruses were obtained from the GenBank. The nucleotide sequences with the identity ≥ 60% to SARS-CoV-2 genome sequence were selected and then analyzed using different algorithms. RESULTS The results showed two recombination events at the beginning and the end of the genome sequence of SARS-CoV-2. Bat-SL-CoVZC21 (GenBank accession number MG772934) was specified as the minor parent for both events with p-values of 8.66 × 10-87 and 3.29 × 10-48, respectively. Furthermore, two recombination regions were detected at the beginning and the middle of the SARS-CoV-2 spike gene. Pangolin-CoV (PCoV_GX-P4L) and Rattus CoV (ChRCoV-HKU24) were determined as the potential parents with the GenBank accession number MT040333 and KM349742, respectively. Analysis of the spike gene revealed more similarity and less nucleotide diversity between SARS-CoV-2 and pangolin-CoVs. CONCLUSION Detection of the ancestors of SARS-CoV-2 in the coronaviruses family can help identify and define the phylogenetic relationships of the family Coronaviridae. Furthermore, constructing a phylogenetic tree based on the recombination regions made changes in the phylogenetic relationships of Betacoronaviruses.
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Affiliation(s)
- Azadeh Lohrasbi-Nejad
- Department of Agricultural Biotechnology, Shahid Bahonar University of Kerman, Kerman, Iran.
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36
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Augustine R, S A, Nayeem A, Salam SA, Augustine P, Dan P, Maureira P, Mraiche F, Gentile C, Hansbro PM, McClements L, Hasan A. Increased complications of COVID-19 in people with cardiovascular disease: Role of the renin-angiotensin-aldosterone system (RAAS) dysregulation. Chem Biol Interact 2022; 351:109738. [PMID: 34740598 PMCID: PMC8563522 DOI: 10.1016/j.cbi.2021.109738] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/19/2021] [Accepted: 11/01/2021] [Indexed: 01/28/2023]
Abstract
The rapid spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19), has had a dramatic negative impact on public health and economies worldwide. Recent studies on COVID-19 complications and mortality rates suggest that there is a higher prevalence in cardiovascular diseases (CVD) patients. Past investigations on the associations between pre-existing CVDs and susceptibility to coronavirus infections including SARS-CoV and the Middle East Respiratory Syndrome coronavirus (MERS-CoV), have demonstrated similar results. However, the underlying mechanisms are poorly understood. This has impeded adequate risk stratification and treatment strategies for CVD patients with SARS-CoV-2 infections. Generally, dysregulation of the expression of angiotensin-converting enzyme (ACE) and the counter regulator, angiotensin-converting enzyme 2 (ACE2) is a hallmark of cardiovascular risk and CVD. ACE2 is the main host receptor for SARS-CoV-2. Although further studies are required, dysfunction of ACE2 after virus binding and dysregulation of the renin-angiotensin-aldosterone system (RAAS) signaling may worsen the outcomes of people affected by COVID-19 and with preexisting CVD. Here, we review the current knowledge and outline the gaps related to the relationship between CVD and COVID-19 with a focus on the RAAS. Improved understanding of the mechanisms regulating viral entry and the role of RAAS may direct future research with the potential to improve the prevention and management of COVID-19.
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Affiliation(s)
- Robin Augustine
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, 2713, Doha, Qatar; Biomedical Research Center (BRC), Qatar University, PO Box 2713, Doha, Qatar.
| | - Abhilash S
- Department of Microbiology, Majlis Arts and Science College, Puramannur, Malappuram, Kerala, 676552, India
| | - Ajisha Nayeem
- Department of Biotechnology, St. Mary's College, Thrissur, 680020, Kerala, India
| | - Shaheen Abdul Salam
- Department of Biosciences, MES College Marampally, Aluva, Ernakulam, 683107, Kerala, India
| | - Priya Augustine
- Department of Zoology, Kongunadu Arts and Science College, Coimbatore, Tamil Nadu, 641029, India
| | - Pan Dan
- Department of Cardiovascular and Transplantation Surgery, Regional Central Hospital of Nancy, Lorraine University, France; Department of Thoracic and Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Pablo Maureira
- Department of Cardiovascular and Transplantation Surgery, Regional Central Hospital of Nancy, Lorraine University, France
| | - Fatima Mraiche
- College of Pharmacy, QU-Health, Qatar University, PO Box 2713, Doha, Qatar
| | - Carmine Gentile
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, NSW, Australia; School of Medicine, Faculty of Medicine and Health, University of Sydney, NSW, Australia; Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, NSW, Australia; School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia
| | - Lana McClements
- School of Life Sciences, Faculty of Science, University of Technology Sydney, NSW, Australia
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, 2713, Doha, Qatar; Biomedical Research Center (BRC), Qatar University, PO Box 2713, Doha, Qatar.
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Mandala WL, Liu MKP. SARS-CoV-2 and HIV-1: Should HIV-1-Infected Individuals in Sub-Saharan Africa Be Considered a Priority Group for the COVID-19 Vaccines? Front Immunol 2021; 12:797117. [PMID: 34858440 PMCID: PMC8630634 DOI: 10.3389/fimmu.2021.797117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 12/23/2022] Open
Abstract
Since its emergence in 2019 SARS-CoV-2 has proven to have a higher level of morbidity and mortality compared to the other prevailing coronaviruses. Although initially most African countries were spared from the devastating effect of SARS-CoV-2, at present almost every country has been affected. Although no association has been established between being HIV-1-infected and being more vulnerable to contracting COVID-19, HIV-1-infected individuals have a greater risk of developing severe COVID-19 and of COVID-19 related mortality. The rapid development of the various types of COVID-19 vaccines has gone a long way in mitigating the devastating effects of the virus and has controlled its spread. However, global vaccine deployment has been uneven particularly in Africa. The emergence of SARS-CoV-2 variants, such as Beta and Delta, which seem to show some subtle resistance to the existing vaccines, suggests COVID-19 will still be a high-risk infection for years. In this review we report on the current impact of COVID-19 on HIV-1-infected individuals from an immunological perspective and attempt to make a case for prioritising COVID-19 vaccination for those living with HIV-1 in Sub-Saharan Africa (SSA) countries like Malawi as one way of minimising the impact of COVID-19 in these countries.
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Affiliation(s)
- Wilson Lewis Mandala
- Academy of Medical Sciences, Malawi University of Science and Technology (MUST), Thyolo, Malawi
| | - Michael K. P. Liu
- Centre for Immunology and Vaccinology, Department of Infectious Disease, Imperial College London, London, United Kingdom
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El-Senousy WM, Shouman M. Human Coronavirus NL63 Among Other Respiratory Viruses in Clinical Specimens of Egyptian Children and Raw Sewage Samples. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:322-328. [PMID: 34086254 PMCID: PMC8176886 DOI: 10.1007/s12560-021-09479-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
The objective of this study was to investigate human coronavirus NL63 (HCoV-NL63) prevalence among the other respiratory viruses such as parainfluenza, respiratory syncytial virus, and non-enteric adenoviruses in clinical specimens of Egyptian children and raw sewage samples. One hundred clinical specimens were collected from Egyptian children suffering from upper and lower respiratory viral infections in the years 2005-2006 to detect HCoV-NL63 genome using RT-PCR. All the specimens were negative for the virus. Also, a complete absence of HCoV-NL63 genome was observed in the twenty-four raw sewage samples collected from two wastewater treatment plants within Greater Cairo from February 2006 to January 2007. Using nested RT-PCR, parainfluenza virus type 1, respiratory syncytial virus type A, adenovirus type 4, and adenovirus type 7 were detected in 3%, 2%, 5%, and 2% of the clinical specimens, respectively. Of these viruses, only adenovirus type 4 was detected in 1/24 (4.17%) of the raw sewage samples, while a complete absence of the other investigated respiratory viruses was observed in the raw sewage samples. The low percentage of positivity in the clinical specimens, the concentration method of the raw sewage samples, and the indirect routes of transmission may be the reasons for the absence of respiratory viruses in raw sewage samples. On the other hand, enteric adenoviruses were detected in 21/24 (87.5%) of the raw sewage samples with a higher prevalence of adenovirus type 41 than adenovirus type 40. A direct route of transmission of enteric viruses to raw sewage may be the reason for the high positivity percentage of enteric adenoviruses in raw sewage samples.
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Affiliation(s)
- Waled Morsy El-Senousy
- Environmental Virology Lab, Water Pollution Research Department, Environmental Research Division and Food-Borne Viruses Group, Centre of Excellence for Advanced Sciences, National Research Centre (NRC), 33 El-Buhouth st., Dokki, Giza, 12622, Egypt.
| | - Mohamed Shouman
- Pediatric Department, Centre of Medical Excellence, Medical Research Division, NRC, Dokki, Giza, Egypt
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Sekharan S, Liu X, Yang Z, Liu X, Deng L, Ruan S, Abramov Y, Sun G, Li S, Zhou T, Shi B, Zeng Q, Zeng Q, Chang C, Jin Y, Shi X. Selecting a stable solid form of remdesivir using microcrystal electron diffraction and crystal structure prediction. RSC Adv 2021; 11:17408-17412. [PMID: 35479679 PMCID: PMC9033196 DOI: 10.1039/d1ra03100g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 12/20/2022] Open
Abstract
Therapeutic options in response to the coronavirus disease 2019 (COVID-19) outbreak are urgently needed. In this communication, we demonstrate how to support selection of a stable solid form of an antiviral drug remdesivir in quick time using the microcrystal electron diffraction (MicroED) technique and a cloud-based and artificial intelligence implemented crystal structure prediction platform. We present the MicroED structures of remdesivir forms II and IV and conclude that form II is more stable than form IV at ambient temperature in agreement with experimental observations. The combined experimental and theoretical study can serve as a template for formulation scientists in the pharmaceutical industry.
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Affiliation(s)
| | - Xuetao Liu
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Zhuocen Yang
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Xiang Liu
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Li Deng
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Shigang Ruan
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Yuriy Abramov
- XtalPi Inc. 245 Main St, Floor 11 Cambridge MA 02142 USA
| | - GuangXu Sun
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Sizhu Li
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Tian Zhou
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Baime Shi
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Qun Zeng
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Qiao Zeng
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Chao Chang
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Yingdi Jin
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
| | - Xuekun Shi
- Jingtai Technology Co. Ltd Floor 4, No. 9, Yifenghua Industrial Zone, 91 Huaning Road, Longhua District Shenzhen Guangdong Province 518109 China
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El-Sayed A, Kamel M. Coronaviruses in humans and animals: the role of bats in viral evolution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:19589-19600. [PMID: 33655480 PMCID: PMC7924989 DOI: 10.1007/s11356-021-12553-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/14/2021] [Indexed: 04/15/2023]
Abstract
Bats act as a natural reservoir for many viruses, including coronaviruses, and have played a crucial epidemiological role in the emergence of many viral diseases. Coronaviruses have been known for 60 years. They are usually responsible for the induction of mild respiratory signs in humans. However, since 2002, the bat-borne virus started to induce fatal epidemics according to WHO reports. In this year, the first serious human coronavirus epidemic (severe acute respiratory syndrome; SARS) occurred (China, 8098 cases, 774 deaths [9.5% of the cases] in 17 countries). The case fatality was higher in elderly patients above 60 years and reached 50% of the cases. SARS epidemic was followed 10 years later by the emergence of the middle east respiratory syndrome (MERS) in Saudi Arabia (in 2012, 2260 cases, 803 deaths [35.5% of the cases] in 27 countries). Finally, in December 2019, a new epidemic in Wuhan, China, (corona virus disease 2019, COVID-19) emerged and could spread to 217 countries infecting more than 86,255,226 cases and killing 1,863,973 people by the end of 2020. There are many reasons why bats are ideal reservoir hosts for viral diseases such as the tolerance of their immune system to the invading viruses for several months. They can actively shed the viruses, although they develop no clinical signs (will be discussed in details later in the review). Bats were directly or indirectly involved in the three previous coronavirus epidemics. The indirect transmission takes place via intermediate hosts including civet cats for SARS and dromedary camels in the case of MERS. Although bats are believed to be the source of COVID-19 pandemic, direct pieces of evidence are still lacking. Therefore, coronaviruses' role in epidemics induction and the epidemiological role of bats are discussed. The current work also presents different evidence (phylogenetic data, animal experiments, bats artificial infection studies, and computerized models of SARS-CoV2 evolution) that underline the involvement of bats in the epidemiology of the pandemic.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Medicine and Infectious Diseases, Cairo University, Giza, 12211, Egypt
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Medicine and Infectious Diseases, Cairo University, Giza, 12211, Egypt.
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Tonelli M, Rienstra C, Anderson TK, Kirchdoerfer R, Henzler-Wildman K. 1H, 13C, and 15N backbone and side chain chemical shift assignments of the SARS-CoV-2 non-structural protein 7. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:73-77. [PMID: 33219414 PMCID: PMC7678775 DOI: 10.1007/s12104-020-09985-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/12/2020] [Indexed: 06/11/2023]
Abstract
The SARS-CoV-2 genome encodes for approximately 30 proteins. Within the international project covid19-nmr, we distribute the spectroscopic analysis of the viral proteins and RNA. Here, we report NMR chemical shift assignments for the protein nsp7. The 83 amino acid nsp7 protein is an essential cofactor in the RNA-dependent RNA polymerase. The polymerase activity and processivity of nsp12 are greatly enhanced by binding 1 copy of nsp7 and 2 copies of nsp8 to form a 160 kD complex. A separate hexadecameric complex of nsp7 and nsp8 (8 copies of each) forms a large ring-like structure. Thus, nsp7 is an important component of several large protein complexes that are required for replication of the large and complex coronavirus genome. We here report the near-complete NMR backbone and sidechain resonance assignment (1H,13C,15N) of isolated nsp7 from SARS-CoV-2 in solution. Further, we derive the secondary structure and compare it to the previously reported assignments and structure of the SARS-CoV nsp7.
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Affiliation(s)
- Marco Tonelli
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin at Madison, Madison, WI, 53706, USA
| | - Chad Rienstra
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin at Madison, Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin at Madison, Madison, WI, 53706, USA
| | - Thomas K Anderson
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin at Madison, Madison, WI, 53706, USA
- Institute for Molecular Virology, University of Wisconsin at Madison, Madison, WI, 53706, USA
| | - Rob Kirchdoerfer
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin at Madison, Madison, WI, 53706, USA
- Institute for Molecular Virology, University of Wisconsin at Madison, Madison, WI, 53706, USA
| | - Katherine Henzler-Wildman
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin at Madison, Madison, WI, 53706, USA.
- Department of Biochemistry, University of Wisconsin at Madison, Madison, WI, 53706, USA.
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Koulgi S, Jani V, V N MU, Sonavane U, Joshi R. Structural insight into the binding interactions of NTPs and nucleotide analogues to RNA dependent RNA polymerase of SARS-CoV-2. J Biomol Struct Dyn 2021; 40:7230-7244. [PMID: 33682633 DOI: 10.1080/07391102.2021.1894985] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
RNA dependent RNA polymerase (RdRP) from positive-stranded RNA viruses has always been a hot target for designing of new drugs. Major class of drugs that are targeted against RdRP are nucleotide analogues. Extensive docking and molecular dynamics study describing the binding of natural nucleotides (NTPs) and its analogues leading to significant structural variation in the RdRP has been presented here. RdRP simulations in its apo, NTP-bound, and analogue-bound form have been performed. Nucleotide analogues included in this study were, favipiravir, galidesivir, lamivudine, ribavirin, remdesivir and sofosbuvir. The conformational flexibility of the RdRP molecule has been explored using principal component (PCA) and Markov state modeling (MSM) analysis. PCA inferred the presence of correlated motions among the conserved motifs of RdRP. Inter-domain distances between the finger and thumb subdomain flanking the nascent RNA template entry site sampled open and closed conformations. The ligand and template binding motifs F and G showed negatively correlated motions. K551, R553, and R555, a part of motif F appear to form strong interactions with the ligand molecules. R836, a primer binding residue was observed to strongly bind to the analogues. MSM analysis helped to extract statistically distinct conformations explored by the RdRP. Ensemble docking of the ligands on the Markov states also suggested the involvement of the above residues in ligand interactions. Markov states obtained clearly demarcated the open/closed conformations of the template entry site. These observations on residues from the conserved motifs involved in binding to the ligands may provide an insight into designing new inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shruti Koulgi
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
| | - Vinod Jani
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
| | - Mallikarjunachari Uppuladinne V N
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
| | - Uddhavesh Sonavane
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
| | - Rajendra Joshi
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
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Suchita W, Tilotma S, Saurabh S, Abhishek K, Sagar S, Lokesh K. Molecular Elucidation and Therapeutic Targeting for combating COVID19: Current Scenario and Future Prospective. Curr Mol Med 2021; 22:894-907. [PMID: 33535951 DOI: 10.2174/1566524021666210203113849] [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: 08/04/2020] [Revised: 11/03/2020] [Accepted: 11/08/2020] [Indexed: 11/22/2022]
Abstract
A corona virus disease 2019 (COVID-19) is a contagious disease which is caused by a novel corona virus. Human corona virus (HCoV) recognized as one of the most rapidly evolving viruses owing to its high genomic nucleotide substitution rates and recombination. Among the severe acute respiratory syndrome (SARS) and Middle-East respiratory syndrome (MERS), COVID-19 has spread more rapidly and increased the level of globalization and adaptation of the virus in every environmental condition due to their high rate of molecular diversity. The whole article highlights the general characteristics of corona virus, their molecular diversity, and molecular protein targeting against COVID-19 with their newer approaches. Through this review, an attempt has made to critically evaluate the recent advances and future aspects helpful to the treatment of COVID-19 based on the present understanding of SARS-CoV-2 infections, which may help offer new insights and potential therapeutic targets for the treatment of the COVID-19.
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Affiliation(s)
- Wamankar Suchita
- ShriRawatpura Sarkar Institute of Pharmacy, Kumhari, Durg,490042,Chhattisgarh. India
| | - Sahu Tilotma
- ShriRawatpura Sarkar Institute of Pharmacy, Kumhari, Durg,490042,Chhattisgarh. India
| | - Shrivastava Saurabh
- ShriRawatpura Sarkar Institute of Pharmacy, Kumhari, Durg,490042,Chhattisgarh. India
| | - Kumar Abhishek
- Division of Pharmacology,KIET School of Pharmacy,KIET Group ofInstitutions,Delhi-NCR,Ghaziabad,201206,Uttar Pradesh. India
| | - Sahu Sagar
- Columbia Institute of Pharmacy, Tekari, Raipur, 493111, Chhattisgarh. India
| | - Kumar Lokesh
- Siddhi Vinayaka Institute of Technology & Sciences (College of Pharmacy), Bilaspur,495001, Chhattisgarh. India
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44
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Pignataro G, Cataldi M, Taglialatela M. Neurological risks and benefits of cytokine-based treatments in coronavirus disease 2019: from preclinical to clinical evidence. Br J Pharmacol 2021; 179:2149-2174. [PMID: 33512003 DOI: 10.1111/bph.15397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 12/15/2022] Open
Abstract
Immunodeficiency and hyperinflammation are responsible for the most frequent and life-threatening forms of coronavirus disease 2019 (COVID-19). Therefore, cytokine-based treatments targeting immuno-inflammatory mechanisms are currently undergoing clinical scrutiny in COVID-19-affected patients. In addition, COVID-19 patients also exhibit a wide range of neurological manifestations (neuro-COVID), which may also benefit from cytokine-based treatments. In fact, such drugs have shown some clinical efficacy also in neuroinflammatory diseases. On the other hand, anti-cytokine drugs are endowed with significant neurological risks, mainly attributable to their immunodepressant effects. Therefore, the aim of the present manuscript is to briefly describe the role of specific cytokines in neuroinflammation, to summarize the efficacy in preclinical models of neuroinflammatory diseases of drugs targeting these cytokines and to review the clinical data regarding the neurological effects of these drugs currently being investigated against COVID-19, in order to raise awareness about their potentially beneficial and/or detrimental neurological consequences.
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Affiliation(s)
- Giuseppe Pignataro
- Division of Pharmacology, Department of Neuroscience, University of Naples "Federico II", Naples, Italy
| | - Mauro Cataldi
- Division of Pharmacology, Department of Neuroscience, University of Naples "Federico II", Naples, Italy
| | - Maurizio Taglialatela
- Division of Pharmacology, Department of Neuroscience, University of Naples "Federico II", Naples, Italy
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45
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Tiwari R, Mishra AR, Gupta A, Nayak D. Structural similarity-based prediction of host factors associated with SARS-CoV-2 infection and pathogenesis. J Biomol Struct Dyn 2021; 40:5868-5879. [PMID: 33506741 PMCID: PMC7852281 DOI: 10.1080/07391102.2021.1874532] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The current pandemic resulted from SARS-CoV-2 still remains as the major public health concern globally. The precise mechanism of viral pathogenesis is not fully understood, which remains a major hurdle for medical intervention. Here we generated an interactome profile of protein-protein interactions based on host and viral protein structural similarities information. Further computational biological study combined with Gene enrichment analysis predicted key enriched pathways associated with viral pathogenesis. The results show that axon guidance, membrane trafficking, vesicle-mediated transport, apoptosis, clathrin-mediated endocytosis, Vpu mediated degradation of CD4 T cell, and interferon-gamma signaling are key events associated in SARS-CoV-2 life cycle. Further, degree centrality analysis reveals that IRF1/9/7, TP53, and CASP3, UBA52, and UBC are vital proteins for IFN-γ-mediated signaling, apoptosis, and proteasomal degradation of CD4, respectively. We crafted chronological events of the virus life cycle. The SARS-CoV-2 enters through clathrin-mediated endocytosis, and the genome is trafficked to the early endosomes in a RAB5-dependent manner. It is predicted to replicate in a double-membrane vesicle (DMV) composed of the endoplasmic reticulum, autophagosome, and ERAD machinery. The SARS-CoV-2 down-regulates host translational machinery by interacting with protein kinase R, PKR-like endoplasmic reticulum kinase, and heme-regulated inhibitor and can phosphorylate eIF2a. The virion assembly occurs in the ER-Golgi intermediate compartment (ERGIC) organized by the spike and matrix protein. Collectively, we have established a spatial link between viral entry, RNA synthesis, assembly, pathogenesis, and their associated diverse host factors, those could pave the way for therapeutic intervention.
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Affiliation(s)
- Ritudhwaj Tiwari
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Anurag R Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Advika Gupta
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Debasis Nayak
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
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46
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Doharey PK, Singh V, Gedda MR, Sahoo AK, Varadwaj PK, Sharma B. In silico study indicates antimalarials as direct inhibitors of SARS-CoV-2-RNA dependent RNA polymerase. J Biomol Struct Dyn 2021; 40:5588-5605. [PMID: 33475021 PMCID: PMC7842134 DOI: 10.1080/07391102.2021.1871956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused a global pandemic. RNA-dependent RNA polymerase (RdRp) is the key component of the replication or transcription machinery of coronavirus. Therefore SARS-CoV-2-RdRp has been chosen as an important target for the development of antiviral drug(s). During the early pandemic of the COVID-19, chloroquine and hydroxychloroquine were suggested by the researchers for the prevention or treatment of SARS-CoV-2. In our study, the antimalarial compounds have been screened and docked against SARS-CoV-2-RdRp (PDB ID: 7BTF), and it was observed that the antimalarials chloroquine, hydroxychloroquine, and amodiaquine exhibit good affinity. Since the crystal structure of SARS-CoV-2-RdRp with its substrate is not available, poliovirus-RdRp crystal structure co-crystallized with its substrate ATP (PDB ID: 2ILY) was used as a reference structure. The superimposition of SARS-CoV-2-RdRp and poliovirus-RdRp structures showed that the active sites of both of the RdRps superimposed very well. The amino acid residues involved in the binding of ATP in the case of poliovirus-RdRp and residues involved in binding with the antimalarial compounds with SARS-CoV-2-RdRp were compared. In both cases, the conserved residues were found to be involved in establishing the interactions. The MMGBSA and molecular dynamic simulation studies were performed to strengthen our docking results. Further residues involved in binding of antimalarials with SARS-CoV-2-RdRp were compared with the residues involved in the SARS-CoV-2-RdRp complexed with remdesivir [PDB ID: 7BV2]. It was observed that co-crystallized remdesivir and docked antimalarials bind in the same pocket of SARS-CoV-2 -RdRp. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
| | - Vishal Singh
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, UP, India
| | - Mallikarjuna Rao Gedda
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, UP, India
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, UP, India
| | - Pritish Kumar Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, UP, India
| | - Bechan Sharma
- Department of Biochemistry, University of Allahabad, Allahabad, UP, India
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47
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Edridge AWD, Kaczorowska J, Hoste ACR, Bakker M, Klein M, Loens K, Jebbink MF, Matser A, Kinsella CM, Rueda P, Ieven M, Goossens H, Prins M, Sastre P, Deijs M, van der Hoek L. Seasonal coronavirus protective immunity is short-lasting. Nat Med 2020. [PMID: 32929268 DOI: 10.1101/2020.05.11.20086439] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A key unsolved question in the current coronavirus disease 2019 (COVID-19) pandemic is the duration of acquired immunity. Insights from infections with the four seasonal human coronaviruses might reveal common characteristics applicable to all human coronaviruses. We monitored healthy individuals for more than 35 years and determined that reinfection with the same seasonal coronavirus occurred frequently at 12 months after infection.
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Affiliation(s)
- Arthur W D Edridge
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Joanna Kaczorowska
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Michelle Klein
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Katherine Loens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
- Department of Microbiology, University Hospital Antwerp, Edegem, Belgium
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Amy Matser
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
| | - Cormac M Kinsella
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Paloma Rueda
- INGENASA, Inmunología y Genética Aplicada S. A., Madrid, Spain
| | - Margareta Ieven
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Herman Goossens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
- Department of Microbiology, University Hospital Antwerp, Edegem, Belgium
| | - Maria Prins
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Department of Infectious Diseases, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Patricia Sastre
- INGENASA, Inmunología y Genética Aplicada S. A., Madrid, Spain
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
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Zhao M, Wang M, Zhang J, Ye J, Xu Y, Wang Z, Ye D, Liu J, Wan J. Advances in the relationship between coronavirus infection and cardiovascular diseases. Biomed Pharmacother 2020; 127:110230. [PMID: 32428835 PMCID: PMC7218375 DOI: 10.1016/j.biopha.2020.110230] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) has once again aroused people's concern about coronavirus. Seven human coronaviruses (HCoVs) have been discovered so far, including HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU115, severe acute respiratory syndrome coronavirus, Middle East respiratory syndrome coronavirus and severe acute respiratory syndrome coronavirus 2. Existing studies show that the cardiovascular disease increased the incidence and severity of coronavirus infection. At the same time, myocardial injury caused by coronavirus infection is one of the main factors contributing to poor prognosis. In this review, the recent clinical findings about the relationship between coronaviruses and cardiovascular diseases and the underlying pathophysiological mechanisms are discussed. This review aimed to provide assistance for the prevention and treatment of COVID-19.
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Affiliation(s)
- Mengmeng Zhao
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan, China; Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Menglong Wang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan, China; Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Jishou Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan, China; Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Jing Ye
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan, China; Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Yao Xu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan, China; Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Zhen Wang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan, China; Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Di Ye
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan, China; Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Jianfang Liu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan, China; Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Jun Wan
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan, China; Hubei Key Laboratory of Cardiology, Wuhan, China.
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49
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Heimdal I, Moe N, Krokstad S, Christensen A, Skanke LH, Nordbø SA, Døllner H. Human Coronavirus in Hospitalized Children With Respiratory Tract Infections: A 9-Year Population-Based Study From Norway. J Infect Dis 2020; 219:1198-1206. [PMID: 30418633 PMCID: PMC7107437 DOI: 10.1093/infdis/jiy646] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/06/2018] [Indexed: 01/29/2023] Open
Abstract
Background The burden of human coronavirus (HCoV)-associated respiratory tract infections (RTIs) in hospitalized children is poorly defined. We studied the occurrence and hospitalization rates of HCoV over 9 years. Methods Children from Sør-Trøndelag County, Norway, hospitalized with RTIs and asymptomatic controls, were prospectively enrolled from 2006 to 2015. Nasopharyngeal aspirates were analyzed with semiquantitative polymerase chain reaction (PCR) tests for HCoV subtypes OC43, 229E, NL63, and HKU1, and 13 other respiratory pathogens. Results HCoV was present in 9.1% (313/3458) of all RTI episodes: 46.6% OC43, 32.3% NL63, 16.0% HKU1, and 5.8% 229E. Hospitalization rates for HCoV-positive children with lower RTIs were 1.5 and 2.8 per 1000 <5 and <1 years of age, respectively. The detection rate among controls was 10.2% (38/373). Codetections occurred in 68.1% of the patients and 68.4% of the controls. In a logistic regression analysis, high HCoV genomic loads (cycle threshold <28 in PCR analysis) were associated with RTIs (odds ratio = 3.12, P = .016) adjusted for relevant factors. Conclusions HCoVs occurred in 1 of 10 hospitalized children with RTIs and asymptomatic controls. A high HCoV genomic load was associated with RTI. HCoVs are associated with a substantial burden of RTIs in need of hospitalization.
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Affiliation(s)
- Inger Heimdal
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim
| | - Nina Moe
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim.,Department of Pediatrics, St Olavs Hospital, Trondheim University Hospital, Norway
| | - Sidsel Krokstad
- Departments of Medical Microbiology, St Olavs Hospital, Trondheim University Hospital, Norway
| | - Andreas Christensen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim.,Departments of Medical Microbiology, St Olavs Hospital, Trondheim University Hospital, Norway
| | - Lars Høsøien Skanke
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim.,Department of Pediatrics, St Olavs Hospital, Trondheim University Hospital, Norway
| | - Svein Arne Nordbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim.,Departments of Medical Microbiology, St Olavs Hospital, Trondheim University Hospital, Norway
| | - Henrik Døllner
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim.,Department of Pediatrics, St Olavs Hospital, Trondheim University Hospital, Norway
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50
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Abstract
Coronaviruses are pathogens with a serious impact on human and animal health. They mostly cause enteric or respiratory disease, which can be severe and life threatening, e.g., in the case of the zoonotic coronaviruses causing severe acute respiratory syndrome (SARS) and Middle East Respiratory Syndrome (MERS) in humans. Despite the economic and societal impact of such coronavirus infections, and the likelihood of future outbreaks of additional pathogenic coronaviruses, our options to prevent or treat coronavirus infections remain very limited. This highlights the importance of advancing our knowledge on the replication of these viruses and their interactions with the host. Compared to other +RNA viruses, coronaviruses have an exceptionally large genome and employ a complex genome expression strategy. Next to a role in basic virus replication or virus assembly, many of the coronavirus proteins expressed in the infected cell contribute to the coronavirus-host interplay. For example, by interacting with the host cell to create an optimal environment for coronavirus replication, by altering host gene expression or by counteracting the host’s antiviral defenses. These coronavirus–host interactions are key to viral pathogenesis and will ultimately determine the outcome of infection. Due to the complexity of the coronavirus proteome and replication cycle, our knowledge of host factors involved in coronavirus replication is still in an early stage compared to what is known for some other +RNA viruses. This review summarizes our current understanding of coronavirus–host interactions at the level of the infected cell, with special attention for the assembly and function of the viral RNA-synthesising machinery and the evasion of cellular innate immune responses.
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