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Liu KZ, Tian G, Ko ACT, Geissler M, Malic L, Moon BU, Clime L, Veres T. Microfluidic methods for the diagnosis of acute respiratory tract infections. Analyst 2024; 150:9-33. [PMID: 39440426 DOI: 10.1039/d4an00957f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
Acute respiratory tract infections (ARTIs) are caused by sporadic or pandemic outbreaks of viral or bacterial pathogens, and continue to be a considerable socioeconomic burden for both developing and industrialized countries alike. Diagnostic methods and technologies serving as the cornerstone for disease management, epidemiological tracking, and public health interventions are evolving continuously to keep up with the demand for higher sensitivity, specificity and analytical throughput. Microfluidics is becoming a key technology in these developments as it allows for integrating, miniaturizing and automating bioanalytical assays at an unprecedented scale, reducing sample and reagent consumption and improving diagnostic performance in terms of sensitivity, throughput and response time. In this article, we describe relevant ARTIs-pneumonia, influenza, severe acute respiratory syndrome, and coronavirus disease 2019-along with their pathogenesis. We provide a summary of established methods for disease diagnosis, involving nucleic acid amplification techniques, antigen detection, serological testing as well as microbial culture. This is followed by a short introduction to microfluidics and how flow is governed at low volume and reduced scale using centrifugation, pneumatic pumping, electrowetting, capillary action, and propagation in porous media through wicking, for each of these principles impacts the design, functioning and performance of diagnostic tools in a particular way. We briefly cover commercial instruments that employ microfluidics for use in both laboratory and point-of-care settings. The main part of the article is dedicated to emerging methods deriving from the use of miniaturized, microfluidic systems for ARTI diagnosis. Finally, we share our thoughts on future perspectives and the challenges associated with validation, approval, and adaptation of microfluidic-based systems.
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Affiliation(s)
- Kan-Zhi Liu
- Life Sciences Division, Medical Devices Research Centre, National Research Council of Canada, 435 Ellice Avenue, Winnipeg, MB, R3B 1Y6, Canada
| | - Ganghong Tian
- Life Sciences Division, Medical Devices Research Centre, National Research Council of Canada, 435 Ellice Avenue, Winnipeg, MB, R3B 1Y6, Canada
| | - Alex C-T Ko
- Life Sciences Division, Medical Devices Research Centre, National Research Council of Canada, 435 Ellice Avenue, Winnipeg, MB, R3B 1Y6, Canada
| | - Matthias Geissler
- Life Sciences Division, Medical Devices Research Centre, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Lidija Malic
- Life Sciences Division, Medical Devices Research Centre, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Byeong-Ui Moon
- Life Sciences Division, Medical Devices Research Centre, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Liviu Clime
- Life Sciences Division, Medical Devices Research Centre, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Teodor Veres
- Life Sciences Division, Medical Devices Research Centre, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
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2
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Benício LFMA, Nascimento ÉCM, Martins JBL. Docking heparan sulfate-based ligands as a promising inhibitor for SARS-CoV-2. J Mol Model 2024; 31:19. [PMID: 39666205 DOI: 10.1007/s00894-024-06236-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 11/26/2024] [Indexed: 12/13/2024]
Abstract
CONTEXT Heparan sulfate (HS) linear polysaccharide glycosaminoglycan compound is linked to components from the cell surface and the extracellular matrix. HS mediates SARS-CoV-2 infection through spike protein binding to cell surface receptors and is required to bind ACE2, prompting the need for electronic structure and molecular docking evaluation of this core system to exploit this attachment in developing new derivatives. Therefore, we have studied five molecules based on HS using molecular docking and electronic structure analysis. Non-covalent interaction analysis shows hydrogen bonding and van der Waals interactions in the binding to RBD-ACE2 interface and 3CLpro. SDM3 and SDM1 molecules present the lowest gap, including solvent effect under 154.6 kcal/mol, and exhibit the most reactivity behavior in this group, potentially leading to enhanced interaction in docking studies. METHODS Heparan sulfate and four derivatives were optimized using B3LYP functional with two basis sets 6-31 + G(d,p) and def2SVP. Electronic structure was used to explore the main interactions and the reactivity of these molecules, and these optimized structures were used in the molecular docking study against 3CLpro, RBD, and ACE2.
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Affiliation(s)
- Luiz F M A Benício
- Department of Pharmacy, Faculty of Health Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Érica C M Nascimento
- Computational Chemistry Laboratory, Institute of Chemistry, University of Brasilia, Brasilia, DF, 70910-900, Brazil
| | - João B L Martins
- Department of Pharmacy, Faculty of Health Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil.
- Computational Chemistry Laboratory, Institute of Chemistry, University of Brasilia, Brasilia, DF, 70910-900, Brazil.
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3
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Sangare K, Liu S, Selvaraj P, Stauft CB, Starost MF, Wang TT. Combined mutations in nonstructural protein 14, envelope, and membrane proteins mitigate the neuropathogenicity of SARS-CoV-2 Omicron BA.1 in K18-hACE2 mice. mSphere 2024:e0072624. [PMID: 39660912 DOI: 10.1128/msphere.00726-24] [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: 08/27/2024] [Accepted: 11/17/2024] [Indexed: 12/12/2024] Open
Abstract
We previously reported that mutations outside the spike protein play a role in the attenuation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.1 variant in human ACE2 transgenic mice (K18-hACE2). Here, we assessed the pathogenicity of SARS-CoV-2 (WA1/2020) containing mutations from the Omicron BA.1 variant in K18-hACE2 mice. At an infection dose of 104 plaque-forming units (PFU), WA1 virus carrying Omicron BA.1 Nsp14(I42V), E(T9I), M(D3G/Q19E/A63T), but not Nsp6(Δ105-107, I189V), substitutions showed significant reduction in lethality. Interestingly, reduction of viral load is more pronounced in the brains than in the lungs. Subsequent analyses suggest that BA.1 E(T9I) and M(D3G/Q19E/A63T) substitutions result in less efficient packaging of virus-like particles. Given that Nsp14(I42V), E(T9I), M(Q19E/A63T) are well preserved in subsequent omicron subvariants, including currently circulating variants, our findings highlight the importance of understanding how non-spike mutations affect the pathogenicity of SARS-CoV-2 variants. IMPORTANCE Inoculation of transgenic mice expressing human angiotensin-converting enzyme 2 (hACE2) with SARS-CoV-2 often leads to a fatal brain infection. Omicron BA.1 variant, however, was found to be non-lethal in this model. Here, we systematically assessed the effect of individual mutations of Omicron BA.1 on the pathogenicity of the virus in hACE2 transgenic mice and found that combination of 5 mutations of Nsp14, E, and M of BA.1 variant significantly lowered brain viral load and reduced lethality. These results provide new insights into how SARS-CoV-2 Omicron BA.1 is attenuated.
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Affiliation(s)
- Kotou Sangare
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Shufeng Liu
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Prabhuanand Selvaraj
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Charles B Stauft
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Matthew F Starost
- Division of Veterinary Resources, Diagnostic and Research Services Branch, National Institutes of Health, Bethesda, Maryland, USA
| | - Tony T Wang
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
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4
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Shteinfer-Kuzmine A, Verma A, Bornshten R, Ben Chetrit E, Ben-Ya'acov A, Pahima H, Rubin E, Mograbi Y, Shteyer E, Shoshan-Barmatz V. Elevated serum mtDNA in COVID-19 patients is linked to SARS-CoV-2 envelope protein targeting mitochondrial VDAC1, inducing apoptosis and mtDNA release. Apoptosis 2024; 29:2025-2046. [PMID: 39375263 PMCID: PMC11550248 DOI: 10.1007/s10495-024-02025-5] [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] [Accepted: 09/23/2024] [Indexed: 10/09/2024]
Abstract
Mitochondria dysfunction is implicated in cell death, inflammation, and autoimmunity. During viral infections, some viruses employ different strategies to disrupt mitochondria-dependent apoptosis, while others, including SARS-CoV-2, induce host cell apoptosis to facilitate replication and immune system modulation. Given mitochondrial DNAs (mtDNA) role as a pro-inflammatory damage-associated molecular pattern in inflammatory diseases, we examined its levels in the serum of COVID-19 patients and found it to be high relative to levels in healthy donors. Furthermore, comparison of serum protein profiles between healthy individuals and SARS-CoV-2-infected patients revealed unique bands in the COVID-19 patients. Using mass spectroscopy, we identified over 15 proteins, whose levels in the serum of COVID-19 patients were 4- to 780-fold higher. As mtDNA release from the mitochondria is mediated by the oligomeric form of the mitochondrial-gatekeeper-the voltage-dependent anion-selective channel 1 (VDAC1)-we investigated whether SARS-CoV-2 protein alters VDAC1 expression. Among the three selected SARS-CoV-2 proteins, small envelope (E), nucleocapsid (N), and accessory 3b proteins, the E-protein induced VDAC1 overexpression, VDAC1 oligomerization, cell death, and mtDNA release. Additionally, this protein led to mitochondrial dysfunction, as evidenced by increased mitochondrial ROS production and cytosolic Ca2+ levels. These findings suggest that SARS-CoV-2 E-protein induces mitochondrial dysfunction, apoptosis, and mtDNA release via VDAC1 modulation. mtDNA that accumulates in the blood activates the cGAS-STING pathway, triggering inflammatory cytokine and chemokine expression that contribute to the cytokine storm and tissue damage seen in cases of severe COVID-19.
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Affiliation(s)
| | - Ankit Verma
- National Institute for Biotechnology in the Negev, Beer-Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Rut Bornshten
- The Shraga Segal Dept. of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Eli Ben Chetrit
- Infectious Diseases Unit, Shaare Zedek Medical Center, Hebrew University School of Medicine, Jerusalem, Israel
| | - Ami Ben-Ya'acov
- Shaare Zedek Medical Center, The Juliet Keidan Institute of Paediatric Gastroenterology, Jerusalem, Israel
| | - Hadas Pahima
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Ethan Rubin
- The Shraga Segal Dept. of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
- Shaare Zedek Medical Center, The Juliet Keidan Institute of Paediatric Gastroenterology, Jerusalem, Israel
| | | | - Eyal Shteyer
- Shaare Zedek Medical Center, The Juliet Keidan Institute of Paediatric Gastroenterology, Jerusalem, Israel
| | - Varda Shoshan-Barmatz
- National Institute for Biotechnology in the Negev, Beer-Sheva, Israel.
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel.
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5
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Yu J, Ge S, Li J, Zhang Y, Xu J, Wang Y, Liu S, Yu X, Wang Z. Interaction between coronaviruses and the autophagic response. Front Cell Infect Microbiol 2024; 14:1457617. [PMID: 39650836 PMCID: PMC11621220 DOI: 10.3389/fcimb.2024.1457617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 10/18/2024] [Indexed: 12/11/2024] Open
Abstract
In recent years, the emergence and widespread dissemination of the coronavirus SARS-CoV-2 has posed a significant threat to global public health and social development. In order to safely and effectively prevent and control the spread of coronavirus diseases, a profound understanding of virus-host interactions is paramount. Cellular autophagy, a process that safeguards cells by maintaining cellular homeostasis under diverse stress conditions. Xenophagy, specifically, can selectively degrade intracellular pathogens, such as bacteria, fungi, viruses, and parasites, thus establishing a robust defense mechanism against such intruders. Coronaviruses have the ability to induce autophagy, and they manipulate this pathway to ensure their efficient replication. While progress has been made in elucidating the intricate relationship between coronaviruses and autophagy, a comprehensive summary of how autophagy either benefits or hinders viral replication remains elusive. In this review, we delve into the mechanisms that govern how different coronaviruses regulate autophagy. We also provide an in-depth analysis of virus-host interactions, particularly focusing on the latest data pertaining to SARS-CoV-2. Our aim is to lay a theoretical foundation for the development of novel coronavirus vaccines and the screening of potential drug targets.
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Affiliation(s)
- Jiarong Yu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Shengqiang Ge
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Jinming Li
- China Animal Health and Epidemiology Center, Qingdao, China
| | | | - Jiao Xu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Yingli Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Shan Liu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Xiaojing Yu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Zhiliang Wang
- China Animal Health and Epidemiology Center, Qingdao, China
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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Dick JK, Sangala JA, Krishna VD, Khaimraj A, Hamel L, Erickson SM, Hicks D, Soigner Y, Covill LE, Johnson AK, Ehrhardt MJ, Ernste K, Brodin P, Koup RA, Khaitan A, Baehr C, Thielen BK, Henzler CM, Skipper C, Miller JS, Bryceson YT, Wu J, John CC, Panoskaltsis-Mortari A, Orioles A, Steiner ME, Cheeran MCJ, Pravetoni M, Hart GT. NK Cell and Monocyte Dysfunction in Multisystem Inflammatory Syndrome in Children. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:1452-1466. [PMID: 39392378 PMCID: PMC11533154 DOI: 10.4049/jimmunol.2400395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 09/16/2024] [Indexed: 10/12/2024]
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a severe complication of SARS-CoV-2 infection characterized by multiorgan involvement and inflammation. Testing of cellular function ex vivo to understand the aberrant immune response in MIS-C is limited. Despite strong Ab production in MIS-C, SARS-CoV-2 nucleic acid testing can remain positive for 4-6 wk postinfection. Therefore, we hypothesized that dysfunctional cell-mediated Ab responses downstream of Ab production may be responsible for delayed clearance of viral products in MIS-C. In MIS-C, monocytes were hyperfunctional for phagocytosis and cytokine production, whereas NK cells were hypofunctional for both killing and cytokine production. The decreased NK cell cytotoxicity correlated with an NK exhaustion marker signature and systemic IL-6 levels. Potentially providing a therapeutic option, cellular engagers of CD16 and SARS-CoV-2 proteins were found to rescue NK cell function in vitro. Taken together, our results reveal dysregulation in Ab-mediated cellular responses of myeloid and NK cells that likely contribute to the immune pathology of this disease.
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Affiliation(s)
- Jenna K. Dick
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
- Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Jules A. Sangala
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
- Center for Immunology, University of Minnesota, Minneapolis, MN
| | | | - Aaron Khaimraj
- Department of Pharmacology, University of Minnesota, Minneapolis, MN
| | - Lydia Hamel
- Division of Critical Care, Children’s Hospital and Clinics of Minnesota, Minneapolis, MN
| | - Spencer M. Erickson
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
| | - Dustin Hicks
- Department of Pharmacology, University of Minnesota, Minneapolis, MN
| | - Yvette Soigner
- Division of Hematology, Oncology, and Transplant, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
| | - Laura E. Covill
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Alexander K. Johnson
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN
| | - Michael J. Ehrhardt
- Division of Bone Marrow Transplantation and Cellular Therapy, Department of Pediatrics, M Health Fairview Masonic Children’s Hospital, Minneapolis, MN
| | - Keenan Ernste
- Virology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Petter Brodin
- Unit for Clinical Pediatrics, Department of Women’s and Children’s Health, Karolinska Institute, Solna, Sweden
- Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Richard A. Koup
- Virology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Alka Khaitan
- Ryan White Center for Pediatric Infectious Diseases & Global Health, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
| | - Carly Baehr
- Department of Pharmacology, University of Minnesota, Minneapolis, MN
| | - Beth K. Thielen
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN
| | | | - Caleb Skipper
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
| | - Jeffrey S. Miller
- Center for Immunology, University of Minnesota, Minneapolis, MN
- Division of Hematology, Oncology, and Transplant, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
| | - Yenan T. Bryceson
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
- Broegelmann Laboratory, Department of Clinical Sciences, University of Bergen, Bergen, Norway
| | - Jianming Wu
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN
| | - Chandy C. John
- Ryan White Center for Pediatric Infectious Diseases & Global Health, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
| | - Angela Panoskaltsis-Mortari
- Division of Bone Marrow Transplantation and Cellular Therapy, Department of Pediatrics, M Health Fairview Masonic Children’s Hospital, Minneapolis, MN
| | - Alberto Orioles
- Division of Critical Care, Children’s Hospital and Clinics of Minnesota, Minneapolis, MN
| | - Marie E. Steiner
- Divisions of Pediatric Critical Care and Pediatric Hematology/Oncology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN
| | - Maxim C. J. Cheeran
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN
| | - Marco Pravetoni
- Department of Pharmacology, University of Minnesota, Minneapolis, MN
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA
| | - Geoffrey T. Hart
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
- Center for Immunology, University of Minnesota, Minneapolis, MN
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Rahmani D, Jafari A, Kesharwani P, Sahebkar A. Molecular targets in SARS-CoV-2 infection: An update on repurposed drug candidates. Pathol Res Pract 2024; 263:155589. [PMID: 39276508 DOI: 10.1016/j.prp.2024.155589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 08/29/2024] [Accepted: 09/06/2024] [Indexed: 09/17/2024]
Abstract
The 2019 widespread contagion of the human coronavirus novel type (SARS-CoV-2) led to a pandemic declaration by the World Health Organization. A daily increase in patient numbers has formed an urgent necessity to find suitable targets and treatment options for the novel coronavirus (COVID-19). Despite scientists' struggles to discover quick treatment solutions, few effective specific drugs are approved to control SARS-CoV-2 infections thoroughly. Drug repositioning or Drug repurposing and target-based approaches are promising strategies for facilitating the drug discovery process. Here, we review current in silico, in vitro, in vivo, and clinical updates regarding proposed drugs for prospective treatment options for COVID-19. Drug targets that can direct pharmaceutical sciences efforts to discover new drugs against SARS-CoV-2 are divided into two categories: Virus-based targets, for example, Spike glycoprotein and Nucleocapsid Protein, and host-based targets, for instance, inflammatory cytokines and cell receptors through which the virus infects the cell. A broad spectrum of drugs has been found to show anti-SARS-CoV-2 potential, including antiviral drugs and monoclonal antibodies, statins, anti-inflammatory agents, and herbal products.
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Affiliation(s)
- Dibachehr Rahmani
- Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Ameneh Jafari
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India.
| | - Amirhossein Sahebkar
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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8
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García‐Arribas AB, Ibáñez‐Freire P, Carlero D, Palacios‐Alonso P, Cantero‐Reviejo M, Ares P, López‐Polín G, Yan H, Wang Y, Sarkar S, Chhowalla M, Oksanen HM, Martín‐Benito J, de Pablo PJ, Delgado‐Buscalioni R. Broad Adaptability of Coronavirus Adhesion Revealed from the Complementary Surface Affinity of Membrane and Spikes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404186. [PMID: 39231361 PMCID: PMC11538687 DOI: 10.1002/advs.202404186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/21/2024] [Indexed: 09/06/2024]
Abstract
Coronavirus stands for a large family of viruses characterized by protruding spikes surrounding a lipidic membrane adorned with proteins. The present study explores the adhesion of transmissible gastroenteritis coronavirus (TGEV) particles on a variety of reference solid surfaces that emulate typical virus-surface interactions. Atomic force microscopy informs about trapping effectivity and the shape of the virus envelope on each surface, revealing that the deformation of TGEV particles spans from 20% to 50% in diameter. Given this large deformation range, experimental Langmuir isotherms convey an unexpectedly moderate variation in the adsorption-free energy, indicating a viral adhesion adaptability which goes beyond the membrane. The combination of an extended Helfrich theory and coarse-grained simulations reveals that, in fact, the envelope and the spikes present complementary adsorption affinities. While strong membrane-surface interaction lead to highly deformed TGEV particles, surfaces with strong spike attraction yield smaller deformations with similar or even larger adsorption-free energies.
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Affiliation(s)
- Aritz B. García‐Arribas
- Departamento de Física de la Materia CondensadaUniversidad Autónoma de MadridMadrid28049Spain
| | - Pablo Ibáñez‐Freire
- Departamento de Física Teórica de la Materia CondensadaUniversidad Autónoma de MadridMadrid28049Spain
| | - Diego Carlero
- Departamento de Estructura de MacromoléculasCentro Nacional de Biotecnología CSICMadrid28049Spain
| | - Pablo Palacios‐Alonso
- Departamento de Física Teórica de la Materia CondensadaUniversidad Autónoma de MadridMadrid28049Spain
| | - Miguel Cantero‐Reviejo
- Departamento de Física Teórica de la Materia CondensadaUniversidad Autónoma de MadridMadrid28049Spain
| | - Pablo Ares
- Departamento de Física Teórica de la Materia CondensadaUniversidad Autónoma de MadridMadrid28049Spain
| | - Guillermo López‐Polín
- Departamento de Física de la Materia CondensadaUniversidad Autónoma de MadridMadrid28049Spain
| | - Han Yan
- Department of Materials Science and MetallurgyUniversity of CambridgeCambridgeCB3 0FSUK
| | - Yan Wang
- Department of Materials Science and MetallurgyUniversity of CambridgeCambridgeCB3 0FSUK
| | - Soumya Sarkar
- Department of Materials Science and MetallurgyUniversity of CambridgeCambridgeCB3 0FSUK
| | - Manish Chhowalla
- Department of Materials Science and MetallurgyUniversity of CambridgeCambridgeCB3 0FSUK
| | - Hanna M. Oksanen
- Faculty of Biological and Environmental SciencesVijkki BiocenterUniversity of HelsinkiHelsinki00014Finland
| | - Jaime Martín‐Benito
- Departamento de Física de la Materia CondensadaUniversidad Autónoma de MadridMadrid28049Spain
| | - Pedro J. de Pablo
- Departamento de Física de la Materia CondensadaUniversidad Autónoma de MadridMadrid28049Spain
- Instituto de Física de la Materia Condensada IFIMACUniversidad Autónoma de MadridMadrid28049Spain
| | - Rafael Delgado‐Buscalioni
- Departamento de Física Teórica de la Materia CondensadaUniversidad Autónoma de MadridMadrid28049Spain
- Instituto de Física de la Materia Condensada IFIMACUniversidad Autónoma de MadridMadrid28049Spain
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9
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El-Maradny YA, Badawy MA, Mohamed KI, Ragab RF, Moharm HM, Abdallah NA, Elgammal EM, Rubio-Casillas A, Uversky VN, Redwan EM. Unraveling the role of the nucleocapsid protein in SARS-CoV-2 pathogenesis: From viral life cycle to vaccine development. Int J Biol Macromol 2024; 279:135201. [PMID: 39216563 DOI: 10.1016/j.ijbiomac.2024.135201] [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: 05/30/2024] [Revised: 08/24/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND The nucleocapsid protein (N protein) is the most abundant protein in SARS-CoV-2. Viral RNA and this protein are bound by electrostatic forces, forming cytoplasmic helical structures known as nucleocapsids. Subsequently, these nucleocapsids interact with the membrane (M) protein, facilitating virus budding into early secretory compartments. SCOPE OF REVIEW Exploring the role of the N protein in the SARS-CoV-2 life cycle, pathogenesis, post-sequelae consequences, and interaction with host immunity has enhanced our understanding of its function and potential strategies for preventing SARS-CoV-2 infection. MAJOR CONCLUSION This review provides an overview of the N protein's involvement in SARS-CoV-2 infectivity, highlighting its crucial role in the virus-host protein interaction and immune system modulation, which in turn influences viral spread. GENERAL SIGNIFICANCE Understanding these aspects identifies the N protein as a promising target for developing effective antiviral treatments and vaccines against SARS-CoV-2.
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Affiliation(s)
- Yousra A El-Maradny
- Pharmaceutical and Fermentation Industries Development Center, City of Scientific Research and Technological Applications (SRTA-City), New Borg EL-Arab, Alexandria 21934, Egypt; Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Moustafa A Badawy
- Industrial Microbiology and Applied Chemistry program, Faculty of Science, Alexandria University, Egypt.
| | - Kareem I Mohamed
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Renad F Ragab
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Hamssa M Moharm
- Genetics, Biotechnology Department, Faculty of Agriculture, Alexandria University, Egypt.
| | - Nada A Abdallah
- Medicinal Plants Department, Faculty of Agriculture, Alexandria University, Egypt.
| | - Esraa M Elgammal
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Alberto Rubio-Casillas
- Autlan Regional Hospital, Health Secretariat, Autlan, JAL 48900, Mexico; Biology Laboratory, Autlan Regional Preparatory School, University of Guadalajara, Autlan, JAL 48900, Mexico.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg EL-Arab, 21934 Alexandria, Egypt.
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10
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Xue W, Chu H, Wang J, Sun Y, Qiu X, Song C, Tan L, Ding C, Liao Y. Coronavirus nucleocapsid protein enhances the binding of p-PKCα to RACK1: Implications for inhibition of nucleocytoplasmic trafficking and suppression of the innate immune response. PLoS Pathog 2024; 20:e1012097. [PMID: 39602452 PMCID: PMC11633972 DOI: 10.1371/journal.ppat.1012097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 12/11/2024] [Accepted: 11/18/2024] [Indexed: 11/29/2024] Open
Abstract
The hallmark of coronavirus infection lies in its ability to evade host immune defenses, a process intricately linked to the nuclear entry of transcription factors crucial for initiating the expression of antiviral genes. Central to this evasion strategy is the manipulation of the nucleocytoplasmic trafficking system, which serves as an effective target for the virus to modulate the expression of immune response-related genes. In this investigation, we discovered that infection with the infectious bronchitis virus (IBV) dynamically impedes the nuclear translocation of several transcription factors such as IRF3, STAT1, STAT2, NF-κB p65, and the p38 MAPK, leading to compromised transcriptional induction of key antiviral genes such as IFNβ, IFITM3, and IL-8. Further examination revealed that during the infection process, components of the nuclear pore complex (NPC), particularly FG-Nups (such as NUP62, NUP153, NUP42, and TPR), undergo cytosolic dispersion from the nuclear envelope; NUP62 undergoes phosphorylation, and NUP42 exhibits a mobility shift in size. These observations suggest a disruption in nucleocytoplasmic trafficking. Screening efforts identified the IBV nucleocapsid (N) protein as the agent responsible for the cytoplasmic distribution of FG-Nups, subsequently hindering the nuclear entry of transcription factors and suppressing the expression of antiviral genes. Interactome analysis further revealed that the IBV N protein interacts with the scaffold protein RACK1, facilitating the recruitment of activated protein kinase C alpha (p-PKCα) to RACK1 and relocating the p-PKCα-RACK1 complex to the cytoplasm. These observations are conserved across diverse coronaviruses N proteins. Concurrently, the presence of both RACK1 and PKCα/β proved essential for the phosphorylation and cytoplasmic dispersion of NUP62, the suppression of antiviral cytokine expression, and efficient virus replication. These findings unveil a novel, highly effective, and evolutionarily conserved mechanism.
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Affiliation(s)
- Wenxiang Xue
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, P. R. China
| | - Hongyan Chu
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, P. R. China
| | - Jiehuang Wang
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, P. R. China
| | - Yingjie Sun
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, P. R. China
| | - Xusheng Qiu
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, P. R. China
| | - Cuiping Song
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, P. R. China
| | - Lei Tan
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, P. R. China
| | - Chan Ding
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, P. R. China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, P. R. China
| | - Ying Liao
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, P. R. China
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11
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Wang Z, Qiu M, Ji Y, Chai K, Liu C, Xu F, Guo F, Tan J, Liu R, Qiao W. Palmitoylation of SARS-CoV-2 Envelope protein is central to virus particle formation. J Virol 2024; 98:e0107224. [PMID: 39287388 PMCID: PMC11495019 DOI: 10.1128/jvi.01072-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 08/25/2024] [Indexed: 09/19/2024] Open
Abstract
The Envelope (E) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an integral structural protein in the virus particles. However, its role in the assembly of virions and the underlying molecular mechanisms are yet to be elucidated, including whether the function of E protein is regulated by post-translational modifications. In the present study, we report that SARS-CoV-2 E protein is palmitoylated at C40, C43, and C44 by palmitoyltransferases zDHHC3, 6, 12, 15, and 20. Mutating these three cysteines to serines (C40/43/44S) reduced the stability of E protein, decreased the interaction of E with structural proteins Spike, Membrane, and Nucleocapsid, and thereby inhibited the production of virus-like particles (VLPs) and VLP-mediated luciferase transcriptional delivery. Specifically, the C40/43/44S mutation of E protein reduced the density of VLPs. Collectively, these results demonstrate that palmitoylation of E protein is vital for its function in the assembly of SARS-CoV-2 particles.IMPORTANCEIn this study, we systematically examined the biochemistry of palmitoylation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) E protein and demonstrated that palmitoylation of SARS-CoV-2 E protein is required for virus-like particle (VLP) production and maintaining normal particle density. These results suggest that palmitoylated E protein is central for proper morphogenesis of SARS-CoV-2 VLPs in densities required for viral infectivity. This study presents a significant advancement in the understanding of how palmitoylation of viral proteins is vital for assembling SARS-CoV-2 particles and supports that palmitoyl acyltransferases can be potential therapeutic targets for the development of SARS-CoV-2 inhibitors.
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Affiliation(s)
- Zhaohuan Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Manman Qiu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yue Ji
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Keli Chai
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenxi Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Fengwen Xu
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
| | - Fei Guo
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
| | - Juan Tan
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Ruikang Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Wentao Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
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12
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Cui H, Sun F, Yu N, Cao Y, Wang X, Zhang D, Chen Z, Wang N, Yuan B, Liu P, Duan W, Qiu W, Yin X, Ma C. TLR2/NF-κB signaling in macrophage/microglia mediated COVID-pain induced by SARS-CoV-2 envelope protein. iScience 2024; 27:111027. [PMID: 39435149 PMCID: PMC11493200 DOI: 10.1016/j.isci.2024.111027] [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: 05/08/2024] [Revised: 06/26/2024] [Accepted: 09/20/2024] [Indexed: 10/23/2024] Open
Abstract
Pain has become a major symptom of long COVID-19 without effective therapy. Apart from viral infection pathological process, SARS-CoV-2 membranal proteins (envelope [S2E], spike [S2S] and membrane [S2M]) also present pro-inflammatory feature independently. Here, we aim to uncover the neuroinflammatory mechanism of COVID-pain induced by SARS-CoV-2 membranal proteins. We detected the three proteins in both peripheral sensory ganglions and spinal dorsal horn of COVID-19 donors. After intradermal and intrathecal injection, only S2E triggered pain behaviors, accompanied with upregulated-phosphorylation nuclear factor kappa B (NF-κB), which was significantly attenuated by minocycline in mice. We further identified Toll-like receptor 2 (TLR2) among TLRs as the target of S2E to evoke inflammatory responses leading to COVID-pain. This study identified the nociceptive effect of S2E through directly interacting with macrophage/microglia TLR2 and inducing the following NF-κB inflammatory storm. Clearing away S2E and inhibiting macrophage/microglia TLR2 served as perspective therapeutic strategies for COVID-19 pain.
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Affiliation(s)
- Huan Cui
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Joint Laboratory of Anesthesia and Pain, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 DongDanSanTiao, Dongcheng District, Beijing 100005, China
| | - Fengrun Sun
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Joint Laboratory of Anesthesia and Pain, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 DongDanSanTiao, Dongcheng District, Beijing 100005, China
| | - Ning Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Joint Laboratory of Anesthesia and Pain, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 DongDanSanTiao, Dongcheng District, Beijing 100005, China
| | - Yan Cao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Joint Laboratory of Anesthesia and Pain, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 DongDanSanTiao, Dongcheng District, Beijing 100005, China
| | - Xue Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Joint Laboratory of Anesthesia and Pain, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 DongDanSanTiao, Dongcheng District, Beijing 100005, China
- National Human Brain Bank for Development and Function, Beijing, China
| | - Di Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Joint Laboratory of Anesthesia and Pain, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 DongDanSanTiao, Dongcheng District, Beijing 100005, China
- National Human Brain Bank for Development and Function, Beijing, China
| | - Zhen Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Joint Laboratory of Anesthesia and Pain, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 DongDanSanTiao, Dongcheng District, Beijing 100005, China
- National Human Brain Bank for Development and Function, Beijing, China
| | - Naili Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Joint Laboratory of Anesthesia and Pain, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 DongDanSanTiao, Dongcheng District, Beijing 100005, China
- National Human Brain Bank for Development and Function, Beijing, China
| | - Bo Yuan
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Joint Laboratory of Anesthesia and Pain, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 DongDanSanTiao, Dongcheng District, Beijing 100005, China
| | - Penghao Liu
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Laboratory of Spinal Cord Injury and Functional Reconstruction, China International Neuroscience Institute (CHINA-INI), Beijing, China
| | - Wanru Duan
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Laboratory of Spinal Cord Injury and Functional Reconstruction, China International Neuroscience Institute (CHINA-INI), Beijing, China
| | - Wenying Qiu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Joint Laboratory of Anesthesia and Pain, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 DongDanSanTiao, Dongcheng District, Beijing 100005, China
- National Human Brain Bank for Development and Function, Beijing, China
| | - Xiangsha Yin
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Joint Laboratory of Anesthesia and Pain, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 DongDanSanTiao, Dongcheng District, Beijing 100005, China
- National Human Brain Bank for Development and Function, Beijing, China
| | - Chao Ma
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Human Anatomy, Histology and Embryology, Neuroscience Center, Joint Laboratory of Anesthesia and Pain, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, No.5 DongDanSanTiao, Dongcheng District, Beijing 100005, China
- National Human Brain Bank for Development and Function, Beijing, China
- Chinese Institute for Brain Research, Beijing 102206, China
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13
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Liu L, Zhang L, Hao X, Wang Y, Zhang X, Ge L, Wang P, Tian B, Zhang M. Coronavirus envelope protein activates TMED10-mediated unconventional secretion of inflammatory factors. Nat Commun 2024; 15:8708. [PMID: 39379362 PMCID: PMC11461611 DOI: 10.1038/s41467-024-52818-0] [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: 03/30/2024] [Accepted: 09/20/2024] [Indexed: 10/10/2024] Open
Abstract
The precise cellular mechanisms underlying heightened proinflammatory cytokine production during coronavirus infection remain incompletely understood. Here we identify the envelope (E) protein in severe coronaviruses (SARS-CoV-2, SARS, or MERS) as a potent inducer of interleukin-1 release, intensifying lung inflammation through the activation of TMED10-mediated unconventional protein secretion (UcPS). In contrast, the E protein of mild coronaviruses (229E, HKU1, or OC43) demonstrates a less pronounced effect. The E protein of severe coronaviruses contains an SS/DS motif, which is not present in milder strains and facilitates interaction with TMED10. This interaction enhances TMED10-oligomerization, facilitating UcPS cargo translocation into the ER-Golgi intermediate compartment (ERGIC)-a pivotal step in interleukin-1 UcPS. Progesterone analogues were identified as compounds inhibiting E-enhanced release of proinflammatory factors and lung inflammation in a Mouse Hepatitis Virus (MHV) infection model. These findings elucidate a molecular mechanism driving coronavirus-induced hyperinflammation, proposing the E-TMED10 interaction as a potential therapeutic target to counteract the adverse effects of coronavirus-induced inflammation.
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Affiliation(s)
- Lei Liu
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Lijingyao Zhang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xinyan Hao
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Yang Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaochun Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Peihui Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Boxue Tian
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Min Zhang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China.
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
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14
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Volovik MV, Batishchev OV. Viral fingerprints of the ion channel evolution: compromise of complexity and function. J Biomol Struct Dyn 2024:1-20. [PMID: 39365745 DOI: 10.1080/07391102.2024.2411523] [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: 01/28/2024] [Accepted: 04/29/2024] [Indexed: 10/06/2024]
Abstract
Evolution from precellular supramolecular assemblies to cellular world originated from the ability to make a barrier between the interior of the cell and the outer environment. This step resulted from the possibility to form a membrane, which preserves the cell like a wall of the castle. However, every castle needs gates for trading, i.e. in the case of cell, for controlled exchange of substances. These 'gates' should have the mechanism of opening and closing, guards, entry rules, and so on. Different structures are known to be able to make membrane permeable to various substances, from ions to macromolecules. They are amphipathic peptides, their assemblies, sophisticated membrane channels with numerous transmembrane domains, etc. Upon evolving, cellular world preserved and selected many variants, which, finally, have provided both prokaryotes and eukaryotes with highly selective and regulated ion channels. However, various simpler variants of ion channels are found in viruses. Despite the origin of viruses is still under debates, they have evolved parallelly with the cellular forms of life. Being initial form of the enveloped organisms, reduction of protocells or their escaped parts, viruses might be fingerprints of the evolutionary steps of cellular structures like ion channels. Therefore, viroporins may provide us a necessary information about selection between high functionality and less complex structure in supporting all the requirements for controlled membrane permeability. In this review we tried to elucidate these compromises and show the possible way of the evolution of ion channels, from peptides to complex multi-subunit structures, basing on viral examples.
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Affiliation(s)
- Marta V Volovik
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Oleg V Batishchev
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
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15
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Patel DK, Kumar H, Sobhia ME. Exploring the binding dynamics of covalent inhibitors within active site of PL pro in SARS-CoV-2. Comput Biol Chem 2024; 112:108132. [PMID: 38959551 DOI: 10.1016/j.compbiolchem.2024.108132] [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: 02/27/2024] [Revised: 06/03/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024]
Abstract
In the global fight against the COVID-19 pandemic caused by the highly transmissible SARS-CoV-2 virus, the search for potent medications is paramount. With a focused investigation on the SARS-CoV-2 papain-like protease (PLpro) as a promising therapeutic target due to its pivotal role in viral replication and immune modulation, the catalytic triad of PLpro comprising Cys111, His272, and Asp286, highlights Cys111 as an intriguing nucleophilic center for potential covalent bonds with ligands. The detailed analysis of the binding site unveils crucial interactions with both hydrophobic and polar residues, demonstrating the structural insights of the cavity and deepening our understanding of its molecular landscape. The sequence of PLpro among variants of concern (Alpha, Beta, Gamma, Delta and Omicron) and the recent variant of interest, JN.1, remains conserved with no mutations at the active site. Moreover, a thorough exploration of apo, non-covalently bound, and covalently bound PLpro conformations exposes significant conformational changes in loop regions, offering invaluable insights into the intricate dynamics of ligand-protein complex formation. Employing strategic in silico medication repurposing, this study swiftly identifies potential molecules for target inhibition. Within the domain of covalent docking studies and molecular dynamics, using reported inhibitors and clinically tested molecules elucidate the formation of stable covalent bonds with the cysteine residue, laying a robust foundation for potential therapeutic applications. These details not only deepen our comprehension of PLpro inhibition but also play a pivotal role in shaping the dynamic landscape of COVID-19 treatment strategies.
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Affiliation(s)
- Deepesh Kumar Patel
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Mohali, Punjab 160062, India
| | - Harish Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Mohali, Punjab 160062, India
| | - M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Mohali, Punjab 160062, India.
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16
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Park H, Lee SM, Jeong SJ, Kweon YC, Shin GW, Kim WY, Lee-Kwon W, Park CY, Kwon HM. A Gain-of-Function Cleavage of TonEBP by Coronavirus NSP5 to Suppress IFN-β Expression. Cells 2024; 13:1614. [PMID: 39404379 PMCID: PMC11476177 DOI: 10.3390/cells13191614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Revised: 09/20/2024] [Accepted: 09/24/2024] [Indexed: 10/19/2024] Open
Abstract
Human coronaviruses (HCoVs) modify host proteins to evade the antiviral defense and sustain viral expansion. Here, we report tonicity-responsive enhancer (TonE) binding protein (TonEBP) as a cellular target of HCoVs. TonEBP was cleaved into N-terminal and C-terminal fragments (TonEBP NT and TonEBP CT, respectively) by NSP5 from all the HCoVs tested. This cleavage resulted in the loss of TonEBP's ability to stimulate the TonE-driven transcription. On the other hand, TonEBP NT promoted viral expansion in association with the suppression of IFN-β expression. TonEBP NT competed away NF-κB binding to the PRD II domain on the IFN-β promoter. A TonEBP mutant resistant to the cleavage by NSP5 did not promote the viral expansion nor suppress the IFN-β expression. These results demonstrate that HCoVs use a common strategy of targeting TonEBP to suppress the host immune defense.
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Affiliation(s)
- Hyun Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; (H.P.); (S.M.L.); (S.J.J.); (Y.C.K.)
| | - Sang Min Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; (H.P.); (S.M.L.); (S.J.J.); (Y.C.K.)
| | - Su Ji Jeong
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; (H.P.); (S.M.L.); (S.J.J.); (Y.C.K.)
| | - Yeong Cheon Kweon
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; (H.P.); (S.M.L.); (S.J.J.); (Y.C.K.)
| | - Go Woon Shin
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; (H.P.); (S.M.L.); (S.J.J.); (Y.C.K.)
| | - Whi Young Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; (H.P.); (S.M.L.); (S.J.J.); (Y.C.K.)
| | - Whaseon Lee-Kwon
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; (H.P.); (S.M.L.); (S.J.J.); (Y.C.K.)
| | - Chan Young Park
- Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hyug Moo Kwon
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; (H.P.); (S.M.L.); (S.J.J.); (Y.C.K.)
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17
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Saleem W, Carpentier N, Hinnekens C, Oh D, Van Vlierberghe S, Braeckmans K, Nauwynck H. Porcine ex-vivo intestinal mucus has age-dependent blocking activity against transmissible gastroenteritis virus. Vet Res 2024; 55:113. [PMID: 39304917 DOI: 10.1186/s13567-024-01374-y] [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: 06/24/2024] [Accepted: 08/27/2024] [Indexed: 09/22/2024] Open
Abstract
Transmissible gastroenteritis virus (TGEV) causes high mortality in young piglets (< 3 days of age). With aging, the susceptibility/morbidity/mortality rates drop. We previously hypothesized that the age-related changes in the intestinal mucus could be responsible for this resistance. Hence, this study investigated the effect of porcine intestinal mucus from 3-day and 3-week-old pigs on the free mobility of the virulent TGEV Miller strain, and on the infection in swine testicle (ST) cells. Single particle tracking (SPT) revealed that TGEV had significantly higher diffusion coefficients in 3-day mucus compared to 3-week mucus. TGEV and charged and uncharged control nanoparticles diffused freely in 3-day mucus but were hindered by 3-week mucus in the diffusion model; TGEV mimicked the diffusion behavior of negatively charged carboxylated particles. Inoculation of ST cells with TGEV in the presence of 3-week mucus resulted in a significantly lower average number of infected cells (30.9 ± 11.9/5 fields) compared with 3-day mucus (84.6 ± 16.4/5 fields). These results show that 3-week mucus has a significant TGEV-blocking activity compared to 3-day mucus in free diffusion and infection of the underlying susceptible cells. Additionally, a label-free proteomics analysis revealed an increased expression of mucin 13, known for negatively regulating the tight junctions in intestinal epithelium, in 3-day-old pigs. In 3-week-old pigs, a higher expression of mucin 2, a type of secreted mucin which is known for inhibiting coronavirus infection, was observed. Concludingly, this study demonstrated a protective effect of 3-week mucus against viral infections.
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Affiliation(s)
- Waqar Saleem
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
| | - Nathan Carpentier
- Polymer Chemistry & Biomaterials Group, Centre of Macromolecular Chemistry, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium
| | - Charlotte Hinnekens
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Dayoung Oh
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Sandra Van Vlierberghe
- Polymer Chemistry & Biomaterials Group, Centre of Macromolecular Chemistry, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Hans Nauwynck
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
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18
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Berta B, Tordai H, Lukács GL, Papp B, Enyedi Á, Padányi R, Hegedűs T. SARS-CoV-2 envelope protein alters calcium signaling via SERCA interactions. Sci Rep 2024; 14:21200. [PMID: 39261533 PMCID: PMC11391011 DOI: 10.1038/s41598-024-71144-5] [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: 03/06/2024] [Accepted: 08/26/2024] [Indexed: 09/13/2024] Open
Abstract
The clinical management of severe COVID-19 cases is not yet well resolved. Therefore, it is important to identify and characterize cell signaling pathways involved in virus pathogenesis that can be targeted therapeutically. Envelope (E) protein is a structural protein of the virus, which is known to be highly expressed in the infected host cell and is a key virulence factor; however, its role is poorly characterized. The E protein is a single-pass transmembrane protein that can assemble into a pentamer forming a viroporin, perturbing Ca2+ homeostasis. Because it is structurally similar to regulins such as, for example, phospholamban, that regulate the sarco/endoplasmic reticulum calcium ATPases (SERCA), we investigated whether the SARS-CoV-2 E protein affects the SERCA system as an exoregulin. Using FRET experiments we demonstrate that E protein can form oligomers with regulins, and thus can alter the monomer/multimer regulin ratio and consequently influence their interactions with SERCAs. We also confirm that a direct interaction between E protein and SERCA2b results in a decrease in SERCA-mediated ER Ca2+ reload. Structural modeling of the complexes indicates an overlapping interaction site for E protein and endogenous regulins. Our results reveal novel links in the host-virus interaction network that play an important role in viral pathogenesis and may provide a new therapeutic target for managing severe inflammatory responses induced by SARS-CoV-2.
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Affiliation(s)
- Blanka Berta
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Hedvig Tordai
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Gergely L Lukács
- Department of Physiology, McGill University, Montréal, QC, Canada
| | - Béla Papp
- INSERM UMR U976, Hôpital Saint-Louis, Paris, France
- Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Université de Paris, Paris, France
- CEA, DRF-Institut Francois Jacob, Department of Hemato-Immunology Research, Hôpital Saint-Louis, Paris, France
| | - Ágnes Enyedi
- Department of Transfusiology, Semmelweis University, Budapest, Hungary
| | - Rita Padányi
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
| | - Tamás Hegedűs
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
- HUN-REN-SU Biophysical Virology Research Group, Eötvös Loránd Research Network, Budapest, Hungary.
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19
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Somberg NH, Sučec I, Medeiros-Silva J, Jo H, Beresis R, Syed AM, Doudna JA, Hong M. Oligomeric State and Drug Binding of the SARS-CoV-2 Envelope Protein Are Sensitive to the Ectodomain. J Am Chem Soc 2024; 146:24537-24552. [PMID: 39167680 DOI: 10.1021/jacs.4c07686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The envelope (E) protein of SARS-CoV-2 is the smallest of the three structural membrane proteins of the virus. E mediates budding of the progeny virus in the endoplasmic reticulum Golgi intermediate compartment of the cell. It also conducts ions, and this channel activity is associated with the pathogenicity of SARS-CoV-2. The structural basis for these functions is still poorly understood. Biochemical studies of E in detergent micelles found a variety of oligomeric states, but recent 19F solid-state NMR data indicated that the transmembrane domain (ETM, residues 8-38) forms pentamers in lipid bilayers. Hexamethylene amiloride (HMA), an E inhibitor, binds the pentameric ETM at the lipid-exposed helix-helix interface. Here, we investigate the oligomeric structure and drug interaction of an ectodomain-containing E construct, ENTM (residues 1-41). Unexpectedly, 19F spin diffusion NMR data reveal that ENTM adopts an average oligomeric state of dimers instead of pentamers in lipid bilayers. A new amiloride inhibitor, AV-352, shows stronger inhibitory activity than HMA in virus-like particle assays. Distance measurements between 13C-labeled protein and a trifluoromethyl group of AV-352 indicate that the drug binds ENTM with a higher stoichiometry than ETM. We measured protein-drug contacts using a sensitivity-enhanced two-dimensional 13C-19F distance NMR technique. The results indicate that AV-352 binds the C-terminal half of the TM domain, similar to the binding region of HMA. These data provide evidence for the existence of multiple oligomeric states of E in lipid bilayers, which may carry out distinct functions and may be differentially targeted by antiviral drugs.
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Affiliation(s)
- Noah H Somberg
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Iva Sučec
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
| | - Richard Beresis
- Department of Pharmaceutical Chemistry, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
| | - Abdullah M Syed
- Gladstone Institute of Data Science and Biotechnology, San Francisco, California 94158, United States
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California 94720, United States
| | - Jennifer A Doudna
- Gladstone Institute of Data Science and Biotechnology, San Francisco, California 94158, United States
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, California 94158, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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20
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Zheng H, Zhao H, Xiong H, Awais MM, Zeng S, Sun J. Bioproduction and immunogenic evaluation of SARS-CoV-2 prototype vaccine in silkworm BmN cells. Int J Biol Macromol 2024; 276:134027. [PMID: 39033889 DOI: 10.1016/j.ijbiomac.2024.134027] [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: 04/08/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 07/23/2024]
Abstract
COVID-19, caused by the novel coronavirus SARS-CoV-2, has presented a significant challenge to global health, security, and the economy. Vaccination is considered a crucial measure in preventing virus transmission. The silkworm bioreactor has gained widespread usage in antigen presentation, monoclonal antibody preparation, and subunit vaccine development due to its safety, efficiency, convenience, and cost-effectiveness. In this study, we employed silkworm BmN cells and the silkworm MultiBac multigene co-expression system to successfully produce two prototype vaccines: a recombinant baculovirus vector vaccine (NPV) co-displaying the SARS-CoV-2 virus capsid protein and a capsid protein virus-like particle (VLP) vaccine. Following the purification of these vaccines, we immunized BALB/c mice to evaluate their immunogenicity. Our results demonstrated that both VLP and NPV prototype vaccines effectively elicited robust immune responses in mice. However, when equal inoculation doses between groups were compared, the recombinant NPV vaccine exhibited significantly higher serum antibody titers and increased expression of spleen cytokines and lymphocyte immune regulatory factors compared to the VLP group. These results suggested an increased immune efficacy of the recombinant NPV vaccine. Conversely, the VLP prototype vaccine displayed more pronounced effects on lymphocyte cell differentiation induction. This study successfully constructed two distinct morphological recombinant vaccine models and systematically elucidated their differences in humoral immune response and lymphocyte differentiation rate. Furthermore, it has fully harnessed the immense potential of silkworm bioreactors for vaccine research and development, providing valuable technical insights for studying mutated viruses like coronaviruses.
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Affiliation(s)
- Hao Zheng
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Hengfeng Zhao
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Haifan Xiong
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Mian Muhammad Awais
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Songrong Zeng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China.
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21
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Sergio MC, Ricciardi S, Guarino AM, Giaquinto L, De Matteis MA. Membrane remodeling and trafficking piloted by SARS-CoV-2. Trends Cell Biol 2024; 34:785-800. [PMID: 38262893 DOI: 10.1016/j.tcb.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024]
Abstract
The molecular mechanisms underlying SARS-CoV-2 host cell invasion and life cycle have been studied extensively in recent years, with a primary focus on viral entry and internalization with the aim of identifying antiviral therapies. By contrast, our understanding of the molecular mechanisms involved in the later steps of the coronavirus life cycle is relatively limited. In this review, we describe what is known about the host factors and viral proteins involved in the replication, assembly, and egress phases of SARS-CoV-2, which induce significant host membrane rearrangements. We also discuss the limits of the current approaches and the knowledge gaps still to be addressed.
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Affiliation(s)
- Maria Concetta Sergio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy
| | | | - Andrea M Guarino
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy
| | - Laura Giaquinto
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy.
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22
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Ferreira J, Fadl S, Cardoso T, Andrade B, Melo T, Silva E, Agarwal A, Turville S, Saksena N, Rabeh W. Boosting immunity: synergistic antiviral effects of luteolin, vitamin C, magnesium and zinc against SARS-CoV-2 3CLpro. Biosci Rep 2024; 44:BSR20240617. [PMID: 39045772 PMCID: PMC11327220 DOI: 10.1042/bsr20240617] [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: 05/17/2024] [Revised: 07/10/2024] [Accepted: 07/23/2024] [Indexed: 07/25/2024] Open
Abstract
SARS-CoV-2 was first discovered in 2019 and has disseminated throughout the globe to pandemic levels, imposing significant health and economic burdens. Although vaccines against SARS-CoV-2 have been developed, their long-term efficacy and specificity have not been determined, and antiviral drugs remain necessary. Flavonoids, which are commonly found in plants, fruits, and vegetables and are part of the human diet, have attracted considerable attention as potential therapeutic agents due to their antiviral and antimicrobial activities and effects on other biological activities, such as inflammation. The present study uses a combination of biochemical, cellular, molecular dynamics, and molecular docking experiments to provide compelling evidence that the flavonoid luteolin (2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one) has antiviral activity against SARS-CoV-2 3-chymotrypsin-like protease (3CLpro) that is synergistically enhanced by magnesium, zinc, and vitamin C. The IC50 of luteolin against 2 µM 3CLpro is 78 µM and decreases 10-fold to 7.6 µM in the presence of zinc, magnesium, and vitamin C. Thermodynamic stability analyses revealed that luteolin has minimal effects on the structure of 3CLpro, whereas metal ions and vitamin C significantly alter the thermodynamic stability of the protease. Interactome analysis uncovered potential host-virus interactions and functional clusters associated with luteolin activity, supporting the relevance of this flavone for combating SARS-CoV-2 infection. This comprehensive investigation sheds light on luteolin's therapeutic potential and provides insights into its mechanisms of action against SARS-CoV-2. The novel formulation of luteolin, magnesium, zinc, and vitamin C may be an effective avenue for treating COVID-19 patients.
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Affiliation(s)
- Juliana C. Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Thyago H.S. Cardoso
- G42 Healthcare Omics Excellence Center, Masdar City, Abu Dhabi, United Arabes Emirates
| | - Bruno Silva Andrade
- UESB - Universidade Estatudal Do Sudoeste da Bahia. Deparmento de Ciencias Biologicas
| | - Tarcisio S. Melo
- UESB - Universidade Estatudal Do Sudoeste da Bahia. Deparmento de Ciencias Biologicas
| | | | | | | | - Nitin K. Saksena
- Victoria University, Footscray Park Campus, Melbourne, VIC, 3134, Australia
- Aegros Therapeutics Pty Ltd, 5-6 Eden Park Drive, Macquarie Park, NSW 2113, Australia
| | - Wael M. Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
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23
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Volovik MV, Denieva ZG, Gifer PK, Rakitina MA, Batishchev OV. Membrane Activity and Viroporin Assembly for the SARS-CoV-2 E Protein Are Regulated by Cholesterol. Biomolecules 2024; 14:1061. [PMID: 39334828 PMCID: PMC11430671 DOI: 10.3390/biom14091061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/20/2024] [Accepted: 08/25/2024] [Indexed: 09/30/2024] Open
Abstract
The SARS-CoV-2 E protein is an enigmatic viral structural protein with reported viroporin activity associated with the acute respiratory symptoms of COVID-19, as well as the ability to deform cell membranes for viral budding. Like many viroporins, the E protein is thought to oligomerize with a well-defined stoichiometry. However, attempts to determine the structure of the protein complex have yielded inconclusive results, suggesting several possible oligomers, ranging from dimers to pentamers. Here, we combined patch-clamp, confocal fluorescence microscopy on giant unilamellar vesicles, and atomic force microscopy to show that E protein can exhibit two modes of membrane activity depending on membrane lipid composition. In the absence or the presence of a low content of cholesterol, the protein forms short-living transient pores, which are seen as semi-transmembrane defects in a membrane by atomic force microscopy. Approximately 30 mol% cholesterol is a threshold for the transition to the second mode of conductance, which could be a stable pentameric channel penetrating the entire lipid bilayer. Therefore, the E-protein has at least two different types of activity on membrane permeabilization, which are regulated by the amount of cholesterol in the membrane lipid composition and could be associated with different types of protein oligomers.
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Affiliation(s)
- Marta V Volovik
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
| | - Zaret G Denieva
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
| | - Polina K Gifer
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
| | - Maria A Rakitina
- N.I. Pirogov Russian National Research Medical University of the Ministry of Health of the Russian Federation, 1 Ostrovityanova Street, 117997 Moscow, Russia
| | - Oleg V Batishchev
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
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24
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Okabe Y, Ohgitani E, Mazda O, Watanabe T. Anti-SARS-CoV-2 activity of microwave solvolysis lignin from woody biomass. Int J Biol Macromol 2024; 275:133556. [PMID: 38955295 DOI: 10.1016/j.ijbiomac.2024.133556] [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: 12/03/2023] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024]
Abstract
The global pandemic caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has had profoundly detrimental effects on our society. To combat this highly pathogenic virus, we turned our attention to an abundant renewable natural aromatic polymer found in wood. Through a chemical modification of Eucalyptus and Japanese cedar wood via acidic microwave solvolysis in equivolume mixture of 2 % (w/w) aqueous H2SO4, ethylene glycol, and toluene at 190 °C. Subsequently, we separated the resulting solvolysis products through extractions with toluene, ethyl acetate, and ethanol. Among these products, the ethyl acetate extract from Eucalyptus wood (eEAE) demonstrated the highest inhibition effects against the novel SARS-CoV-2. We further divided eEAE into four fractions, and a hexane extract from the ethanol-soluble portion, termed eEAE3, exhibited the most substantial inhibitory rate at 93.0 % when tested at a concentration of 0.5 mg/mL. Analyzing eEAE3 using pyrolysis gas chromatography-mass spectrometry revealed that its primary components are derived from lignin. Additionally, 1H-13C edited-heteronuclear single quantum coherence nuclear magnetic resonance analysis showed that the solvolysis process cleaved major lignin interunit linkages. Considering the abundance and renewability of lignin, the lignin-derived anti-SARS-CoV-2 agent presents a promising potential for application in suppressing infections within our everyday environment.
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Affiliation(s)
- Yumi Okabe
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan
| | - Eriko Ohgitani
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo, Kyoto 602-8566, Japan
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo, Kyoto 602-8566, Japan
| | - Takashi Watanabe
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan.
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25
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Dutta M, Su Y, Plescia CB, Voth GA, Stahelin RV. The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes. J Biol Chem 2024; 300:107456. [PMID: 38866325 PMCID: PMC11298601 DOI: 10.1016/j.jbc.2024.107456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 06/14/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N), and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we used several lipid binding assays and found the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, we show lipid binding occurs in the N protein C-terminal domain, which is supported by extensive in silico analysis. We demonstrate anionic lipid binding occurs for both the free and the N oligomeric forms, suggesting N can associate with membranes in the nucleocapsid form. Based on these results, we present a lipid-dependent model based on in vitro, cellular, and in silico data for the recruitment of N to assembly sites in the lifecycle of SARS-CoV-2.
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Affiliation(s)
- Mandira Dutta
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA
| | - Yuan Su
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA
| | - Caroline B Plescia
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA
| | - Gregory A Voth
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA; Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, Illinois, USA.
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
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26
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Roohi A, Gharagozlou S. Vitamin D supplementation and calcium: Many-faced gods or nobody in fighting against Corona Virus Disease 2019. Clin Nutr ESPEN 2024; 62:172-184. [PMID: 38901939 DOI: 10.1016/j.clnesp.2024.05.015] [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: 11/15/2023] [Revised: 05/07/2024] [Accepted: 05/22/2024] [Indexed: 06/22/2024]
Abstract
In December 2019, Corona Virus Disease 2019 (COVID-19) was first identified and designated as a pandemic in March 2020 due to rapid spread of the virus globally. At the beginning of the pandemic, only a few treatment options, mainly focused on supportive care and repurposing medications, were available. Due to its effects on immune system, vitamin D was a topic of interest during the pandemic, and researchers investigated its potential impact on COVID-19 outcomes. However, the results of studies about the impact of vitamin D on the disease are inconclusive. In the present narrative review, different roles of vitamin D regarding the COVID-19 have been discussed to show that vitamin D supplementation should be recommended carefully.
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Affiliation(s)
- Azam Roohi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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27
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Kononova PA, Selyutina OY, Fomenko VV, Salakhutdinov NF, Polyakov NE. The mutual lipid-mediated effect of the transmembrane domain of SARS-CoV-2 E-protein and glycyrrhizin nicotinate derivatives on the localization in the lipid bilayer. Arch Biochem Biophys 2024; 758:110080. [PMID: 38960345 DOI: 10.1016/j.abb.2024.110080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/27/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024]
Abstract
Glycyrrhizinic acid (GA) is one of the active substances in licorice root. It exhibits antiviral activity against various enveloped viruses, for example, SARS-CoV-2. GA derivatives are promising biologically active compounds from perspective of developing broad-spectrum antiviral agents. Given that GA nicotinate derivatives (Glycyvir) demonstrate activity against various DNA- and RNA-viruses, a search for a possible mechanism of action of these compounds is required. In the present paper, the interaction of Glycyvir with the transmembrane domain of the SARS-CoV-2 E-protein (ETM) in a model lipid membrane was investigated by NMR spectroscopy and molecular dynamics simulation. The lipid-mediated influence on localization of the SARS-CoV-2 E-protein by Glycyvir was observed. The presence of Glycyvir leads to deeper immersion of the ETM in lipid bilayer. Taking into account that E-protein plays a significant role in virus production and takes part in virion assembly and budding, the data on the effect of potential antiviral agents on ETM localization and structure in the lipid environment may provide a basis for further studies of potential coronavirus E-protein inhibitors.
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Affiliation(s)
- Polina A Kononova
- V. V. Voevodsky Institute of Chemical Kinetics and Combustion, 3 Institutskaya St., 630090, Novosibirsk, Russia
| | - Olga Yu Selyutina
- V. V. Voevodsky Institute of Chemical Kinetics and Combustion, 3 Institutskaya St., 630090, Novosibirsk, Russia; Institute of Solid State Chemistry and Mechanochemistry, 18 Kutateladze St., 630128, Novosibirsk, Russia.
| | - Vladislav V Fomenko
- V. V. Voevodsky Institute of Chemical Kinetics and Combustion, 3 Institutskaya St., 630090, Novosibirsk, Russia; N. N. Vorozhtsov Institute of Organic Chemistry, 9 Lavrentiev Ave, 630090, Novosibirsk, Russia
| | - Nariman F Salakhutdinov
- N. N. Vorozhtsov Institute of Organic Chemistry, 9 Lavrentiev Ave, 630090, Novosibirsk, Russia
| | - Nikolay E Polyakov
- V. V. Voevodsky Institute of Chemical Kinetics and Combustion, 3 Institutskaya St., 630090, Novosibirsk, Russia; Institute of Solid State Chemistry and Mechanochemistry, 18 Kutateladze St., 630128, Novosibirsk, Russia
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28
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Cheng L, Rui Y, Wang Y, Chen S, Su J, Yu XF. A glimpse into viral warfare: decoding the intriguing role of highly pathogenic coronavirus proteins in apoptosis regulation. J Biomed Sci 2024; 31:70. [PMID: 39003473 PMCID: PMC11245872 DOI: 10.1186/s12929-024-01062-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 06/18/2024] [Indexed: 07/15/2024] Open
Abstract
Coronaviruses employ various strategies for survival, among which the activation of endogenous or exogenous apoptosis stands out, with viral proteins playing a pivotal role. Notably, highly pathogenic coronaviruses such as SARS-CoV-2, SARS-CoV, and MERS-CoV exhibit a greater array of non-structural proteins compared to low-pathogenic strains, facilitating their ability to induce apoptosis via multiple pathways. Moreover, these viral proteins are adept at dampening host immune responses, thereby bolstering viral replication and persistence. This review delves into the intricate interplay between highly pathogenic coronaviruses and apoptosis, systematically elucidating the molecular mechanisms underpinning apoptosis induction by viral proteins. Furthermore, it explores the potential therapeutic avenues stemming from apoptosis inhibition as antiviral agents and the utilization of apoptosis-inducing viral proteins as therapeutic modalities. These insights not only shed light on viral pathogenesis but also offer novel perspectives for cancer therapy.
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Affiliation(s)
- Leyi Cheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yajuan Rui
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yanpu Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Shiqi Chen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jiaming Su
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Xiao-Fang Yu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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Jarghon AEM, Damayanti NA, Dhamanti I, Notobroto HB, Hidajah AC, Awad AMM. Mapping Vulnerability to Potential Crisis Events in Surabaya City: A GIS-Based Approach. F1000Res 2024; 13:465. [PMID: 39165351 PMCID: PMC11333876 DOI: 10.12688/f1000research.145182.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/27/2024] [Indexed: 08/22/2024] Open
Abstract
Background This study aims to develop a vulnerability map for Surabaya using GIS-based Multi-Criteria Decision Analysis (MCDA) to assess the city's vulnerability to COVID-19. Methods Six key factors influencing vulnerability were identified and their relative importance determined through the Analytic Hierarchy Process (AHP) pairwise comparison matrix. GIS was utilized to classify Surabaya's vulnerability into five levels: very low, low, medium, high, and very high. Results The resulting vulnerability map provides essential insights for decision-makers, healthcare professionals, and disaster management teams. It enables strategic resource allocation, targeted interventions, and formulation of comprehensive response strategies tailored to specific needs of vulnerable districts. Conclusions Through these measures, Surabaya can enhance its resilience and preparedness, ensuring the well-being of its residents in the face of potential emergency outbreaks.
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Affiliation(s)
- Ali E. M. Jarghon
- Faculty of public Health, Airlangga University, Surabaya, East Java, 60114, Indonesia
| | | | - Inge Dhamanti
- Faculty of public Health, Airlangga University, Surabaya, East Java, 60114, Indonesia
| | - Hari Basuki Notobroto
- Faculty of public Health, Airlangga University, Surabaya, East Java, 60114, Indonesia
| | - Atik Choirul Hidajah
- Faculty of public Health, Airlangga University, Surabaya, East Java, 60114, Indonesia
| | - Anas M. M. Awad
- faculty of Geodesy and Geomatics Engineering, Institut Teknologi Bandung, Bandung, West Java, 40132, Indonesia
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Payen SH, Adhikari K, Petereit J, Uppal T, Rossetto CC, Verma SC. SARS-CoV-2 superinfection in CD14 + monocytes with latent human cytomegalovirus (HCMV) promotes inflammatory cascade. Virus Res 2024; 345:199375. [PMID: 38642618 PMCID: PMC11061749 DOI: 10.1016/j.virusres.2024.199375] [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: 02/16/2024] [Revised: 04/07/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 2019 (COVID-19), has posed significant challenges to global health. While much attention has been directed towards understanding the primary mechanisms of SARS-CoV-2 infection, emerging evidence suggests co-infections or superinfections with other viruses may contribute to increased morbidity and mortality, particularly in severe cases of COVID-19. Among viruses that have been reported in patients with SARS-CoV-2, seropositivity for Human cytomegalovirus (HCMV) is associated with increased COVID-19 risk and hospitalization. HCMV is a ubiquitous beta-herpesvirus with a seroprevalence of 60-90 % worldwide and one of the leading causes of mortality in immunocompromised individuals. The primary sites of latency for HCMV include CD14+ monocytes and CD34+ hematopoietic cells. In this study, we sought to investigate SARS-CoV-2 infection of CD14+ monocytes latently infected with HCMV. We demonstrate that CD14+ cells are susceptible and permissive to SARS-CoV-2 infection and detect subgenomic transcripts indicative of replication. To further investigate the molecular changes triggered by SARS-CoV-2 infection in HCMV-latent CD14+ monocytes, we conducted RNA sequencing coupled with bioinformatic differential gene analysis. The results revealed significant differences in cytokine-cytokine receptor interactions and inflammatory pathways in cells superinfected with replication-competent SARS-CoV-2 compared to the heat-inactivated and mock controls. Notably, there was a significant upregulation in transcripts associated with pro-inflammatory response factors and a decrease in anti-inflammatory factors. Taken together, these findings provide a basis for the heightened inflammatory response, offering potential avenues for targeted therapeutic interventions among HCMV-infected severe cases of COVID-19. SUMMARY: COVID-19 patients infected with secondary viruses have been associated with a higher prevalence of severe symptoms. Individuals seropositive for human cytomegalovirus (HCMV) infection are at an increased risk for severe COVID-19 disease and hospitalization. HCMV reactivation has been reported in severe COVID-19 cases with respiratory failure and could be the result of co-infection with SARS-CoV-2 and HCMV. In a cell culture model of superinfection, HCMV has previously been shown to increase infection of SARS-CoV-2 of epithelial cells by upregulating the human angiotensin-converting enzyme-2 (ACE2) receptor. In this study, we utilize CD14+ monocytes, a major cell type that harbors latent HCMV, to investigate co-infection of SARS-CoV-2 and HCMV. This study is a first step toward understanding the mechanism that may facilitate increased COVID-19 disease severity in patients infected with SARS-CoV-2 and HCMV.
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Affiliation(s)
- Shannon Harger Payen
- Reno School of Medicine, Department of Microbiology & Immunology/MS 320, University of Nevada, Reno, NV 89557, United States
| | - Kabita Adhikari
- Reno School of Medicine, Department of Microbiology & Immunology/MS 320, University of Nevada, Reno, NV 89557, United States
| | - Juli Petereit
- Nevada Bioinformatics Center (RRID:SCR_017802), University of Nevada, Reno, NV 89557, United States
| | - Timsy Uppal
- Reno School of Medicine, Department of Microbiology & Immunology/MS 320, University of Nevada, Reno, NV 89557, United States
| | - Cyprian C Rossetto
- Reno School of Medicine, Department of Microbiology & Immunology/MS 320, University of Nevada, Reno, NV 89557, United States
| | - Subhash C Verma
- Reno School of Medicine, Department of Microbiology & Immunology/MS 320, University of Nevada, Reno, NV 89557, United States.
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Bepler T, Barrera MD, Rooney MT, Xiong Y, Kuang H, Goodell E, Goodwin MJ, Harbron E, Fu R, Mihailescu M, Narayanan A, Cotten ML. Antiviral activity of the host defense peptide piscidin 1: investigating a membrane-mediated mode of action. Front Chem 2024; 12:1379192. [PMID: 38988727 PMCID: PMC11233706 DOI: 10.3389/fchem.2024.1379192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/08/2024] [Indexed: 07/12/2024] Open
Abstract
Outbreaks of viral diseases are on the rise, fueling the search for antiviral therapeutics that act on a broad range of viruses while remaining safe to human host cells. In this research, we leverage the finding that the plasma membranes of host cells and the lipid bilayers surrounding enveloped viruses differ in lipid composition. We feature Piscidin 1 (P1), a cationic host defense peptide (HDP) that has antimicrobial effects and membrane activity associated with its N-terminal region where a cluster of aromatic residues and copper-binding motif reside. While few HDPs have demonstrated antiviral activity, P1 acts in the micromolar range against several enveloped viruses that vary in envelope lipid composition. Notably, it inhibits HIV-1, a virus that has an envelope enriched in cholesterol, a lipid associated with higher membrane order and stability. Here, we first document through plaque assays that P1 boasts strong activity against SARS-CoV-2, which has an envelope low in cholesterol. Second, we extend previous studies done with homogeneous bilayers and devise cholesterol-containing zwitterionic membranes that contain the liquid disordered (Ld; low in cholesterol) and ordered (Lo, rich in cholesterol) phases. Using dye leakage assays and cryo-electron microscopy on vesicles, we show that P1 has dramatic permeabilizing capability on the Lo/Ld, an effect matched by a strong ability to aggregate, fuse, and thin the membranes. Differential scanning calorimetry and NMR experiments demonstrate that P1 mixes the lipid content of vesicles and alters the stability of the Lo. Structural studies by NMR indicate that P1 interacts with the Lo/Ld by folding into an α-helix that lies parallel to the membrane surface. Altogether, these results show that P1 is more disruptive to phase-separated than homogenous cholesterol-containing bilayers, suggesting an ability to target domain boundaries. Overall, this multi-faceted research highlights how a peptide that interacts strongly with membranes through an aromatic-rich N-terminal motif disrupt viral envelope mimics. This represents an important step towards the development of novel peptides with broad-spectrum antiviral activity.
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Affiliation(s)
- Tristan Bepler
- New York Structural Biology Center, New York, NY, United States
| | - Michael D. Barrera
- School of Systems Biology, George Mason University, Manassas, VA, United States
| | - Mary T. Rooney
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
- Department of Chemistry, Hofstra University, Hempstead, NY, United States
| | - Yawei Xiong
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, United States
| | - Evan Goodell
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
| | - Matthew J. Goodwin
- Department of Chemistry, William & Mary, Williamsburg, VA, United States
| | - Elizabeth Harbron
- Department of Chemistry, William & Mary, Williamsburg, VA, United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL, United States
| | - Mihaela Mihailescu
- Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Aarthi Narayanan
- Department of Biology, George Mason University, Manassas, VA, United States
| | - Myriam L. Cotten
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
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Geanes ES, McLennan R, Pierce SH, Menden HL, Paul O, Sampath V, Bradley T. SARS-CoV-2 envelope protein regulates innate immune tolerance. iScience 2024; 27:109975. [PMID: 38827398 PMCID: PMC11140213 DOI: 10.1016/j.isci.2024.109975] [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: 11/28/2023] [Revised: 03/01/2024] [Accepted: 05/10/2024] [Indexed: 06/04/2024] Open
Abstract
Severe COVID-19 often leads to secondary infections and sepsis that contribute to long hospital stays and mortality. However, our understanding of the precise immune mechanisms driving severe complications after SARS-CoV-2 infection remains incompletely understood. Here, we provide evidence that the SARS-CoV-2 envelope (E) protein initiates innate immune inflammation, via toll-like receptor 2 signaling, and establishes a sustained state of innate immune tolerance following initial activation. Monocytes in this tolerant state exhibit reduced responsiveness to secondary stimuli, releasing lower levels of cytokines and chemokines. Mice exposed to E protein before secondary lipopolysaccharide challenge show diminished pro-inflammatory cytokine expression in the lung, indicating that E protein drives this tolerant state in vivo. These findings highlight the potential of the SARS-CoV-2 E protein to induce innate immune tolerance, contributing to long-term immune dysfunction that could lead to susceptibility to subsequent infections, and uncovers therapeutic targets aimed at restoring immune function following SARS-CoV-2 infection.
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Affiliation(s)
- Eric S. Geanes
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Rebecca McLennan
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Stephen H. Pierce
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Heather L. Menden
- Division of Neonatology, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Oishi Paul
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
| | - Venkatesh Sampath
- Division of Neonatology, Children’s Mercy Research Institute, Kansas City, MO, USA
- Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA
| | - Todd Bradley
- Genomic Medicine Center, Children’s Mercy Research Institute, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA
- Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA
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Shao HH, Yin RX. Pathogenic mechanisms of cardiovascular damage in COVID-19. Mol Med 2024; 30:92. [PMID: 38898389 PMCID: PMC11186295 DOI: 10.1186/s10020-024-00855-2] [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: 03/09/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND COVID-19 is a new infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS CoV-2). Since the outbreak in December 2019, it has caused an unprecedented world pandemic, leading to a global human health crisis. Although SARS CoV-2 mainly affects the lungs, causing interstitial pneumonia and severe acute respiratory distress syndrome, a number of patients often have extensive clinical manifestations, such as gastrointestinal symptoms, cardiovascular damage and renal dysfunction. PURPOSE This review article discusses the pathogenic mechanisms of cardiovascular damage in COVID-19 patients and provides some useful suggestions for future clinical diagnosis, treatment and prevention. METHODS An English-language literature search was conducted in PubMed and Web of Science databases up to 12th April, 2024 for the terms "COVID-19", "SARS CoV-2", "cardiovascular damage", "myocardial injury", "myocarditis", "hypertension", "arrhythmia", "heart failure" and "coronary heart disease", especially update articles in 2023 and 2024. Salient medical literatures regarding the cardiovascular damage of COVID-19 were selected, extracted and synthesized. RESULTS The most common cardiovascular damage was myocarditis and pericarditis, hypertension, arrhythmia, myocardial injury and heart failure, coronary heart disease, stress cardiomyopathy, ischemic stroke, blood coagulation abnormalities, and dyslipidemia. Two important pathogenic mechanisms of the cardiovascular damage may be direct viral cytotoxicity as well as indirect hyperimmune responses of the body to SARS CoV-2 infection. CONCLUSIONS Cardiovascular damage in COVID-19 patients is common and portends a worse prognosis. Although the underlying pathophysiological mechanisms of cardiovascular damage related to COVID-19 are not completely clear, two important pathogenic mechanisms of cardiovascular damage may be the direct damage of the SARSCoV-2 infection and the indirect hyperimmune responses.
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Affiliation(s)
- Hong-Hua Shao
- Department of Infectious Diseases, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, No. 1 Erli, Changgang Road, Nanning, Guangxi, 530023, People's Republic of China
| | - Rui-Xing Yin
- Department of Infectious Diseases, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, No. 1 Erli, Changgang Road, Nanning, Guangxi, 530023, People's Republic of China.
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi, 530021, People's Republic of China.
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Monarca L, Ragonese F, Biagini A, Sabbatini P, Pacini M, Zucchi A, Spaccapelo R, Ferrari P, Nicolini A, Fioretti B. Electrophysiological Impact of SARS-CoV-2 Envelope Protein in U251 Human Glioblastoma Cells: Possible Implications in Gliomagenesis? Int J Mol Sci 2024; 25:6669. [PMID: 38928376 PMCID: PMC11203726 DOI: 10.3390/ijms25126669] [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: 04/12/2024] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
SARS-CoV-2 is the causative agent of the COVID-19 pandemic, the acute respiratory disease which, so far, has led to over 7 million deaths. There are several symptoms associated with SARS-CoV-2 infections which include neurological and psychiatric disorders, at least in the case of pre-Omicron variants. SARS-CoV-2 infection can also promote the onset of glioblastoma in patients without prior malignancies. In this study, we focused on the Envelope protein codified by the virus genome, which acts as viroporin and that is reported to be central for virus propagation. In particular, we characterized the electrophysiological profile of E-protein transfected U251 and HEK293 cells through the patch-clamp technique and FURA-2 measurements. Specifically, we observed an increase in the voltage-dependent (Kv) and calcium-dependent (KCa) potassium currents in HEK293 and U251 cell lines, respectively. Interestingly, in both cellular models, we observed a depolarization of the mitochondrial membrane potential in accordance with an alteration of U251 cell growth. We, therefore, investigated the transcriptional effect of E protein on the signaling pathways and found several gene alterations associated with apoptosis, cytokines and WNT pathways. The electrophysiological and transcriptional changes observed after E protein expression could explain the impact of SARS-CoV-2 infection on gliomagenesis.
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Affiliation(s)
- Lorenzo Monarca
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06123 Perugia, Italy; (L.M.); (F.R.); (A.B.); (P.S.)
- Department of Medicine and Surgery, Perugia Medical School, University of Perugia, 06132 Perugia, Italy;
| | - Francesco Ragonese
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06123 Perugia, Italy; (L.M.); (F.R.); (A.B.); (P.S.)
| | - Andrea Biagini
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06123 Perugia, Italy; (L.M.); (F.R.); (A.B.); (P.S.)
- Department of Medicine and Surgery, Perugia Medical School, University of Perugia, 06132 Perugia, Italy;
| | - Paola Sabbatini
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06123 Perugia, Italy; (L.M.); (F.R.); (A.B.); (P.S.)
| | - Matteo Pacini
- Urology Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (A.Z.)
| | - Alessandro Zucchi
- Urology Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy; (M.P.); (A.Z.)
| | - Roberta Spaccapelo
- Department of Medicine and Surgery, Perugia Medical School, University of Perugia, 06132 Perugia, Italy;
- Interuniversity Consortium for Biotechnology (C.I.B.), 34148 Trieste, Italy
| | - Paola Ferrari
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, 56126 Pisa, Italy;
| | - Andrea Nicolini
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, 56126 Pisa, Italy;
| | - Bernard Fioretti
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06123 Perugia, Italy; (L.M.); (F.R.); (A.B.); (P.S.)
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Nimer NA, Nimer SN. Immunization against Medically Important Human Coronaviruses of Public Health Concern. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2024; 2024:9952803. [PMID: 38938549 PMCID: PMC11208815 DOI: 10.1155/2024/9952803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/14/2024] [Accepted: 05/20/2024] [Indexed: 06/29/2024]
Abstract
SARS-CoV-2 is a virus that affects the human immune system. It was observed to be on the rise since the beginning of 2020 and turned into a life-threatening pandemic. Scientists have tried to develop a possible preventive and therapeutic drug against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and other related coronaviruses by assessing COVID-19-recovered persons' immunity. This study aims to review immunization against SARS-CoV-2, along with exploring the interventions that have been developed for the prevention of SARS-CoV-2. This study also highlighted the role of phototherapy in treating SARS-CoV infection. The study adopted a review approach to gathering the information available and the progress that has been made in the treatment and prevention of COVID-19. Various vaccinations, including nucleotide, subunit, and vector-based vaccines, as well as attenuated and inactivated forms that have already been shown to have prophylactic efficacy against the Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV, have been summarized. Neutralizing and non-neutralizing antibodies are all associated with viral infections. Because there is no specific antiviral vaccine or therapies for coronaviruses, the main treatment strategy is supportive care, which is reinforced by combining broad-spectrum antivirals, convalescent plasma, and corticosteroids. COVID-19 has been a challenge to keep reconsidering the usual approaches to regulatory evaluation as a result of getting mixed and complicated findings on the vaccines, as well as licensing procedures. However, it is observed that medicinal herbs also play an important role in treating infection of the upper respiratory tract, the principal symptom of SARS-CoV due to their natural bioactive composite. However, some Traditional Chinese Medicines contain mutagens and nephrotoxins and the toxicological properties of the majority of Chinese herbal remedies are unknown. Therefore, to treat the COVID-19 infection along with conventional treatment, it is recommended that herb-drug interaction be examined thoroughly.
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Affiliation(s)
- Nabil A. Nimer
- Faculty of Pharmacy, Philadelphia University, Amman, Jordan
| | - Seema N. Nimer
- School of Medicine, The University of Jordan, Amman, Jordan
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Lu W, Yan L, Tang X, Wang X, Du J, Zou Z, Li L, Ye J, Zhou L. Efficacy and safety of mesenchymal stem cells therapy in COVID-19 patients: a systematic review and meta-analysis of randomized controlled trials. J Transl Med 2024; 22:550. [PMID: 38851730 PMCID: PMC11162060 DOI: 10.1186/s12967-024-05358-6] [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: 04/14/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) has become a serious public health issue. In COVID-19 patients, the elevated levels of inflammatory cytokines lead to the manifestation of COVID-19 symptoms, such as lung tissue edema, lung diffusion dysfunction, acute respiratory distress syndrome (ARDS), secondary infection, and ultimately mortality. Mesenchymal stem cells (MSCs) exhibit anti-inflammatory and immunomodulatory properties, thus providing a potential treatment option for COVID-19. The number of clinical trials of MSCs for COVID-19 has been rising. However, the treatment protocols and therapeutic effects of MSCs for COVID-19 patients are inconsistent. This meta-analysis was performed to systematically determine the safety and efficacy of MSC infusion in COVID-19 patients. METHODS We conducted a comprehensive literature search from PubMed/Medline, Web of Science, EMBASE, and Cochrane Library up to 22 November 2023 to screen for eligible randomized controlled trials. Inclusion and exclusion criteria for searched literature were formulated according to the PICOS principle, followed by the use of literature quality assessment tools to assess the risk of bias. Finally, outcome measurements including therapeutic efficacy, clinical symptoms, and adverse events of each study were extracted for statistical analysis. RESULTS A total of 14 randomized controlled trials were collected. The results of enrolled studies demonstrated that patients with COVID-19 pneumonia who received MSC inoculation showed a decreased mortality compared with counterparts who received conventional treatment (RR: 0.76; 95% CI [0.60, 0.96]; p = 0.02). Reciprocally, MSC inoculation improved the clinical symptoms in patients (RR: 1.28; 95% CI [1.06, 1.55]; p = 0.009). In terms of immune biomarkers, MSC treatment inhibited inflammation responses in COVID-19 patients, as was indicated by the decreased levels of CRP and IL-6. Importantly, our results showed that no significant differences in the incidence of adverse reactions or serious adverse events were monitored in patients after MSC inoculation. CONCLUSION This meta-analysis demonstrated that MSC inoculation is effective and safe in the treatment of patients with COVID-19 pneumonia. Without increasing the incidence of adverse events or serious adverse events, MSC treatment decreased patient mortality and inflammatory levels and improved the clinical symptoms in COVID-19 patients. However, large-cohort randomized controlled trials with expanded numbers of patients are required to further confirm our results.
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Affiliation(s)
- Wenming Lu
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China
- School of Rehabilitation Medicine, Gannan Medical University, GanZhou City, 341000, Jiangxi, People's Republic of China
- The First Clinical College of Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China
| | - Longxiang Yan
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China
- School of Rehabilitation Medicine, Gannan Medical University, GanZhou City, 341000, Jiangxi, People's Republic of China
- The First Clinical College of Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China
| | - Xingkun Tang
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China
- School of Rehabilitation Medicine, Gannan Medical University, GanZhou City, 341000, Jiangxi, People's Republic of China
| | - Xuesong Wang
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China
- School of Rehabilitation Medicine, Gannan Medical University, GanZhou City, 341000, Jiangxi, People's Republic of China
| | - Jing Du
- School of Rehabilitation Medicine, Gannan Medical University, GanZhou City, 341000, Jiangxi, People's Republic of China
| | - Zhengwei Zou
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China
- Ganzhou Key Laboratory of Stem Cell and Regenerative Medicine, Ganzhou, 341000, Jiangxi, People's Republic of China
| | - Lincai Li
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China
- Ganzhou Key Laboratory of Stem Cell and Regenerative Medicine, Ganzhou, 341000, Jiangxi, People's Republic of China
| | - Junsong Ye
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China
- Ganzhou Key Laboratory of Stem Cell and Regenerative Medicine, Ganzhou, 341000, Jiangxi, People's Republic of China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China
- Jiangxi Provincal Key Laboratory of Tissue Engineering, Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China
| | - Lin Zhou
- Subcenter for Stem Cell Clinical Translation, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China.
- Ganzhou Key Laboratory of Stem Cell and Regenerative Medicine, Ganzhou, 341000, Jiangxi, People's Republic of China.
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China.
- Jiangxi Provincal Key Laboratory of Tissue Engineering, Gannan Medical University, Ganzhou, 341000, Jiangxi, People's Republic of China.
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Giacon N, Lo Cascio E, Pennacchietti V, De Maio F, Santarelli G, Sibilia D, Tiberio F, Sanguinetti M, Lattanzi W, Toto A, Arcovito A. PDZ2-conjugated-PLGA nanoparticles are tiny heroes in the battle against SARS-CoV-2. Sci Rep 2024; 14:13059. [PMID: 38844490 PMCID: PMC11156922 DOI: 10.1038/s41598-024-63239-w] [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: 03/22/2024] [Accepted: 05/27/2024] [Indexed: 06/09/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has highlighted the urgent need for innovative antiviral strategies to fight viral infections. Although a substantial part of the overall effort has been directed at the Spike protein to create an effective global vaccination strategy, other proteins have also been examined and identified as possible therapeutic targets. Among them, although initially underestimated, there is the SARS-CoV-2 E-protein, which turned out to be a key factor in viral pathogenesis due to its role in virus budding, assembly and spreading. The C-terminus of E-protein contains a PDZ-binding motif (PBM) that plays a key role in SARS-CoV-2 virulence as it is recognized and bound by the PDZ2 domain of the human tight junction protein ZO-1. The binding between the PDZ2 domain of ZO-1 and the C-terminal portion of SARS-CoV-2 E-protein has been extensively characterized. Our results prompted us to develop a possible adjuvant therapeutic strategy aimed at slowing down or inhibiting virus-mediated pathogenesis. Such innovation consists in the design and synthesis of externally PDZ2-ZO1 functionalized PLGA-based nanoparticles to be used as intracellular decoy. Contrary to conventional strategies, this innovative approach aims to capitalize on the E protein-PDZ2 interaction to prevent virus assembly and replication. In fact, the conjugation of the PDZ2 domain to polymeric nanoparticles increases the affinity toward the E protein effectively creating a "molecular sponge" able to sequester E proteins within the intracellular environment of infected cells. Our in vitro studies on selected cellular models, show that these nanodevices significantly reduce SARS-CoV-2-mediated virulence, emphasizing the importance of exploiting viral-host interactions for therapeutic benefit.
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Affiliation(s)
- Noah Giacon
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
| | - Ettore Lo Cascio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
| | - Valeria Pennacchietti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Flavio De Maio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Giulia Santarelli
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Diego Sibilia
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
| | - Federica Tiberio
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Wanda Lattanzi
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
- Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy.
| | - Alessandro Arcovito
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy.
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy.
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Cui L, Li T, Xue W, Zhang S, Wang H, Liu H, Gu Y, Xia N, Li S. Comprehensive Overview of Broadly Neutralizing Antibodies against SARS-CoV-2 Variants. Viruses 2024; 16:900. [PMID: 38932192 PMCID: PMC11209230 DOI: 10.3390/v16060900] [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: 04/08/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Currently, SARS-CoV-2 has evolved into various variants, including the numerous highly mutated Omicron sub-lineages, significantly increasing immune evasion ability. The development raises concerns about the possibly diminished effectiveness of available vaccines and antibody-based therapeutics. Here, we describe those representative categories of broadly neutralizing antibodies (bnAbs) that retain prominent effectiveness against emerging variants including Omicron sub-lineages. The molecular characteristics, epitope conservation, and resistance mechanisms of these antibodies are further detailed, aiming to offer suggestion or direction for the development of therapeutic antibodies, and facilitate the design of vaccines with broad-spectrum potential.
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Affiliation(s)
- Lingyan Cui
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Tingting Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Wenhui Xue
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Sibo Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Hong Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Hongjing Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ying Gu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Shaowei Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
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Tolksdorf B, Heinze J, Niemeyer D, Röhrs V, Berg J, Drosten C, Kurreck J. Development of a highly stable, active small interfering RNA with broad activity against SARS-CoV viruses. Antiviral Res 2024; 226:105879. [PMID: 38599550 DOI: 10.1016/j.antiviral.2024.105879] [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: 02/02/2024] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Treatment options for COVID-19 remain limited. Here, we report the optimization of an siRNA targeting the highly conserved leader region of SARS-CoV-2. The siRNA was rendered nuclease resistant by the introduction of modified nucleotides without loss of activity. Importantly, the siRNA also retained its inhibitory activity against the emerged omicron sublineage variant BA.2, which occurred after the siRNA was designed and is resistant to other antiviral agents such as antibodies. In addition, we show that a second highly active siRNA designed against the viral 5'-UTR can be applied as a rescue molecule, to minimize the spread of escape mutations. We therefore consider our siRNA-based molecules to be promising broadly active candidates for the treatment of current and future SARS-CoV-2 variants.
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Affiliation(s)
- Beatrice Tolksdorf
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany
| | - Julian Heinze
- German Center for Infection Research (DZIF), Charitéplatz 1, 10117, Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, 10117, Germany
| | - Daniela Niemeyer
- German Center for Infection Research (DZIF), Charitéplatz 1, 10117, Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, 10117, Germany
| | - Viola Röhrs
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany
| | - Johanna Berg
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany
| | - Christian Drosten
- German Center for Infection Research (DZIF), Charitéplatz 1, 10117, Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, 10117, Germany
| | - Jens Kurreck
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany.
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40
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Yu R, Dong S, Chen B, Si F, Li C. Developing Next-Generation Live Attenuated Vaccines for Porcine Epidemic Diarrhea Using Reverse Genetic Techniques. Vaccines (Basel) 2024; 12:557. [PMID: 38793808 PMCID: PMC11125984 DOI: 10.3390/vaccines12050557] [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: 04/12/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is the etiology of porcine epidemic diarrhea (PED), a highly contagious digestive disease in pigs and especially in neonatal piglets, in which a mortality rate of up to 100% will be induced. Immunizing pregnant sows remains the most promising and effective strategy for protecting their neonatal offspring from PEDV. Although half a century has passed since its first report in Europe and several prophylactic vaccines (inactivated or live attenuated) have been developed, PED still poses a significant economic concern to the swine industry worldwide. Hence, there is an urgent need for novel vaccines in clinical practice, especially live attenuated vaccines (LAVs) that can induce a strong protective lactogenic immune response in pregnant sows. Reverse genetic techniques provide a robust tool for virological research from the function of viral proteins to the generation of rationally designed vaccines. In this review, after systematically summarizing the research progress on virulence-related viral proteins, we reviewed reverse genetics techniques for PEDV and their application in the development of PED LAVs. Then, we probed into the potential methods for generating safe, effective, and genetically stable PED LAV candidates, aiming to provide new ideas for the rational design of PED LAVs.
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Affiliation(s)
| | | | | | - Fusheng Si
- Institute of Animal Husbandry and Veterinary Medicine, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai 201106, China; (R.Y.); (S.D.); (B.C.)
| | - Chunhua Li
- Institute of Animal Husbandry and Veterinary Medicine, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai 201106, China; (R.Y.); (S.D.); (B.C.)
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41
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Zhao Z, Bashiri S, Ziora ZM, Toth I, Skwarczynski M. COVID-19 Variants and Vaccine Development. Viruses 2024; 16:757. [PMID: 38793638 PMCID: PMC11125726 DOI: 10.3390/v16050757] [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: 04/22/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), the global pandemic caused by severe acute respiratory syndrome 2 virus (SARS-CoV-2) infection, has caused millions of infections and fatalities worldwide. Extensive SARS-CoV-2 research has been conducted to develop therapeutic drugs and prophylactic vaccines, and even though some drugs have been approved to treat SARS-CoV-2 infection, treatment efficacy remains limited. Therefore, preventive vaccination has been implemented on a global scale and represents the primary approach to combat the COVID-19 pandemic. Approved vaccines vary in composition, although vaccine design has been based on either the key viral structural (spike) protein or viral components carrying this protein. Therefore, mutations of the virus, particularly mutations in the S protein, severely compromise the effectiveness of current vaccines and the ability to control COVID-19 infection. This review begins by describing the SARS-CoV-2 viral composition, the mechanism of infection, the role of angiotensin-converting enzyme 2, the host defence responses against infection and the most common vaccine designs. Next, this review summarizes the common mutations of SARS-CoV-2 and how these mutations change viral properties, confer immune escape and influence vaccine efficacy. Finally, this review discusses global strategies that have been employed to mitigate the decreases in vaccine efficacy encountered against new variants.
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Affiliation(s)
- Ziyao Zhao
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Sahra Bashiri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
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42
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Nagahawatta DP, Liyanage NM, Jayawardena TU, Jayawardhana HHACK, Jeong SH, Kwon HJ, Jeon YJ. Role of marine natural products in the development of antiviral agents against SARS-CoV-2: potential and prospects. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:280-297. [PMID: 38827130 PMCID: PMC11136918 DOI: 10.1007/s42995-023-00215-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 10/17/2023] [Indexed: 06/04/2024]
Abstract
A novel coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has surfaced and caused global concern owing to its ferocity. SARS-CoV-2 is the causative agent of coronavirus disease 2019; however, it was only discovered at the end of the year and was considered a pandemic by the World Health Organization. Therefore, the development of novel potent inhibitors against SARS-CoV-2 and future outbreaks is urgently required. Numerous naturally occurring bioactive substances have been studied in the clinical setting for diverse disorders. The intricate infection and replication mechanism of SARS-CoV-2 offers diverse therapeutic drug targets for developing antiviral medicines by employing natural products that are safer than synthetic compounds. Marine natural products (MNPs) have received increased attention in the development of novel drugs owing to their high diversity and availability. Therefore, this review article investigates the infection and replication mechanisms, including the function of the SARS-CoV-2 genome and structure. Furthermore, we highlighted anti-SARS-CoV-2 therapeutic intervention efforts utilizing MNPs and predicted SARS-CoV-2 inhibitor design. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00215-9.
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Affiliation(s)
- D. P. Nagahawatta
- Department of Marine Life Sciences, Jeju National University, Jeju, 690-756 Republic of Korea
| | - N. M. Liyanage
- Department of Marine Life Sciences, Jeju National University, Jeju, 690-756 Republic of Korea
| | - Thilina U. Jayawardena
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 4M3 Canada
| | | | - Seong-Hun Jeong
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Hyung-Jun Kwon
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - You-Jin Jeon
- Department of Marine Life Sciences, Jeju National University, Jeju, 690-756 Republic of Korea
- Marine Science Institute, Jeju National University, Jeju, 63333 Republic of Korea
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Wang TH, Shao HP, Zhao BQ, Zhai HL. Molecular Insights into the Variability in Infection and Immune Evasion Capabilities of SARS-CoV-2 Variants: A Sequence and Structural Investigation of the RBD Domain. J Chem Inf Model 2024; 64:3503-3523. [PMID: 38517012 DOI: 10.1021/acs.jcim.3c01730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continuously emerge, an increasing number of mutations are accumulating in the Spike protein receptor-binding domain (RBD) region. Through sequence analysis of various Variants of Concern (VOC), we identified that they predominantly fall within the ο lineage although recent variants introduce any novel mutations in the RBD. Molecular dynamics simulations were employed to compute the binding free energy of these variants with human Angiotensin-converting enzyme 2 (ACE2). Structurally, the binding interface of the ο RBD displays a strong positive charge, complementing the negatively charged binding interface of ACE2, resulting in a significant enhancement in the electrostatic potential energy for the ο variants. Although the increased potential energy is partially offset by the rise in polar solvation free energy, enhanced electrostatic potential contributes to the long-range recognition between the ο variant's RBD and ACE2. We also conducted simulations of glycosylated ACE2-RBD proteins. The newly emerged ο (JN.1) variant has added a glycosylation site at N-354@RBD, which significantly weakened its binding affinity with ACE2. Further, our interaction studies with three monoclonal antibodies across multiple SARS-CoV-2 strains revealed a diminished neutralization efficacy against the ο variants, primarily attributed to the electrostatic repulsion between the antibodies and RBD interface. Considering the characteristics of the ο variant and the trajectory of emerging strains, we propose that newly developed antibodies against SARS-CoV-2 RBD should have surfaces rich in negative potential and, postbinding, exhibit strong van der Waals interactions. These findings provide invaluable guidance for the formulation of future therapeutic strategies.
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Affiliation(s)
- Tian Hua Wang
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Hai Ping Shao
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Bing Qiang Zhao
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Hong Lin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
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Hillung J, Olmo-Uceda MJ, Muñoz-Sánchez JC, Elena SF. Accumulation Dynamics of Defective Genomes during Experimental Evolution of Two Betacoronaviruses. Viruses 2024; 16:644. [PMID: 38675984 PMCID: PMC11053736 DOI: 10.3390/v16040644] [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: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Virus-encoded replicases often generate aberrant RNA genomes, known as defective viral genomes (DVGs). When co-infected with a helper virus providing necessary proteins, DVGs can multiply and spread. While DVGs depend on the helper virus for propagation, they can in some cases disrupt infectious virus replication, impact immune responses, and affect viral persistence or evolution. Understanding the dynamics of DVGs alongside standard viral genomes during infection remains unclear. To address this, we conducted a long-term experimental evolution of two betacoronaviruses, the human coronavirus OC43 (HCoV-OC43) and the murine hepatitis virus (MHV), in cell culture at both high and low multiplicities of infection (MOI). We then performed RNA-seq at regular time intervals, reconstructed DVGs, and analyzed their accumulation dynamics. Our findings indicate that DVGs evolved to exhibit greater diversity and abundance, with deletions and insertions being the most common types. Notably, some high MOI deletions showed very limited temporary existence, while others became prevalent over time. We observed differences in DVG abundance between high and low MOI conditions in HCoV-OC43 samples. The size distribution of HCoV-OC43 genomes with deletions differed between high and low MOI passages. In low MOI lineages, short and long DVGs were the most common, with an additional cluster in high MOI lineages which became more prevalent along evolutionary time. MHV also showed variations in DVG size distribution at different MOI conditions, though they were less pronounced compared to HCoV-OC43, suggesting a more random distribution of DVG sizes. We identified hotspot regions for deletions that evolved at a high MOI, primarily within cistrons encoding structural and accessory proteins. In conclusion, our study illustrates the widespread formation of DVGs during betacoronavirus evolution, influenced by MOI and cell- and virus-specific factors.
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Affiliation(s)
- Julia Hillung
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-UV, Catedrático Agustín Escardino Benlloch 9, 46980 Paterna, Valencia, Spain; (J.H.); (M.J.O.-U.); (J.C.M.-S.)
| | - María J. Olmo-Uceda
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-UV, Catedrático Agustín Escardino Benlloch 9, 46980 Paterna, Valencia, Spain; (J.H.); (M.J.O.-U.); (J.C.M.-S.)
| | - Juan C. Muñoz-Sánchez
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-UV, Catedrático Agustín Escardino Benlloch 9, 46980 Paterna, Valencia, Spain; (J.H.); (M.J.O.-U.); (J.C.M.-S.)
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-UV, Catedrático Agustín Escardino Benlloch 9, 46980 Paterna, Valencia, Spain; (J.H.); (M.J.O.-U.); (J.C.M.-S.)
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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Zakiyyah SN, Irkham, Einaga Y, Gultom NS, Fauzia RP, Kadja GTM, Gaffar S, Ozsoz M, Hartati YW. Green Synthesis of Ceria Nanoparticles from Cassava Tubers for Electrochemical Aptasensor Detection of SARS-CoV-2 on a Screen-Printed Carbon Electrode. ACS APPLIED BIO MATERIALS 2024; 7:2488-2498. [PMID: 38577953 DOI: 10.1021/acsabm.4c00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Green synthesis approaches for making nanosized ceria using starch from cassava as template molecules to control the particle size are reported. The results of the green synthesis of ceria with an optimum calcination temperature of 800 °C shows a size distribution of each particle of less than 30 nm with an average size of 9.68 nm, while the ratio of Ce3+ to Ce4+ was 25.6%. The green-synthesized nanoceria are applied to increase the sensitivity and attach biomolecules to the electrode surface of the electrochemical aptasensor system for coronavirus disease (COVID-19). The response of the aptasensor to the receptor binding domain of the virus was determined with the potassium ferricyanide redox system. The screen-printed carbon electrode that has been modified with green-synthesized nanoceria shows 1.43 times higher conductivity than the bare electrode, while those modified with commercial ceria increase only 1.18 times. Using an optimized parameter for preparing the aptasensors, the detection and quantification limits were 1.94 and 5.87 ng·mL-1, and the accuracy and precision values were 98.5 and 89.1%. These results show that green-synthesized ceria could be a promising approach for fabricating an electrochemical aptasensor.
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Affiliation(s)
- Salma Nur Zakiyyah
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jl. Raya Bandung-Sumedang Km 21, Jatinangor, Sumedang, West Java 45363, Indonesia
| | - Irkham
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jl. Raya Bandung-Sumedang Km 21, Jatinangor, Sumedang, West Java 45363, Indonesia
| | - Yasuaki Einaga
- Department of Chemistry, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Noto Susanto Gultom
- Department of Physics, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jl. Raya Bandung-Sumedang Km 21, Jatinangor, Sumedang, West Java 45363, Indonesia
| | - Retna Putri Fauzia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jl. Raya Bandung-Sumedang Km 21, Jatinangor, Sumedang, West Java 45363, Indonesia
| | - Grandprix Thomreys Marth Kadja
- Division of Inorganic and Physical Chemistry, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha no. 10, Bandung 40132, Indonesia
- Research Center for Nanosciences and Nanotechnology, Institut Teknologi Bandung, Jl. Ganesha no. 10, Bandung 40132, Indonesia
| | - Shabarni Gaffar
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jl. Raya Bandung-Sumedang Km 21, Jatinangor, Sumedang, West Java 45363, Indonesia
| | - Mehmet Ozsoz
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jl. Raya Bandung-Sumedang Km 21, Jatinangor, Sumedang, West Java 45363, Indonesia
- Department of Biomedical Engineering, Near East University, Mersin 99138, Turkey
| | - Yeni Wahyuni Hartati
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jl. Raya Bandung-Sumedang Km 21, Jatinangor, Sumedang, West Java 45363, Indonesia
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Pearson GJ, Mears HV, Broncel M, Snijders AP, Bauer DLV, Carlton JG. ER-export and ARFRP1/AP-1-dependent delivery of SARS-CoV-2 Envelope to lysosomes controls late stages of viral replication. SCIENCE ADVANCES 2024; 10:eadl5012. [PMID: 38569033 PMCID: PMC10990277 DOI: 10.1126/sciadv.adl5012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
The β-coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the global COVID-19 pandemic. Coronaviral Envelope (E) proteins are pentameric viroporins that play essential roles in assembly, release, and pathogenesis. We developed a nondisruptive tagging strategy for SARS-CoV-2 E and find that, at steady state, it localizes to the Golgi and to lysosomes. We identify sequences in E, conserved across Coronaviridae, responsible for endoplasmic reticulum-to-Golgi export, and relate this activity to interaction with COP-II via SEC24. Using proximity biotinylation, we identify an ADP ribosylation factor 1/adaptor protein-1 (ARFRP1/AP-1)-dependent pathway allowing Golgi-to-lysosome trafficking of E. We identify sequences in E that bind AP-1, are conserved across β-coronaviruses, and allow E to be trafficked from Golgi to lysosomes. We show that E acts to deacidify lysosomes and, by developing a trans-complementation assay for SARS-CoV-2 structural proteins, that lysosomal delivery of E and its viroporin activity is necessary for efficient viral replication and release.
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Affiliation(s)
- Guy J. Pearson
- Organelle Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- School of Cancer & Pharmaceutical Sciences, King’s College London, Great Maze Pond, London SE1 1UL, UK
| | - Harriet V. Mears
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Malgorzata Broncel
- Proteomic Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P. Snijders
- Proteomic Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David L. V. Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jeremy G. Carlton
- Organelle Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- School of Cancer & Pharmaceutical Sciences, King’s College London, Great Maze Pond, London SE1 1UL, UK
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Shaikh SB, Prabhu A, Akarsha B, Rahamathulla MP, Sha M, Bhandary YP. Lung as a target for COVID-19: Mechanistic insights and probable candidate molecules for cure. J Infect Public Health 2024; 17:573-578. [PMID: 38367571 DOI: 10.1016/j.jiph.2024.01.014] [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: 09/12/2023] [Revised: 01/01/2024] [Accepted: 01/21/2024] [Indexed: 02/19/2024] Open
Abstract
Novel coronavirus (SARS nCoV2), belonging to the family coronaviridae, remains a dreadful pathogen affecting the respiratory tract and lungs. COVID-19 declared a global pandemic by WHO, has become a serious cause of concern for clinicians and researchers, who need to understand the significant biology and pathogenicity of this virus to design better treatment modalities. Existing antiretroviral drugs remain partially ineffective in critical subjects with associated co-morbidities. This review provides an insight into the molecular mechanisms by which SARS-CoV2 targets the lungs leading to ARDS in severe cases. This also addresses the possible drug targets and certain anti-inflammatory natural compounds that can be looked upon as promising adjuvant therapeutics for COVID-19.
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Affiliation(s)
- Sadiya Bi Shaikh
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore 575 018, Karnataka, India
| | - Ashwini Prabhu
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore 575 018, Karnataka, India
| | - Akarsha B
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore 575 018, Karnataka, India.
| | - Mohamudha Parveen Rahamathulla
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, Al Kharj 11942, Kingdom of Saudi Arabia.
| | - Mohemmed Sha
- Department of Software Engineering, College of Computer Engineering and Sciences, Prince Sattam bin Abdulaziz University, Al Kharj 11942, Kingdom of Saudi Arabia
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Nguyen TH, Thai QM, Pham MQ, Minh PTH, Phung HTT. Machine learning combines atomistic simulations to predict SARS-CoV-2 Mpro inhibitors from natural compounds. Mol Divers 2024; 28:553-561. [PMID: 36823394 PMCID: PMC9950021 DOI: 10.1007/s11030-023-10601-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/04/2023] [Indexed: 02/25/2023]
Abstract
To date, the COVID-19 pandemic has still been infectious around the world, continuously causing social and economic damage on a global scale. One of the most important therapeutic targets for the treatment of COVID-19 is the main protease (Mpro) of SARS-CoV-2. In this study, we combined machine-learning (ML) model with atomistic simulations to computationally search for highly promising SARS-CoV-2 Mpro inhibitors from the representative natural compounds of the National Cancer Institute (NCI) Database. First, the trained ML model was used to scan the library quickly and reliably for possible Mpro inhibitors. The ML output was then confirmed using atomistic simulations integrating molecular docking and molecular dynamic simulations with the linear interaction energy scheme. The results turned out to show that there was evidently good agreement between ML and atomistic simulations. Ten substances were proposed to be able to inhibit SARS-CoV-2 Mpro. Seven of them have high-nanomolar affinity and are very potential inhibitors. The strategy has been proven to be reliable and appropriate for fast prediction of SARS-CoV-2 Mpro inhibitors, benefiting for new emerging SARS-CoV-2 variants in the future accordingly.
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Affiliation(s)
- Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Quynh Mai Thai
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Pham Thi Hong Minh
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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Salemi MH, Alipour A. Investigation of Neuropsychological Dysfunction Among Recovered Nurses: The COVID-19. Cureus 2024; 16:e58929. [PMID: 38800204 PMCID: PMC11123473 DOI: 10.7759/cureus.58929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
OBJECTIVE This investigation aimed to compare the neuropsychological dysfunctions of coronavirus (COVID-19)-recovered nurses to those of healthy nurses. METHODOLOGY The present research method was descriptive and causal-comparative, in which the statistical population consisted of nurses with a history of COVID disease and working in the COVID department of public hospitals in Isfahan city. The available method selected 30 nurses with a history of illness and compared them with 30 other nurses from the same hospitals. We collected data using the "go/no go" test, the Wisconsin card sorting test (WCST), and direct and inverted word reading tests. We also analyzed the collected data using multivariate analysis of variance. RESULTS The results showed a significant difference between nurses with a history of COVID disease and normal nurses in memory performance, the total error of the Wisconsin card sorting test, and the error of committing and inappropriately inhibiting the go/no go task (P < 0.01). However, there is no significant difference between the two groups in the number of classes, the error of perseveration in the Wisconsin test, or the reaction time of the go/no task (P < 0.05). CONCLUSION Therefore, the present study's results indicate that nurses recovering from COVID-19 perform worse than normal nurses in memory functions, cognitive flexibility, and response inhibition within one to three months of recovery.
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Affiliation(s)
| | - Ahmad Alipour
- Department of Psychology, Payame Noor University, Tehran, IRN
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50
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Kaygısız Yiğit M, Akyol R, Yalvaç B, Etöz M. Dental radiographic changes in individuals with COVID-19: a controlled retrospective study. Oral Radiol 2024; 40:148-157. [PMID: 37733163 DOI: 10.1007/s11282-023-00713-7] [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: 05/02/2023] [Accepted: 09/04/2023] [Indexed: 09/22/2023]
Abstract
OBJECTIVE The aim of this study is to compare the pre-COVID-19 and post-COVID-19 dental radiological findings of individuals with positive rRT-PCR test results and with healthy controls using the apical periodontitis grade scale (APGS), radiographic-based periodontal bone loss (R-PBL), and radiographic DMFT indices, and to investigate the relatively long-term dental effects of COVID-19. METHODS This study included people who had two panoramic radiographs taken between 2018 and 2022. There are 52 patients with positive rRT-PCR tests in the study group. The control group included 50 individuals. Study and control groups were compared using the apical periodontitis grade scale (APGS), radiographic-based periodontal bone loss (R-PBL), and radiographic DMFT indices. RESULTS Although results showed a significant difference in percentage R-PBL value and R-PBL types in the study group, there was no significant difference in percentage R-PBL value and R-PBL types in the control group. Also, both groups showed a significant difference in the DMFT index. CONCLUSIONS According to the results of this study, it can be said that COVID-19 increases the incidence of periodontitis, and it can be interpreted that the pandemic may adversely affect the general oral health of all people.
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Affiliation(s)
- Meryem Kaygısız Yiğit
- Department of Oral and Maxillofacial Radiology, Faculty of Dentistry, Erciyes University, 38039, Kayseri, Turkey.
| | - Rıdvan Akyol
- Department of Oral and Maxillofacial Radiology, Faculty of Dentistry, Nuh Naci Yazgan University, Kayseri, Turkey
| | - Beyza Yalvaç
- Department of Oral and Maxillofacial Radiology, Faculty of Dentistry, Erciyes University, 38039, Kayseri, Turkey
| | - Meryem Etöz
- Department of Oral and Maxillofacial Radiology, Faculty of Dentistry, Erciyes University, 38039, Kayseri, Turkey
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