1
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Yang S, Tian M, Dai Y, Wang R, Yamada S, Feng S, Wang Y, Chhangani D, Ou T, Li W, Guo X, McAdow J, Rincon-Limas DE, Yin X, Tai W, Cheng G, Johnson A. Infection and chronic disease activate a systemic brain-muscle signaling axis. Sci Immunol 2024; 9:eadm7908. [PMID: 38996009 DOI: 10.1126/sciimmunol.adm7908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/18/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024]
Abstract
Infections and neurodegenerative diseases induce neuroinflammation, but affected individuals often show nonneural symptoms including muscle pain and muscle fatigue. The molecular pathways by which neuroinflammation causes pathologies outside the central nervous system (CNS) are poorly understood. We developed multiple models to investigate the impact of CNS stressors on motor function and found that Escherichia coli infections and SARS-CoV-2 protein expression caused reactive oxygen species (ROS) to accumulate in the brain. ROS induced expression of the cytokine Unpaired 3 (Upd3) in Drosophila and its ortholog, IL-6, in mice. CNS-derived Upd3/IL-6 activated the JAK-STAT pathway in skeletal muscle, which caused muscle mitochondrial dysfunction and impaired motor function. We observed similar phenotypes after expressing toxic amyloid-β (Aβ42) in the CNS. Infection and chronic disease therefore activate a systemic brain-muscle signaling axis in which CNS-derived cytokines bypass the connectome and directly regulate muscle physiology, highlighting IL-6 as a therapeutic target to treat disease-associated muscle dysfunction.
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Affiliation(s)
- Shuo Yang
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Department of Genetics and Genetics Engineering, School of Life Science, Fudan University, Shanghai 200438, China
| | - Meijie Tian
- Genetics Branch, Oncogenomics Section, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yulong Dai
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Rong Wang
- Department of Genetics and Genetics Engineering, School of Life Science, Fudan University, Shanghai 200438, China
| | - Shigehiro Yamada
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Shengyong Feng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yunyun Wang
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Deepak Chhangani
- Department of Neurology and McKnight Brain Institute, Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, Genetics Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida College of Medicine, Gainesville, FL 32611, USA
| | - Tiffany Ou
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Wenle Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Xuan Guo
- Life Science Institute, Jinzhou Medical University, Jinzhou 121001, China
| | - Jennifer McAdow
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Diego E Rincon-Limas
- Department of Neurology and McKnight Brain Institute, Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease, Genetics Institute, and Norman Fixel Institute for Neurological Diseases, University of Florida College of Medicine, Gainesville, FL 32611, USA
| | - Xin Yin
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Wanbo Tai
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
- Southwest United Graduate School, Kunming 650092, China
| | - Aaron Johnson
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
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2
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Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant MG, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nat Methods 2024; 21:1340-1348. [PMID: 38918604 DOI: 10.1038/s41592-024-02321-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein-nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: Escherichia coli beta-galactosidase with inhibitor, SARS-CoV-2 virus RNA-dependent RNA polymerase with covalently bound nucleotide analog and SARS-CoV-2 virus ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. The quality of submitted ligand models and surrounding atoms were analyzed by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics and contact scores. A composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.
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Affiliation(s)
- Catherine L Lawson
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | | | - Grigore D Pintilie
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Stephen K Burley
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- RCSB Protein Data Bank and San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA
| | - Jiří Černý
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic
| | - Vincent B Chen
- Department of Biochemistry, Duke University, Durham, NC, USA
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Alberto Gobbi
- Discovery Chemistry, Genentech Inc., San Francisco, CA, USA
- , Berlin, Germany
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Sigrid Noreng
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
- Protein Science, Septerna, South San Francisco, CA, USA
| | | | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | - Alexis L Rohou
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Bohdan Schneider
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic
| | - Benjamin D Sellers
- Discovery Chemistry, Genentech Inc., San Francisco, CA, USA
- Computational Chemistry, Vilya, South San Francisco, CA, USA
| | - Chenghua Shao
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | | | | | | | - Ying Yang
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Venkat Abbaraju
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Pavel V Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Paul S Bond
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Burnley
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Arthur Campbell
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Renzhi Cao
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | | | - K D Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Reza Esmaeeli
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Nabin Giri
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Soon Wen Hoh
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Jie Hou
- Department of Computer Science, Saint Louis University, St. Louis, MO, USA
| | - Corey F Hryc
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Carola Hunte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Maxim Igaev
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Agnel P Joseph
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Wei-Chun Kao
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Dilip Kumar
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Lijun Lang
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
- The Chinese University of Hong Kong, Hong Kong, China
| | - Sean Lin
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Sumit Mittal
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal, India
| | - Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
- National Renewable Energy Laboratory (NREL), Golden, CO, USA
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew Muenks
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Robert A Nicholls
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Mateusz Olek
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Colin M Palmer
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Emmi Pohjolainen
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karunakar R Pothula
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | | | - Daipayan Sarkar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
- MSU-DOE Plant Research Laboratory, East Lansing, MI, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Luisa U Schäfer
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Christopher J Schlicksup
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Gunnar F Schröder
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mrinal Shekhar
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Dong Si
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Oleg V Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Andrea C Vaiana
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Nature's Toolbox (NTx), Rio Rancho, NM, USA
| | | | - Jacob Verburgt
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | | | - Martyn D Winn
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Simone Weyand
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Michael F Schmid
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Helen M Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Wah Chiu
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
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3
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Ferdoush J, Abdul Kadir R, Simay Kaplanoglu S, Osborn M. SARS-CoV-2 and UPS with potentials for therapeutic interventions. Gene 2024; 912:148377. [PMID: 38490508 DOI: 10.1016/j.gene.2024.148377] [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: 01/19/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
The Ubiquitin proteasome system (UPS), an essential eukaryotic/host/cellular post-translational modification (PTM), plays a critical role in the regulation of diverse cellular functions including regulation of protein stability, immune signaling, antiviral activity, as well as virus replication. Although UPS regulation of viral proteins may be utilized by the host as a defense mechanism to invade viruses, viruses may have adapted to take advantage of the host UPS. This system can be manipulated by viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) to stimulate various steps of the viral replication cycle and facilitate pathogenesis, thereby causing the respiratory disease COVID-19. Many SARS-CoV-2 encoded proteins including open reading frame 3a (ORF3a), ORF6, ORF7a, ORF9b, and ORF10 interact with the host's UPS machinery, influencing host immune signaling and apoptosis. Moreover, SARS-CoV-2 encoded papain-like protease (PLpro) interferes with the host UPS to facilitate viral replication and to evade the host's immune system. These alterations in SARS-CoV-2 infected cells have been revealed by various proteomic studies, suggesting potential targets for clinical treatment. To provide insight into the underlying causes of COVID-19 and suggest possible directions for therapeutic interventions, this paper reviews the intricate relationship between SARS-CoV-2 and UPS. Promising treatment strategies are also investigated in this paper including targeting PLpro with zinc-ejector drugs, as well as targeting viral non-structural protein (nsp12) via heat treatment associated ubiquitin-mediated proteasomal degradation to reduce viral pathogenesis.
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Affiliation(s)
- Jannatul Ferdoush
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA.
| | - Rizwaan Abdul Kadir
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Selin Simay Kaplanoglu
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Morgan Osborn
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
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4
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Lundrigan E, Toudic C, Pennock E, Pezacki JP. SARS-CoV-2 Protein Nsp9 Is Involved in Viral Evasion through Interactions with Innate Immune Pathways. ACS OMEGA 2024; 9:26428-26438. [PMID: 38911767 PMCID: PMC11191075 DOI: 10.1021/acsomega.4c02631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/13/2024] [Accepted: 04/23/2024] [Indexed: 06/25/2024]
Abstract
The suppression of the host's innate antiviral immune response by SARS-CoV-2, a contributing factor to the severity of disease, has been considerably studied in recent years. Many of these studies have focused on the actions of the structural proteins of the virus because of their accessibility to host immunological components. However, less is known about SARS-CoV-2 nonstructural and accessory proteins in relation to viral evasion. Herein, we study SARS-CoV-2 nonstructural proteins Orf3a, Orf6, and Nsp9 in a mimicked virus-infected state using poly(I:C), a synthetic analog of viral dsRNA, that elicits the antiviral immune response. Through genome-wide expression profiling, we determined that Orf3a, Orf6, and Nsp9 all modulate the host antiviral signaling transcriptome to varying extents, uniquely suppressing aspects of innate immune signaling. Our data suggest that SARS-CoV-2 Nsp9 hinders viral detection through suppression of RIG-I expression and antagonizes the interferon antiviral cascade by downregulating NF-kB and TBK1. Our data point to unique molecular mechanisms through which the different SARS-CoV-2 proteins suppress immune signaling and promote viral evasion. Nsp9 in particular acts on major elements of the host antiviral pathways to impair the antiviral immune response.
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Affiliation(s)
- Eryn Lundrigan
- Department of Chemistry and
Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Caroline Toudic
- Department of Chemistry and
Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Emily Pennock
- Department of Chemistry and
Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and
Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
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5
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Carvajal JJ, García-Castillo V, Cuellar SV, Campillay-Véliz CP, Salazar-Ardiles C, Avellaneda AM, Muñoz CA, Retamal-Díaz A, Bueno SM, González PA, Kalergis AM, Lay MK. New insights into the pathogenesis of SARS-CoV-2 during and after the COVID-19 pandemic. Front Immunol 2024; 15:1363572. [PMID: 38911850 PMCID: PMC11190347 DOI: 10.3389/fimmu.2024.1363572] [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: 12/31/2023] [Accepted: 04/24/2024] [Indexed: 06/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the respiratory distress condition known as COVID-19. This disease broadly affects several physiological systems, including the gastrointestinal, renal, and central nervous (CNS) systems, significantly influencing the patient's overall quality of life. Additionally, numerous risk factors have been suggested, including gender, body weight, age, metabolic status, renal health, preexisting cardiomyopathies, and inflammatory conditions. Despite advances in understanding the genome and pathophysiological ramifications of COVID-19, its precise origins remain elusive. SARS-CoV-2 interacts with a receptor-binding domain within angiotensin-converting enzyme 2 (ACE2). This receptor is expressed in various organs of different species, including humans, with different abundance. Although COVID-19 has multiorgan manifestations, the main pathologies occur in the lung, including pulmonary fibrosis, respiratory failure, pulmonary embolism, and secondary bacterial pneumonia. In the post-COVID-19 period, different sequelae may occur, which may have various causes, including the direct action of the virus, alteration of the immune response, and metabolic alterations during infection, among others. Recognizing the serious adverse health effects associated with COVID-19, it becomes imperative to comprehensively elucidate and discuss the existing evidence surrounding this viral infection, including those related to the pathophysiological effects of the disease and the subsequent consequences. This review aims to contribute to a comprehensive understanding of the impact of COVID-19 and its long-term effects on human health.
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Affiliation(s)
- Jonatan J. Carvajal
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Valeria García-Castillo
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Shelsy V. Cuellar
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | | | - Camila Salazar-Ardiles
- Center for Research in Physiology and Altitude Medicine (FIMEDALT), Biomedical Department, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Andrea M. Avellaneda
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Department of Basic Sciences, Faculty of Sciences, Universidad Santo Tomás, Antofagasta, Chile
| | - Christian A. Muñoz
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Angello Retamal-Díaz
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Susan M. Bueno
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo A. González
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Margarita K. Lay
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
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6
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Guarnieri JW, Haltom JA, Albrecht YES, Lie T, Olali AZ, Widjaja GA, Ranshing SS, Angelin A, Murdock D, Wallace DC. SARS-CoV-2 mitochondrial metabolic and epigenomic reprogramming in COVID-19. Pharmacol Res 2024; 204:107170. [PMID: 38614374 DOI: 10.1016/j.phrs.2024.107170] [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: 02/06/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/15/2024]
Abstract
To determine the effects of SARS-CoV-2 infection on cellular metabolism, we conducted an exhaustive survey of the cellular metabolic pathways modulated by SARS-CoV-2 infection and confirmed their importance for SARS-CoV-2 propagation by cataloging the effects of specific pathway inhibitors. This revealed that SARS-CoV-2 strongly inhibits mitochondrial oxidative phosphorylation (OXPHOS) resulting in increased mitochondrial reactive oxygen species (mROS) production. The elevated mROS stabilizes HIF-1α which redirects carbon molecules from mitochondrial oxidation through glycolysis and the pentose phosphate pathway (PPP) to provide substrates for viral biogenesis. mROS also induces the release of mitochondrial DNA (mtDNA) which activates innate immunity. The restructuring of cellular energy metabolism is mediated in part by SARS-CoV-2 Orf8 and Orf10 whose expression restructures nuclear DNA (nDNA) and mtDNA OXPHOS gene expression. These viral proteins likely alter the epigenome, either by directly altering histone modifications or by modulating mitochondrial metabolite substrates of epigenome modification enzymes, potentially silencing OXPHOS gene expression and contributing to long-COVID.
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Affiliation(s)
- Joseph W Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jeffrey A Haltom
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yentli E Soto Albrecht
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Timothy Lie
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arnold Z Olali
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Gabrielle A Widjaja
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sujata S Ranshing
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Deborah Murdock
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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7
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Hartmann S, Radochonski L, Ye C, Martinez-Sobrido L, Chen J. SARS-CoV-2 ORF3a drives dynamic dense body formation for optimal viral infectivity. RESEARCH SQUARE 2024:rs.3.rs-4292014. [PMID: 38798602 PMCID: PMC11118709 DOI: 10.21203/rs.3.rs-4292014/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
SARS-CoV-2 uses the double-membrane vesicles as replication organelles. However, how virion assembly occurs has not been fully understood. Here we identified a SARS-CoV-2-driven membrane structure named the 3a dense body (3DB). 3DBs have unusual electron-dense and dynamic inner structures, and their formation is driven by the accessory protein ORF3a via hijacking a specific subset of the trans-Golgi network (TGN) and early endosomal membranes. 3DB formation is conserved in related bat and pangolin coronaviruses yet lost during the evolution to SARS-CoV. 3DBs recruit the viral structural proteins spike (S) and membrane (M) and undergo dynamic fusion/fission to facilitate efficient virion assembly. A recombinant SARS-CoV-2 virus with an ORF3a mutant specifically defective in 3DB formation showed dramatically reduced infectivity for both extracellular and cell-associated virions. Our study uncovers the crucial role of 3DB in optimal SARS-CoV-2 infectivity and highlights its potential as a target for COVID-19 prophylactics and therapeutics.
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Affiliation(s)
- Stella Hartmann
- Department of Microbiology, University of Chicago, Chicago, IL, USA 60637
- Howard Taylor Ricketts Laboratory, University of Chicago, Lemont, IL, USA 60439
| | - Lisa Radochonski
- Department of Microbiology, University of Chicago, Chicago, IL, USA 60637
- Howard Taylor Ricketts Laboratory, University of Chicago, Lemont, IL, USA 60439
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX, USA 78227
| | | | - Jueqi Chen
- Department of Microbiology, University of Chicago, Chicago, IL, USA 60637
- Howard Taylor Ricketts Laboratory, University of Chicago, Lemont, IL, USA 60439
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8
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Jia L, Ruben EA, Suarez HJ, Olsen SK, Wasmuth EV. Single particle cryo-electron microscopy with an enhanced 200 kV cryo-TEM configuration achieves near-atomic resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.593029. [PMID: 38766263 PMCID: PMC11100677 DOI: 10.1101/2024.05.07.593029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Single particle cryogenic electron microscopy (cryo-EM) as a structural biology methodology has become increasingly attractive and accessible to investigators in both academia and industry as this ever-advancing technology enables successful structural determination of a wide range of protein and nucleic acid targets. Although data for many high resolution cryo-EM structures are still obtained using a 300 kV cryogenic transmission electron microscope (cryo-TEM), a modern 200 kV cryo-TEM equipped with an advanced direct electron detector and energy filter is a cost-effective choice for most single particle applications, routinely achieving sub 3 angstrom (Å) resolution. Here, we systematically evaluate performance of one such high-end configuration - a 200 kV Glacios microscope coupled with a Falcon 4 direct electron detector and Selectris energy filter (Glacios-F4-S). First, we evaluated data quality on the standard benchmarking sample, rabbit muscle aldolase, using three of the most frequently used cryo-EM data collection software: SerialEM, Leginon and EPU, and found that - despite sample heterogeneity - all final reconstructions yield same overall resolutions of 2.6 Å and map quality when using either of the three software. Furthermore, comparison between Glacios-F4-S and a 300 kV cryo-TEM (Titan Krios with Falcon 4) revealed nominal resolution differences in overall reconstructions of a reconstituted human nucleosome core particle, achieving 2.8 and 2.5 Å, respectively. Finally, we performed comparative data analysis on the human RAD51 paralog complex, BCDX2, a four-protein complex of approximately 150 kilodaltons, and found that a small dataset (≤1,000 micrographs) was sufficient to generate a 3.3 Å reconstruction, with sufficient detail to resolve co-bound ligands, AMP-PNP and Mg +2 . In summary, this study provides evidence that the Glacios-F4-S operates equally well with all standard data collection software, and is sufficient to obtain high resolution structural information of novel macromolecular complexes, readily acquiring single particle data rivaling that of 300 kV cryo-TEMs.
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9
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Giri N, Wang L, Cheng J. Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures. Sci Data 2024; 11:458. [PMID: 38710720 PMCID: PMC11074267 DOI: 10.1038/s41597-024-03299-9] [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: 01/08/2024] [Accepted: 04/23/2024] [Indexed: 05/08/2024] Open
Abstract
The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structures of biological macromolecules and their complexes significantly expedite biomedical research and drug discovery. However, automatically and accurately building atomic models from high-resolution cryo-EM density maps is still time-consuming and challenging when template-based models are unavailable. Artificial intelligence (AI) methods such as deep learning trained on limited amount of labeled cryo-EM density maps generate inaccurate atomic models. To address this issue, we created a dataset called Cryo2StructData consisting of 7,600 preprocessed cryo-EM density maps whose voxels are labelled according to their corresponding known atomic structures for training and testing AI methods to build atomic models from cryo-EM density maps. Cryo2StructData is larger than existing, publicly available datasets for training AI methods to build atomic protein structures from cryo-EM density maps. We trained and tested deep learning models on Cryo2StructData to validate its quality showing that it is ready for being used to train and test AI methods for building atomic models.
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Affiliation(s)
- Nabin Giri
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, USA
- Roy Blunt NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA
| | - Liguo Wang
- Laboratory for BioMolecular Structure (LBMS), Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, USA.
- Roy Blunt NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA.
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10
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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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11
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Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
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Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
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12
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Nogales E, Mahamid J. Bridging structural and cell biology with cryo-electron microscopy. Nature 2024; 628:47-56. [PMID: 38570716 PMCID: PMC11211576 DOI: 10.1038/s41586-024-07198-2] [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: 07/18/2023] [Accepted: 02/13/2024] [Indexed: 04/05/2024]
Abstract
Most life scientists would agree that understanding how cellular processes work requires structural knowledge about the macromolecules involved. For example, deciphering the double-helical nature of DNA revealed essential aspects of how genetic information is stored, copied and repaired. Yet, being reductionist in nature, structural biology requires the purification of large amounts of macromolecules, often trimmed off larger functional units. The advent of cryogenic electron microscopy (cryo-EM) greatly facilitated the study of large, functional complexes and generally of samples that are hard to express, purify and/or crystallize. Nevertheless, cryo-EM still requires purification and thus visualization outside of the natural context in which macromolecules operate and coexist. Conversely, cell biologists have been imaging cells using a number of fast-evolving techniques that keep expanding their spatial and temporal reach, but always far from the resolution at which chemistry can be understood. Thus, structural and cell biology provide complementary, yet unconnected visions of the inner workings of cells. Here we discuss how the interplay between cryo-EM and cryo-electron tomography, as a connecting bridge to visualize macromolecules in situ, holds great promise to create comprehensive structural depictions of macromolecules as they interact in complex mixtures or, ultimately, inside the cell itself.
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Affiliation(s)
- Eva Nogales
- Molecular and Cell Biology Department, Institute for Quantitative Biomedicine, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Howard Hughes Medical Institute, Berkeley, CA, USA.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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13
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Trepte P, Secker C, Olivet J, Blavier J, Kostova S, Maseko SB, Minia I, Silva Ramos E, Cassonnet P, Golusik S, Zenkner M, Beetz S, Liebich MJ, Scharek N, Schütz A, Sperling M, Lisurek M, Wang Y, Spirohn K, Hao T, Calderwood MA, Hill DE, Landthaler M, Choi SG, Twizere JC, Vidal M, Wanker EE. AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor. Mol Syst Biol 2024; 20:428-457. [PMID: 38467836 PMCID: PMC10987651 DOI: 10.1038/s44320-024-00019-8] [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: 02/09/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 03/13/2024] Open
Abstract
Protein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays or AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold-Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.
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Affiliation(s)
- Philipp Trepte
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany.
- Brain Development and Disease, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030, Vienna, Austria.
| | - Christopher Secker
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany.
- Zuse Institute Berlin, Berlin, Germany.
| | - Julien Olivet
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Jeremy Blavier
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
| | - Simona Kostova
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Sibusiso B Maseko
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
| | - Igor Minia
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125, Berlin, Germany
| | - Eduardo Silva Ramos
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Patricia Cassonnet
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique (CNRS), Université de Paris, Paris, France
| | - Sabrina Golusik
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Martina Zenkner
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Stephanie Beetz
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Mara J Liebich
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Nadine Scharek
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Anja Schütz
- Protein Production & Characterization, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Marcel Sperling
- Multifunctional Colloids and Coating, Fraunhofer Institute for Applied Polymer Research (IAP), 14476, Potsdam-Golm, Germany
| | - Michael Lisurek
- Structural Chemistry and Computational Biophysics, Leibniz-Institut für Molekulare Pharmakologie (FMP), 13125, Berlin, Germany
| | - Yang Wang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, 13125, Berlin, Germany
| | - Soon Gang Choi
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium.
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium.
- Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
| | - Erich E Wanker
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany.
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14
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Greber BJ. High-resolution cryo-EM of a small protein complex: The structure of the human CDK-activating kinase. Structure 2024:S0969-2126(24)00085-6. [PMID: 38565138 DOI: 10.1016/j.str.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/27/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
The human CDK-activating kinase (CAK) is a multifunctional protein complex and key regulator of cell growth and division. Because of its critical functions in regulating the cell cycle and transcription initiation, it is a key target for multiple cancer drug discovery programs. However, the structure of the active human CAK, insights into its regulation, and its interactions with cellular substrates and inhibitors remained elusive until recently due to the lack of high-resolution structures of the intact complex. This review covers the progress in structure determination of the human CAK by cryogenic electron microscopy (cryo-EM), from early efforts to recent near-atomic resolution maps routinely resolved at 2Å or better. These results were enabled by the latest cryo-EM technologies introduced after the initial phase of the "resolution revolution" and allowed the application of high-resolution methods to new classes of molecular targets, including small protein complexes that were intractable using earlier technology.
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Affiliation(s)
- Basil J Greber
- Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, UK.
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15
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Rosenbaum JC, Carlson AE. The SARS coronavirus accessory protein ORF3a rescues potassium conductance in yeast. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001129. [PMID: 38525126 PMCID: PMC10958204 DOI: 10.17912/micropub.biology.001129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/26/2024]
Abstract
ORF3a is an accessory protein expressed by all human pathogen coronaviruses and is the only accessory protein that strongly affects viral fitness. Its deletion reduces severity in both alpha- and beta-coronaviruses, demonstrating a conserved function across the superfamily. Initially regarded as a non-selective cation channel, ORF3a's function is now disputed. Here, we show that ORF3a from SARS, but not SARS-CoV-2, promotes potassium conductance in a yeast model system commonly used to study potassium channels. ORF3a-mediated potassium conductance is also sensitive to inhibitors, including emodin, carbamazepine, and nifedipine. This model may be used in future studies on ORF3a and related proteins.
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Affiliation(s)
- Joel C. Rosenbaum
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Anne E. Carlson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
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16
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Walia K, Sharma A, Paul S, Chouhan P, Kumar G, Ringe R, Sharma M, Tuli A. SARS-CoV-2 virulence factor ORF3a blocks lysosome function by modulating TBC1D5-dependent Rab7 GTPase cycle. Nat Commun 2024; 15:2053. [PMID: 38448435 PMCID: PMC10918171 DOI: 10.1038/s41467-024-46417-2] [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: 06/12/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
SARS-CoV-2, the causative agent of COVID-19, uses the host endolysosomal system for entry, replication, and egress. Previous studies have shown that the SARS-CoV-2 virulence factor ORF3a interacts with the lysosomal tethering factor HOPS complex and blocks HOPS-mediated late endosome and autophagosome fusion with lysosomes. Here, we report that SARS-CoV-2 infection leads to hyperactivation of the late endosomal and lysosomal small GTP-binding protein Rab7, which is dependent on ORF3a expression. We also observed Rab7 hyperactivation in naturally occurring ORF3a variants encoded by distinct SARS-CoV-2 variants. We found that ORF3a, in complex with Vps39, sequesters the Rab7 GAP TBC1D5 and displaces Rab7 from this complex. Thus, ORF3a disrupts the GTP hydrolysis cycle of Rab7, which is beneficial for viral production, whereas the Rab7 GDP-locked mutant strongly reduces viral replication. Hyperactivation of Rab7 in ORF3a-expressing cells impaired CI-M6PR retrieval from late endosomes to the trans-Golgi network, disrupting the biosynthetic transport of newly synthesized hydrolases to lysosomes. Furthermore, the tethering of the Rab7- and Arl8b-positive compartments was strikingly reduced upon ORF3a expression. As SARS-CoV-2 egress requires Arl8b, these findings suggest that ORF3a-mediated hyperactivation of Rab7 serves a multitude of functions, including blocking endolysosome formation, interrupting the transport of lysosomal hydrolases, and promoting viral egress.
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Affiliation(s)
- Kshitiz Walia
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Abhishek Sharma
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Sankalita Paul
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Priya Chouhan
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Gaurav Kumar
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Rajesh Ringe
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Mahak Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Amit Tuli
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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17
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Cebi E, Lee J, Subramani VK, Bak N, Oh C, Kim KK. Cryo-electron microscopy-based drug design. Front Mol Biosci 2024; 11:1342179. [PMID: 38501110 PMCID: PMC10945328 DOI: 10.3389/fmolb.2024.1342179] [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: 11/21/2023] [Accepted: 01/31/2024] [Indexed: 03/20/2024] Open
Abstract
Structure-based drug design (SBDD) has gained popularity owing to its ability to develop more potent drugs compared to conventional drug-discovery methods. The success of SBDD relies heavily on obtaining the three-dimensional structures of drug targets. X-ray crystallography is the primary method used for solving structures and aiding the SBDD workflow; however, it is not suitable for all targets. With the resolution revolution, enabling routine high-resolution reconstruction of structures, cryogenic electron microscopy (cryo-EM) has emerged as a promising alternative and has attracted increasing attention in SBDD. Cryo-EM offers various advantages over X-ray crystallography and can potentially replace X-ray crystallography in SBDD. To fully utilize cryo-EM in drug discovery, understanding the strengths and weaknesses of this technique and noting the key advancements in the field are crucial. This review provides an overview of the general workflow of cryo-EM in SBDD and highlights technical innovations that enable its application in drug design. Furthermore, the most recent achievements in the cryo-EM methodology for drug discovery are discussed, demonstrating the potential of this technique for advancing drug development. By understanding the capabilities and advancements of cryo-EM, researchers can leverage the benefits of designing more effective drugs. This review concludes with a discussion of the future perspectives of cryo-EM-based SBDD, emphasizing the role of this technique in driving innovations in drug discovery and development. The integration of cryo-EM into the drug design process holds great promise for accelerating the discovery of new and improved therapeutic agents to combat various diseases.
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Affiliation(s)
| | | | | | | | - Changsuk Oh
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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18
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Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant M, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. RESEARCH SQUARE 2024:rs.3.rs-3864137. [PMID: 38343795 PMCID: PMC10854310 DOI: 10.21203/rs.3.rs-3864137/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein/nucleic-acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: E. coli beta-galactosidase with inhibitor, SARS-CoV-2 RNA-dependent RNA polymerase with covalently bound nucleotide analog, and SARS-CoV-2 ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. We found that (1) the quality of submitted ligand models and surrounding atoms varied, as judged by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics, and contact scores, and (2) a composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.
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Affiliation(s)
- Catherine L. Lawson
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | | | - Grigore D. Pintilie
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Stephen K. Burley
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ USA
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA USA
| | - Jiří Černý
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, CZ
| | | | - Paul Emsley
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Alberto Gobbi
- Discovery Chemistry, Genentech Inc, South San Francisco, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Sigrid Noreng
- Structural Biology, Genentech Inc, South San Francisco, USA
| | | | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | | | - Bohdan Schneider
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, CZ
| | | | - Chenghua Shao
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | | | | | | | - Ying Yang
- Structural Biology, Genentech Inc, South San Francisco, USA
| | - Venkat Abbaraju
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew L. Baker
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Paul S. Bond
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Burnley
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Arthur Campbell
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Renzhi Cao
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | | | - Kevin D. Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Reza Esmaeeli
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Nabin Giri
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Soon Wen Hoh
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Jie Hou
- Department of Computer Science, Saint Louis University, St. Louis, MO, USA
| | - Corey F. Hryc
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Carola Hunte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Maxim Igaev
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Agnel P. Joseph
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Wei-Chun Kao
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Dilip Kumar
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Lijun Lang
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Sean Lin
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Sumit Mittal
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal, India
| | - Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew Muenks
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | | | - Mateusz Olek
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Colin M. Palmer
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Emmi Pohjolainen
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karunakar R. Pothula
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | | | - Daipayan Sarkar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Luisa U. Schäfer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Christopher J. Schlicksup
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Gunnar F. Schröder
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mrinal Shekhar
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Dong Si
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Andrea C. Vaiana
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Nature’s Toolbox (NTx), Rio Rancho, NM, USA
| | | | - Jacob Verburgt
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiao Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | - Martyn D. Winn
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Simone Weyand
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Michael F. Schmid
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Helen M. Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Wah Chiu
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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19
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Zhang J, Hom K, Zhang C, Nasr M, Gerzanich V, Zhang Y, Tang Q, Xue F, Simard JM, Zhao RY. SARS-CoV-2 ORF3a Protein as a Therapeutic Target against COVID-19 and Long-Term Post-Infection Effects. Pathogens 2024; 13:75. [PMID: 38251382 PMCID: PMC10819734 DOI: 10.3390/pathogens13010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has posed unparalleled challenges due to its rapid transmission, ability to mutate, high mortality and morbidity, and enduring health complications. Vaccines have exhibited effectiveness, but their efficacy diminishes over time while new variants continue to emerge. Antiviral medications offer a viable alternative, but their success has been inconsistent. Therefore, there remains an ongoing need to identify innovative antiviral drugs for treating COVID-19 and its post-infection complications. The ORF3a (open reading frame 3a) protein found in SARS-CoV-2, represents a promising target for antiviral treatment due to its multifaceted role in viral pathogenesis, cytokine storms, disease severity, and mortality. ORF3a contributes significantly to viral pathogenesis by facilitating viral assembly and release, essential processes in the viral life cycle, while also suppressing the body's antiviral responses, thus aiding viral replication. ORF3a also has been implicated in triggering excessive inflammation, characterized by NF-κB-mediated cytokine production, ultimately leading to apoptotic cell death and tissue damage in the lungs, kidneys, and the central nervous system. Additionally, ORF3a triggers the activation of the NLRP3 inflammasome, inciting a cytokine storm, which is a major contributor to the severity of the disease and subsequent mortality. As with the spike protein, ORF3a also undergoes mutations, and certain mutant variants correlate with heightened disease severity in COVID-19. These mutations may influence viral replication and host cellular inflammatory responses. While establishing a direct link between ORF3a and mortality is difficult, its involvement in promoting inflammation and exacerbating disease severity likely contributes to higher mortality rates in severe COVID-19 cases. This review offers a comprehensive and detailed exploration of ORF3a's potential as an innovative antiviral drug target. Additionally, we outline potential strategies for discovering and developing ORF3a inhibitor drugs to counteract its harmful effects, alleviate tissue damage, and reduce the severity of COVID-19 and its lingering complications.
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Affiliation(s)
- Jiantao Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (J.Z.); (C.Z.)
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA; (K.H.); (F.X.)
| | - Chenyu Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (J.Z.); (C.Z.)
| | - Mohamed Nasr
- Drug Development and Clinical Sciences Branch, Division of AIDS, NIAID, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Volodymyr Gerzanich
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (V.G.); (J.M.S.)
| | - Yanjin Zhang
- Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA;
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC 20059, USA;
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA; (K.H.); (F.X.)
| | - J. Marc Simard
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (V.G.); (J.M.S.)
- Research & Development Service, VA Maryland Health Care System, Baltimore, MD 21201, USA
| | - Richard Y. Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (J.Z.); (C.Z.)
- Research & Development Service, VA Maryland Health Care System, Baltimore, MD 21201, USA
- Department of Microbiology-Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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20
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Elnosary ME, Shreadah MA, Ashour ML, Nabil-Adam A. Predictions based on inflammatory cytokine profiling of Egyptian COVID-19 with 2 potential therapeutic effects of certain marine-derived compounds. Int Immunopharmacol 2024; 126:111072. [PMID: 38006751 DOI: 10.1016/j.intimp.2023.111072] [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: 11/12/2022] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUNDS A worldwide coronavirus pandemic has affected many healthcare systems in 2019 (COVID-19). Following viral activation, cytokines and chemokines are released, causing inflammation and tissue death, particularly in the lungs, resulting in severe COVID-19 symptoms such as pneumonia and ARDS. COVID-19 induces the release of several chemokines and cytokines in different organs, such as the cardiovascular system and lungs. RESEARCH IDEA COVID-19 and its more severe effects, such as an elevated risk of death, are more common in patients with metabolic syndrome and the elderly. Cytokine storm and COVID-19 severity may be mitigated by immunomodulation targeting NF-κB activation in conjunction with TNF- α -inhibition. In severe cases of COVID-19, inhibiting the NF-κB/TNF- α, the pathway may be employed as a therapeutic option. MATERIAL AND METHODS The study will elaborate on the Egyptian pattern for COVID-19 patients in the first part of our study. An Egyptian patient with COVID-19 inflammatory profiling will be discussed in the second part of this article using approved marine drugs selected to inhabit the significant inflammatory signals. A biomarker profiling study is currently being performed on Egyptian patients with SARS-COV-2. According to the severity of the infection, participants were divided into four groups. The First Group was non-infected with SARS-CoV-2 (Control, n = 16), the Second Group was non-intensive care patients (non-ICU, n = 16), the Third Group was intensive care patients (ICU, n = 16), and the Fourth Group was ICU with endotracheal intubation (ICU + EI, n = 16). To investigate COVID-19 inflammatory biomarkers for Egyptian patients, several inflammatory, oxidative, antioxidant, and anti-inflammatory biomarkers were measured. The following are examples of blood tests: CRP, Ferritin, D-dimer, TNF-α, IL-8, IL-6., IL-Ib, CD8, NF-κB, MDA, and total antioxidants. RESULTS AND DISCUSSION The results of the current study revealed many logical findings, such as the elevation of CRP, Ferritin, D-dimer, TNF- α, CD8, IL-6, IL-, NF-κB, and MDA. Where a significant increase showed in ICU group results (23.05 ± 0.30, 2.35 ± 0.86, 433.4 ± 159.3, 26.67 ± 3.51, 7.52 ± 1.48, 7.49 ± 1.04, 5.76 ± 1.31, 7.41 ± 0.73) respectively, and also ICU group results (54.75 ± 3.44, 0.65 ± 0.13, 460.2 ± 121.42, 27.43 ± 2.52, 8.63 ± 2.68, 10.65 ± 2.75, 5.93 ± 1.4, 10.64 ± 0.86) respectively, as well as ICU + EI group results (117.63 ± 11.89, 1.22 ± 0.65, 918.8 ± 159.27, 26.68 ± 2.00, 6.68 ± 1.08, 11.68 ± 6.16, 6.23 ± 0.07, 22.41 ± 1.39),respectively.The elevation in laboratory biomarkers of cytokines storm in three infected groups with remarkable increases in the ICU + EI group was due to the elevation of oxidative stress and inflammatory storm molecules, which lead to highly inflammatory responses, specifically in severe patients of COVID-19. Another approach to be used in the current study is investigating new computational drug compounds for SARS-COV-2 protective agents from the marine environment. The results revealed that (Imatinib and Indinavir) had the highest affinity toward Inflammatory molecules and COVID-19 proteins (PDB ID: -7CZ4 and 7KJR), which may be used in the future as possible COVID-19 drug candidates. CONCLUSION The investigated inflammatory biomarkers in Egyptian COVID-19 patients showed a strong correlation between IL6, TNF-α, NF-κB, CRB, DHL, and ferritin as COVID-19 biomarkers and determined the severity of the infection. Also, the oxidative /antioxidant showed good biomarkers for infection recovery and progression of the patients.
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Affiliation(s)
- Mohamed E Elnosary
- Al-Azhar University, Faculty of Science, Botany and Microbiology Department, 11884 Nasr City, Cairo, Egypt.
| | - Mohamed Attia Shreadah
- Marine Biotechnology and Natural Products Laboratory, National Institute of Oceanography & Fisheries, Egypt
| | - Mohamed L Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Abbasia, Cairo 11566, Egypt; Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia.
| | - Asmaa Nabil-Adam
- Marine Biotechnology and Natural Products Laboratory, National Institute of Oceanography & Fisheries, Egypt.
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Dalal V, Arcario MJ, Petroff JT, Tan BK, Dietzen NM, Rau MJ, Fitzpatrick JAJ, Brannigan G, Cheng WWL. Lipid nanodisc scaffold and size alter the structure of a pentameric ligand-gated ion channel. Nat Commun 2024; 15:25. [PMID: 38167383 PMCID: PMC10762164 DOI: 10.1038/s41467-023-44366-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: 11/20/2022] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Lipid nanodiscs have become a standard tool for studying membrane proteins, including using single particle cryo-electron microscopy (cryo-EM). We find that reconstituting the pentameric ligand-gated ion channel (pLGIC), Erwinia ligand-gated ion channel (ELIC), in different nanodiscs produces distinct structures by cryo-EM. The effect of the nanodisc on ELIC structure extends to the extracellular domain and agonist binding site. Additionally, molecular dynamic simulations indicate that nanodiscs of different size impact ELIC structure and that the nanodisc scaffold directly interacts with ELIC. These findings suggest that the nanodisc plays a crucial role in determining the structure of pLGICs, and that reconstitution of ion channels in larger nanodiscs may better approximate a lipid membrane environment.
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Affiliation(s)
- Vikram Dalal
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Mark J Arcario
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - John T Petroff
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Brandon K Tan
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Noah M Dietzen
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Michael J Rau
- Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
| | - James A J Fitzpatrick
- Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
- Department of Physics, Rutgers University, Camden, NJ, USA
| | - Wayland W L Cheng
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.
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22
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Hong J, Li T, Chao Y, Xu Y, Zhu Z, Zhou Z, Gu W, Qu Q, Li D. Molecular basis of the inositol deacylase PGAP1 involved in quality control of GPI-AP biogenesis. Nat Commun 2024; 15:8. [PMID: 38167496 PMCID: PMC10761859 DOI: 10.1038/s41467-023-44568-2] [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: 08/17/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
The secretion and quality control of glycosylphosphatidylinositol-anchored proteins (GPI-APs) necessitates post-attachment remodeling initiated by the evolutionarily conserved PGAP1, which deacylates the inositol in nascent GPI-APs. Impairment of PGAP1 activity leads to developmental diseases in humans and fatality and infertility in animals. Here, we present three PGAP1 structures (2.66-2.84 Å), revealing its 10-transmembrane architecture and product-enzyme interaction details. PGAP1 holds GPI-AP acyl chains in an optimally organized, guitar-shaped cavity with apparent energetic penalties from hydrophobic-hydrophilic mismatches. However, abundant glycan-mediated interactions in the lumen counterbalance these repulsions, likely conferring substrate fidelity and preventing off-target hydrolysis of bulk membrane lipids. Structural and biochemical analyses uncover a serine hydrolase-type catalysis with atypical features and imply mechanisms for substrate entrance and product release involving a drawing compass movement of GPI-APs. Our findings advance the mechanistic understanding of GPI-AP remodeling.
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Affiliation(s)
- Jingjing Hong
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Tingting Li
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Yulin Chao
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, Shanghai, 200032, China
| | - Yidan Xu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Zhini Zhu
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, Shanghai, 200032, China
| | - Zixuan Zhou
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, Shanghai, 200032, China
| | - Weijie Gu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Qianhui Qu
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, Shanghai, 200032, China.
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
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23
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Giri N, Wang L, Cheng J. Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.14.545024. [PMID: 37398020 PMCID: PMC10312718 DOI: 10.1101/2023.06.14.545024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structures of biological macromolecules and their complexes significantly expedite biomedical research and drug discovery. However, automatically and accurately building atomic models from high-resolution cryo-EM density maps is still time-consuming and challenging when template-based models are unavailable. Artificial intelligence (AI) methods such as deep learning trained on limited amount of labeled cryo-EM density maps generate inaccurate atomic models. To address this issue, we created a dataset called Cryo2StructData consisting of 7,600 preprocessed cryo-EM density maps whose voxels are labelled according to their corresponding known atomic structures for training and testing AI methods to build atomic models from cryo-EM density maps. It is larger and of higher quality than any existing, publicly available dataset. We trained and tested deep learning models on Cryo2StructData to make sure it is ready for the large-scale development of AI methods for building atomic models from cryo-EM density maps.
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Affiliation(s)
- Nabin Giri
- University of Missouri, Electrical Engineering and Computer Science, Columbia, 65211, USA
- NextGen Precision Health Institute, Columbia, 65211, USA
| | - Liguo Wang
- Laboratory for Biological Structure, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Jianlin Cheng
- University of Missouri, Electrical Engineering and Computer Science, Columbia, 65211, USA
- NextGen Precision Health Institute, Columbia, 65211, USA
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24
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Chen YM, Lu CT, Wang CW, Fischer WB. Repurposing dye ligands as antivirals via a docking approach on viral membrane and globular proteins - SARS-CoV-2 and HPV-16. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184220. [PMID: 37657640 DOI: 10.1016/j.bbamem.2023.184220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
A series of dye ligands are docked to three different proteins, E and 3a of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) and E6 of human papilloma virus type 16 (HPV-16) using three different software. A four-level selection algorithm is used based on nonparametric statistics of numerical key values such as the "rank" derived from (i) averaged estimated binding energies (EBEs) and (ii) absolute EBE value of each of the software, (iii) frequency of ranking and (iv) rank of the area-under-curve values (AUCs) from decoy docking. A series of repurposing drugs and known antivirals used in experimental studies are docked for comparison. One dye ligand is ranked best for all proteins using the selection algorithm levels i - iii. Another three dye ligands are ranked top for the proteins individually when using all four levels.
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Affiliation(s)
- Yi-Ming Chen
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ching-Tai Lu
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chia-Wen Wang
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wolfgang B Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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25
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Stewart H, Palmulli R, Johansen KH, McGovern N, Shehata OM, Carnell GW, Jackson HK, Lee JS, Brown JC, Burgoyne T, Heeney JL, Okkenhaug K, Firth AE, Peden AA, Edgar JR. Tetherin antagonism by SARS-CoV-2 ORF3a and spike protein enhances virus release. EMBO Rep 2023; 24:e57224. [PMID: 37818801 PMCID: PMC10702813 DOI: 10.15252/embr.202357224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/23/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023] Open
Abstract
The antiviral restriction factor, tetherin, blocks the release of several different families of enveloped viruses, including the Coronaviridae. Tetherin is an interferon-induced protein that forms parallel homodimers between the host cell and viral particles, linking viruses to the surface of infected cells and inhibiting their release. We demonstrate that SARS-CoV-2 infection causes tetherin downregulation and that tetherin depletion from cells enhances SARS-CoV-2 viral titres. We investigate the potential viral proteins involved in abrogating tetherin function and find that SARS-CoV-2 ORF3a reduces tetherin localisation within biosynthetic organelles where Coronaviruses bud, and increases tetherin localisation to late endocytic organelles via reduced retrograde recycling. We also find that expression of Spike protein causes a reduction in cellular tetherin levels. Our results confirm that tetherin acts as a host restriction factor for SARS-CoV-2 and highlight the multiple distinct mechanisms by which SARS-CoV-2 subverts tetherin function.
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Affiliation(s)
- Hazel Stewart
- Department of PathologyUniversity of CambridgeCambridgeUK
| | | | - Kristoffer H Johansen
- Department of PathologyUniversity of CambridgeCambridgeUK
- Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Naomi McGovern
- Department of PathologyUniversity of CambridgeCambridgeUK
| | - Ola M Shehata
- Department of Biomedical ScienceUniversity of Sheffield, Firth CourtSheffieldUK
| | - George W Carnell
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | | | - Jin S Lee
- Department of PathologyUniversity of CambridgeCambridgeUK
| | | | - Thomas Burgoyne
- Royal Brompton HospitalGuy's and St Thomas' NHS Foundation TrustLondonUK
- UCL Institute of OphthalmologyUniversity College LondonLondonUK
| | | | | | - Andrew E Firth
- Department of PathologyUniversity of CambridgeCambridgeUK
| | - Andrew A Peden
- Department of Biomedical ScienceUniversity of Sheffield, Firth CourtSheffieldUK
| | - James R Edgar
- Department of PathologyUniversity of CambridgeCambridgeUK
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26
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Arya R, Tripathi P, Nayak K, Ganesh J, Bihani SC, Ghosh B, Prashar V, Kumar M. Insights into the evolution of mutations in SARS-CoV-2 non-spike proteins. Microb Pathog 2023; 185:106460. [PMID: 37995880 DOI: 10.1016/j.micpath.2023.106460] [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: 06/12/2023] [Revised: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
The COVID-19 pandemic has been driven by the emergence of SARS-CoV-2 variants with mutations across all the viral proteins. Although mutations in the spike protein have received significant attention, understanding the prevalence and potential impact of mutations in other viral proteins is essential for comprehending the evolution of SARS-CoV-2. Here, we conducted a comprehensive analysis of approximately 14 million sequences of SARS-CoV-2 deposited in the GISAID database until December 2022 to identify prevalent mutations in the non-spike proteins at the global and country levels. Additionally, we evaluated the energetics of each mutation to better understand their impact on protein stability. While the consequences of many mutations remain unclear, we discuss potential structural and functional significance of some mutations. Our study highlights the ongoing evolutionary process of SARS-CoV-2 and underscores the importance of understanding changes in non-spike proteins.
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Affiliation(s)
- Rimanshee Arya
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Preeti Tripathi
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Karthik Nayak
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; School of Chemical Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari, Mumbai, 400098, India
| | - Janani Ganesh
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Subhash C Bihani
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Biplab Ghosh
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India; Beamline Development & Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Vishal Prashar
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
| | - Mukesh Kumar
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
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27
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Pitsillou E, Beh RC, Liang JJ, Tang TS, Zhou X, Siow YY, Ma Y, Hu Z, Wu Z, Hung A, Karagiannis TC. EpiMed Coronabank Chemical Collection: Compound selection, ADMET analysis, and utilisation in the context of potential SARS-CoV-2 antivirals. J Mol Graph Model 2023; 125:108602. [PMID: 37597309 DOI: 10.1016/j.jmgm.2023.108602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/21/2023]
Abstract
Antiviral drugs are important for the coronavirus disease 2019 (COVID-19) response, as vaccines and antibodies may have reduced efficacy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Antiviral drugs that have been made available for use, albeit with questionable efficacy, include remdesivir (Veklury®), nirmatrelvir-ritonavir (Paxlovid™), and molnupiravir (Lagevrio®). To expand the options available for COVID-19 and prepare for future pandemics, there is a need to investigate new uses for existing drugs and design novel compounds. To support these efforts, we have created a comprehensive library of 750 molecules that have been sourced from in vitro, in vivo, and in silico studies. It is publicly available at our dedicated website (https://epimedlab.org/crl/). The EpiMed Coronabank Chemical Collection consists of compounds that have been divided into 10 main classes based on antiviral properties, as well as the potential to be used for the management, prevention, or treatment of COVID-19 related complications. A detailed description of each compound is provided, along with the molecular formula, canonical SMILES, and U.S. Food and Drug Administration approval status. The chemical structures have been obtained and are available for download. Moreover, the pharmacokinetic properties of the ligands have been characterised. To demonstrate an application of the EpiMed Coronabank Chemical Collection, molecular docking was used to evaluate the binding characteristics of ligands against SARS-CoV-2 nonstructural and accessory proteins. Overall, our database can be used to aid the drug repositioning process, and for gaining further insight into the molecular mechanisms of action of potential compounds of interest.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Raymond C Beh
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Julia J Liang
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Thinh Sieu Tang
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Xun Zhou
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ya Yun Siow
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yinghao Ma
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Zifang Hu
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Zifei Wu
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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28
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Federico L, Malone B, Tennøe S, Chaban V, Osen JR, Gainullin M, Smorodina E, Kared H, Akbar R, Greiff V, Stratford R, Clancy T, Munthe LA. Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence. Front Immunol 2023; 14:1265044. [PMID: 38045681 PMCID: PMC10691274 DOI: 10.3389/fimmu.2023.1265044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/01/2023] [Indexed: 12/05/2023] Open
Abstract
During the COVID-19 pandemic we utilized an AI-driven T cell epitope prediction tool, the NEC Immune Profiler (NIP) to scrutinize and predict regions of T cell immunogenicity (hotspots) from the entire SARS-CoV-2 viral proteome. These immunogenic regions offer potential for the development of universally protective T cell vaccine candidates. Here, we validated and characterized T cell responses to a set of minimal epitopes from these AI-identified universal hotspots. Utilizing a flow cytometry-based T cell activation-induced marker (AIM) assay, we identified 59 validated screening hits, of which 56% (33 peptides) have not been previously reported. Notably, we found that most of these novel epitopes were derived from the non-spike regions of SARS-CoV-2 (Orf1ab, Orf3a, and E). In addition, ex vivo stimulation with NIP-predicted peptides from the spike protein elicited CD8+ T cell response in PBMC isolated from most vaccinated donors. Our data confirm the predictive accuracy of AI platforms modelling bona fide immunogenicity and provide a novel framework for the evaluation of vaccine-induced T cell responses.
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Affiliation(s)
- Lorenzo Federico
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | - Viktoriia Chaban
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Julie Røkke Osen
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Murat Gainullin
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eva Smorodina
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Oslo University Hospital, Oslo, Norway
| | - Hassen Kared
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Rahmad Akbar
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Oslo University Hospital, Oslo, Norway
| | - Victor Greiff
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Oslo University Hospital, Oslo, Norway
| | | | | | - Ludvig Andre Munthe
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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29
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Busscher BM, Befekadu HB, Liu Z, Xiao TS. SARS-CoV-2 ORF3a-Mediated NF-κB Activation Is Not Dependent on TRAF-Binding Sequence. Viruses 2023; 15:2229. [PMID: 38005906 PMCID: PMC10675646 DOI: 10.3390/v15112229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/31/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus Disease 2019 (COVID-19). Excessive inflammation is a hallmark of severe COVID-19, and several proteins encoded in the SARS-CoV-2 genome are capable of stimulating inflammatory pathways. Among these, the accessory protein open reading frame 3a (ORF3a) has been implicated in COVID-19 pathology. Here we investigated the roles of ORF3a in binding to TNF receptor-associated factor (TRAF) proteins and inducing nuclear factor kappa B (NF-κB) activation. X-ray crystallography and a fluorescence polarization assay revealed low-affinity binding between an ORF3a N-terminal peptide and TRAFs, and a dual-luciferase assay demonstrated NF-κB activation by ORF3a. Nonetheless, mutation of the N-terminal TRAF-binding sequence PIQAS in ORF3a did not significantly diminish NF-κB activation in our assay. Our results thus suggest that the SARS-CoV-2 protein may activate NF-κB through alternative mechanisms.
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Affiliation(s)
- Brianna M. Busscher
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (B.M.B.); (Z.L.)
| | - Henock B. Befekadu
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Zhonghua Liu
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (B.M.B.); (Z.L.)
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Tsan Sam Xiao
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (B.M.B.); (Z.L.)
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30
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Macauslane KL, Pegg CL, Short KR, Schulz BL. Modulation of endoplasmic reticulum stress response pathways by respiratory viruses. Crit Rev Microbiol 2023:1-19. [PMID: 37934111 DOI: 10.1080/1040841x.2023.2274840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/15/2023] [Indexed: 11/08/2023]
Abstract
Acute respiratory infections (ARIs) are amongst the leading causes of death and disability, and the greatest burden of disease impacts children, pregnant women, and the elderly. Respiratory viruses account for the majority of ARIs. The unfolded protein response (UPR) is a host homeostatic defence mechanism primarily activated in response to aberrant endoplasmic reticulum (ER) resident protein accumulation in cell stresses including viral infection. The UPR has been implicated in the pathogenesis of several respiratory diseases, as the respiratory system is particularly vulnerable to chronic and acute activation of the ER stress response pathway. Many respiratory viruses therefore employ strategies to modulate the UPR during infection, with varying effects on the host and the pathogens. Here, we review the specific means by which respiratory viruses affect the host UPR, particularly in association with the high production of viral glycoproteins, and the impact of UPR activation and subversion on viral replication and disease pathogenesis. We further review the activation of UPR in common co-morbidities of ARIs and discuss the therapeutic potential of modulating the UPR in virally induced respiratory diseases.
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Affiliation(s)
- Kyle L Macauslane
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
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31
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Grand RJ. SARS-CoV-2 and the DNA damage response. J Gen Virol 2023; 104:001918. [PMID: 37948194 PMCID: PMC10768691 DOI: 10.1099/jgv.0.001918] [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: 09/01/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is characterized by respiratory distress, multiorgan dysfunction and, in some cases, death. The virus is also responsible for post-COVID-19 condition (commonly referred to as 'long COVID'). SARS-CoV-2 is a single-stranded, positive-sense RNA virus with a genome of approximately 30 kb, which encodes 26 proteins. It has been reported to affect multiple pathways in infected cells, resulting, in many cases, in the induction of a 'cytokine storm' and cellular senescence. Perhaps because it is an RNA virus, replicating largely in the cytoplasm, the effect of SARS-Cov-2 on genome stability and DNA damage responses (DDRs) has received relatively little attention. However, it is now becoming clear that the virus causes damage to cellular DNA, as shown by the presence of micronuclei, DNA repair foci and increased comet tails in infected cells. This review considers recent evidence indicating how SARS-CoV-2 causes genome instability, deregulates the cell cycle and targets specific components of DDR pathways. The significance of the virus's ability to cause cellular senescence is also considered, as are the implications of genome instability for patients suffering from long COVID.
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Affiliation(s)
- Roger J. Grand
- Institute for Cancer and Genomic Science, The Medical School, University of Birmingham, Birmingham, UK
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32
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D'Anna L, Miclot T, Bignon E, Perricone U, Barone G, Monari A, Terenzi A. Resolving a guanine-quadruplex structure in the SARS-CoV-2 genome through circular dichroism and multiscale molecular modeling. Chem Sci 2023; 14:11332-11339. [PMID: 37886086 PMCID: PMC10599604 DOI: 10.1039/d3sc04004f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/08/2023] [Indexed: 10/28/2023] Open
Abstract
The genome of SARS-CoV-2 coronavirus is made up of a single-stranded RNA fragment that can assume a specific secondary structure, whose stability can influence the virus's ability to reproduce. Recent studies have identified putative guanine quadruplex sequences in SARS-CoV-2 genome fragments that are involved in coding for both structural and non-structural proteins. In this contribution, we focus on a specific G-rich sequence referred to as RG-2, which codes for the non-structural protein 10 (Nsp10) and assumes a guanine-quadruplex (G4) arrangement. We provide the secondary structure of RG-2 G4 at atomistic resolution by molecular modeling and simulation, validated by the superposition of experimental and calculated electronic circular dichroism spectra. Through both experimental and simulation approaches, we have demonstrated that pyridostatin (PDS), a widely recognized G4 binder, can bind to and stabilize RG-2 G4 more strongly than RG-1, another G4 forming sequence that was previously proposed as a potential target for antiviral drug candidates. Overall, this study highlights RG-2 as a valuable target to inhibit the translation and replication of SARS-CoV-2, paving the way towards original therapeutic approaches against emerging RNA viruses.
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Affiliation(s)
- Luisa D'Anna
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo Viale delle Scienze, Ed. 17 90128 Palermo Italy
| | - Tom Miclot
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo Viale delle Scienze, Ed. 17 90128 Palermo Italy
- Université de Lorraine and CNRS UMR 7019 LPCT F-54000 Nancy France
| | | | - Ugo Perricone
- Fondazione Ri.MED Via Filippo Marini 14 90128 Palermo Italy
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo Viale delle Scienze, Ed. 17 90128 Palermo Italy
| | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS F-75006 Paris France
| | - Alessio Terenzi
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo Viale delle Scienze, Ed. 17 90128 Palermo Italy
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33
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Yuan C, Ma Z, Xie J, Li W, Su L, Zhang G, Xu J, Wu Y, Zhang M, Liu W. The role of cell death in SARS-CoV-2 infection. Signal Transduct Target Ther 2023; 8:357. [PMID: 37726282 PMCID: PMC10509267 DOI: 10.1038/s41392-023-01580-8] [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: 01/20/2023] [Revised: 06/09/2023] [Accepted: 07/31/2023] [Indexed: 09/21/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), showing high infectiousness, resulted in an ongoing pandemic termed coronavirus disease 2019 (COVID-19). COVID-19 cases often experience acute respiratory distress syndrome, which has caused millions of deaths. Apart from triggering inflammatory and immune responses, many viral infections can cause programmed cell death in infected cells. Cell death mechanisms have a vital role in maintaining a suitable environment to achieve normal cell functionality. Nonetheless, these processes are dysregulated, potentially contributing to disease pathogenesis. Over the past decades, multiple cell death pathways are becoming better understood. Growing evidence suggests that the induction of cell death by the coronavirus may significantly contributes to viral infection and pathogenicity. However, the interaction of SARS-CoV-2 with cell death, together with its associated mechanisms, is yet to be elucidated. In this review, we summarize the existing evidence concerning the molecular modulation of cell death in SARS-CoV-2 infection as well as viral-host interactions, which may shed new light on antiviral therapy against SARS-CoV-2.
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Affiliation(s)
- Cui Yuan
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhenling Ma
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jiufeng Xie
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wenqing Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Lijuan Su
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Guozhi Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jun Xu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yaru Wu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Min Zhang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Wei Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China.
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Justo Arevalo S, Castillo-Chávez A, Uribe Calampa CS, Zapata Sifuentes D, Huallpa CJ, Landa Bianchi G, Garavito-Salini Casas R, Quiñones Aguilar M, Pineda Chavarría R. What do we know about the function of SARS-CoV-2 proteins? Front Immunol 2023; 14:1249607. [PMID: 37790934 PMCID: PMC10544941 DOI: 10.3389/fimmu.2023.1249607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 10/05/2023] Open
Abstract
The COVID-19 pandemic has highlighted the importance in the understanding of the biology of SARS-CoV-2. After more than two years since the first report of COVID-19, it remains crucial to continue studying how SARS-CoV-2 proteins interact with the host metabolism to cause COVID-19. In this review, we summarize the findings regarding the functions of the 16 non-structural, 6 accessory and 4 structural SARS-CoV-2 proteins. We place less emphasis on the spike protein, which has been the subject of several recent reviews. Furthermore, comprehensive reviews about COVID-19 therapeutic have been also published. Therefore, we do not delve into details on these topics; instead we direct the readers to those other reviews. To avoid confusions with what we know about proteins from other coronaviruses, we exclusively report findings that have been experimentally confirmed in SARS-CoV-2. We have identified host mechanisms that appear to be the primary targets of SARS-CoV-2 proteins, including gene expression and immune response pathways such as ribosome translation, JAK/STAT, RIG-1/MDA5 and NF-kβ pathways. Additionally, we emphasize the multiple functions exhibited by SARS-CoV-2 proteins, along with the limited information available for some of these proteins. Our aim with this review is to assist researchers and contribute to the ongoing comprehension of SARS-CoV-2's pathogenesis.
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Affiliation(s)
- Santiago Justo Arevalo
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru
- Departmento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Daniela Zapata Sifuentes
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru
- Departmento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | - César J. Huallpa
- Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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Islam MJ, Alom MS, Hossain MS, Ali MA, Akter S, Islam S, Ullah MO, Halim MA. Unraveling the impact of ORF3a Q57H mutation on SARS-CoV-2: insights from molecular dynamics. J Biomol Struct Dyn 2023:1-14. [PMID: 37649361 DOI: 10.1080/07391102.2023.2252908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
ORF3a is a conserved accessory protein of SARS-CoV-2, linked to viral infection and pathogenesis, with acquired mutations at various locations. Previous studies have shown that the occurrence of the Q57H mutation is higher in comparison to other positions in ORF3a. This mutation is known to induce conformational changes, yet the extent of structural alteration and its role in the viral adaptation process remain unknown. Here we performed molecular dynamics (MD) simulations of wt-ORF3a, Q57H, and Q57A mutants to analyze structural changes caused by mutations compared to the native protein. The MD analysis revealed that Q57H and Q57A mutants show significant structural changes in the dimer conformation than the wt-ORF3a. This dimer conformer narrows down the ion channel cavity, which reduces Na + or K + permeability leading to decrease the antigenic response that can help the virus to escape the host immune system. Non-bonding interaction analysis shows the Q57H mutant has more interacting residues, resulting in more stability within dimer conformation than the wt-ORF3a and Q57A. Moreover, both mutant dimers (Q57H and Q57A) form a novel salt-bridge interaction at the same position between A:Asp142 and B:Lys61, whereas such an interaction is absent in the wt-ORF3a dimer. We have also noticed that the TM3 domain's flexibility in Q57H is increased because of strong inter-domain interactions of TM1 and TM2 within the dimer conformation. These unusual interactions and flexibility of Q57H mutant can have significant impacts on the SARS-CoV-2 adaptations, virulence, transmission, and immune system evasion. Our findings are consistent with the previous experimental data and provided details information on the structural perturbation in ORF3a caused by mutations, which can help better understand the structural change at the molecular level as well as the reason for the high virulence properties of this variant.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Jahirul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Md Siddik Alom
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Md Shahadat Hossain
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, USA
| | - Shaila Akter
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Shafiqul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, USA
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36
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Lee YB, Jung M, Kim J, Charles A, Christ W, Kang J, Kang MG, Kwak C, Klingström J, Smed-Sörensen A, Kim JS, Mun JY, Rhee HW. Super-resolution proximity labeling reveals anti-viral protein network and its structural changes against SARS-CoV-2 viral proteins. Cell Rep 2023; 42:112835. [PMID: 37478010 DOI: 10.1016/j.celrep.2023.112835] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 05/31/2023] [Accepted: 07/05/2023] [Indexed: 07/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in human cells by interacting with host factors following infection. To understand the virus and host interactome proximity, we introduce a super-resolution proximity labeling (SR-PL) method with a "plug-and-playable" PL enzyme, TurboID-GBP (GFP-binding nanobody protein), and we apply it for interactome mapping of SARS-CoV-2 ORF3a and membrane protein (M), which generates highly perturbed endoplasmic reticulum (ER) structures. Through SR-PL analysis of the biotinylated interactome, 224 and 272 peptides are robustly identified as ORF3a and M interactomes, respectively. Within the ORF3a interactome, RNF5 co-localizes with ORF3a and generates ubiquitin modifications of ORF3a that can be involved in protein degradation. We also observe that the SARS-CoV-2 infection rate is efficiently reduced by the overexpression of RNF5 in host cells. The interactome data obtained using the SR-PL method are presented at https://sarscov2.spatiomics.org. We hope that our method will contribute to revealing virus-host interactions of other viruses in an efficient manner.
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Affiliation(s)
- Yun-Bin Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jeesoo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea
| | - Afandi Charles
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Wanda Christ
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14183 Stockholm, Sweden
| | - Jiwoong Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Chulhwan Kwak
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Jonas Klingström
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14183 Stockholm, Sweden; Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Anna Smed-Sörensen
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea.
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea.
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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37
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Jiao S, Miranda P, Li Y, Maric D, Holmgren M. Some aspects of the life of SARS-CoV-2 ORF3a protein in mammalian cells. Heliyon 2023; 9:e18754. [PMID: 37609425 PMCID: PMC10440475 DOI: 10.1016/j.heliyon.2023.e18754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/24/2023] Open
Abstract
The accessory protein ORF3a, from SARS-CoV-2, plays a critical role in viral infection and pathogenesis. Here, we characterized ORF3a assembly, ion channel activity, subcellular localization, and interactome. At the plasma membrane, ORF3a exists mostly as monomers and dimers, which do not alter the native cell membrane conductance, suggesting that ORF3a does not function as a viroporin at the cell surface. As a membrane protein, ORF3a is synthesized at the ER and sorted via a canonical route. ORF3a overexpression induced an approximately 25% increase in cell death. By developing an APEX2-based proximity labeling assay, we uncovered proteins proximal to ORF3a, suggesting that ORF3a recruits some host proteins to weaken the cell. In addition, it exposed a set of mitochondria related proteins that triggered mitochondrial fission. Overall, this work can be an important instrument in understanding the role of ORF3a in the virus pathogenicity and searching for potential therapeutic treatments for COVID-19.
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Affiliation(s)
- Song Jiao
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Pablo Miranda
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
| | - Miguel Holmgren
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Maryland, MD, USA
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38
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Henke W, Kalamvoki M, Stephens EB. The Role of the Tyrosine-Based Sorting Signals of the ORF3a Protein of SARS-CoV-2 on Intracellular Trafficking, Autophagy, and Apoptosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.550379. [PMID: 37547007 PMCID: PMC10402054 DOI: 10.1101/2023.07.24.550379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The open reading frame 3a (ORF3a) is an accessory transmembrane protein that is important to the pathogenicity of SARS-CoV-2. The cytoplasmic domain of ORF3a has three canonical tyrosine-based sorting signals (YxxΦ; where x is any amino acid and Φ is a hydrophobic amino acid with a bulky -R group). They have been implicated in the trafficking of membrane proteins to the cell plasma membrane and to intracellular organelles. Previous studies have indicated that mutation of the 160YSNV163 motif abrogated plasma membrane expression and inhibited ORF3a-induced apoptosis. However, two additional canonical tyrosine-based sorting motifs (211YYQL213, 233YNKI236) exist in the cytoplasmic domain of ORF3a that have not been assessed. We removed all three potential tyrosine-based motifs and systematically restored them to assess the importance of each motif or combination of motifs that restored efficient trafficking to the cell surface and lysosomes. Our results indicate that the YxxΦ motif at position 160 was insufficient for the trafficking of ORF3a to the cell surface. Our studies also showed that ORF3a proteins with an intact YxxΦ at position 211 or at 160 and 211 were most important. We found that ORF3a cell surface expression correlated with the co-localization of ORF3a with LAMP-1 near the cell surface. These results suggest that YxxΦ motifs within the cytoplasmic domain may act cooperatively in ORF3a transport to the plasma membrane and endocytosis to lysosomes. Further, our results indicate that certain tyrosine mutants failed to activate caspase 3 and did not correlate with autophagy functions associated with this protein.
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Affiliation(s)
- Wyatt Henke
- Department of Microbiology, Molecular Genetics, and Immunology, 2000 Hixon Hall, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, Kansas 66160
| | - Maria Kalamvoki
- Department of Microbiology, Molecular Genetics, and Immunology, 2000 Hixon Hall, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, Kansas 66160
| | - Edward B Stephens
- Department of Microbiology, Molecular Genetics, and Immunology, 2000 Hixon Hall, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, Kansas 66160
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39
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Moradi S, Wu Y, Walden P, Cui Z, Johnston WA, Petrov D, Alexandrov K. In Vitro Reconstitution and Analysis of SARS-CoV-2/Host Protein-Protein Interactions. ACS OMEGA 2023; 8:25009-25019. [PMID: 37483225 PMCID: PMC10357528 DOI: 10.1021/acsomega.3c01625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023]
Abstract
The emergence of viral threats such as Ebola, ZIKA, and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) requires a rapid and efficient approach for elucidating mechanisms of pathogenesis and development of therapeutics. In this context, cell-free protein synthesis (CFPS) holds a promise to resolve the bottlenecks of multiplexed protein production and interaction analysis among host and pathogen proteins. Here, we applied a eukaryotic CFPS system based on Leishmania tarentolae extract (LTE) protein expression in combination with AlphaLISA proximity-based protein interaction technology to identify intraviral and viral-human protein interactions of SARS-CoV-2 virus that can potentially be targeted by the existing or novel antiviral therapeutics. We produced and tested 54 putative human-viral protein pairs in vitro and identified 45 direct binary protein interactions. As a casing example of the assay's suitability for drug development applications, we analyzed the effect of a putative biologic on the human angiotensin-converting enzyme 2/receptor-binding domain (hACE2/RBD) interaction. This suggests that the presented pathogen characterization platform can facilitate the development of new therapeutic agents.
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Affiliation(s)
- Shayli
Varasteh Moradi
- CSIRO-QUT
Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic
Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics
and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Yue Wu
- CSIRO-QUT
Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic
Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics
and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Patricia Walden
- CSIRO-QUT
Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic
Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics
and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Zhenling Cui
- CSIRO-QUT
Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic
Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics
and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Wayne A. Johnston
- CSIRO-QUT
Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic
Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics
and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Dmitri Petrov
- Department
of Biology, Stanford University, Stanford, California 94305-5020, United
States
| | - Kirill Alexandrov
- CSIRO-QUT
Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic
Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics
and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
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40
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Chen GL, Li J, Zhang J, Zeng B. To Be or Not to Be an Ion Channel: Cryo-EM Structures Have a Say. Cells 2023; 12:1870. [PMID: 37508534 PMCID: PMC10378246 DOI: 10.3390/cells12141870] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
Ion channels are the second largest class of drug targets after G protein-coupled receptors. In addition to well-recognized ones like voltage-gated Na/K/Ca channels in the heart and neurons, novel ion channels are continuously discovered in both excitable and non-excitable cells and demonstrated to play important roles in many physiological processes and diseases such as developmental disorders, neurodegenerative diseases, and cancer. However, in the field of ion channel discovery, there are an unignorable number of published studies that are unsolid and misleading. Despite being the gold standard of a functional assay for ion channels, electrophysiological recordings are often accompanied by electrical noise, leak conductance, and background currents of the membrane system. These unwanted signals, if not treated properly, lead to the mischaracterization of proteins with seemingly unusual ion-conducting properties. In the recent ten years, the technical revolution of cryo-electron microscopy (cryo-EM) has greatly advanced our understanding of the structures and gating mechanisms of various ion channels and also raised concerns about the pore-forming ability of some previously identified channel proteins. In this review, we summarize cryo-EM findings on ion channels with molecular identities recognized or disputed in recent ten years and discuss current knowledge of proposed channel proteins awaiting cryo-EM analyses. We also present a classification of ion channels according to their architectures and evolutionary relationships and discuss the possibility and strategy of identifying more ion channels by analyzing structures of transmembrane proteins of unknown function. We propose that cross-validation by electrophysiological and structural analyses should be essentially required for determining molecular identities of novel ion channels.
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Affiliation(s)
- Gui-Lan Chen
- Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China
| | - Bo Zeng
- Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
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41
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Shariq M, Malik AA, Sheikh JA, Hasnain SE, Ehtesham NZ. Regulation of autophagy by SARS-CoV-2: The multifunctional contributions of ORF3a. J Med Virol 2023; 95:e28959. [PMID: 37485696 DOI: 10.1002/jmv.28959] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/01/2023] [Accepted: 07/04/2023] [Indexed: 07/25/2023]
Abstract
Severe acute respiratory syndrome-coronavirus-1 (SARS-CoV-2) regulates autophagic flux by blocking the fusion of autophagosomes with lysosomes, causing the accumulation of membranous vesicles for replication. Multiple SARS-CoV-2 proteins regulate autophagy with significant roles attributed to ORF3a. Mechanistically, open reading frame 3a (ORF3a) forms a complex with UV radiation resistance associated, regulating the functions of the PIK3C3-1 and PIK3C3-2 lipid kinase complexes, thereby modulating autophagosome biogenesis. ORF3a sequesters VPS39 onto the late endosome/lysosome, inhibiting assembly of the soluble NSF attachement protein REceptor (SNARE) complex and preventing autolysosome formation. ORF3a promotes the interaction between BECN1 and HMGB1, inducing the assembly of PIK3CA kinases into the ER (endoplasmic reticulum) and activating reticulophagy, proinflammatory responses, and ER stress. ORF3a recruits BORCS6 and ARL8B to lysosomes, initiating the anterograde transport of the virus to the plasma membrane. ORF3a also activates the SNARE complex (STX4-SNAP23-VAMP7), inducing fusion of lysosomes with the plasma membrane for viral egress. These mechanistic details can provide multiple targets for inhibiting SARS-CoV-2 by developing host- or host-pathogen interface-based therapeutics.
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Affiliation(s)
- Mohd Shariq
- Inflammation Biology and Cell Signalling Laboratory, ICMR-National Institute of Pathology, New Delhi, India
| | - Asrar A Malik
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Javaid A Sheikh
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi, India
| | - Seyed E Hasnain
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Nasreen Z Ehtesham
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
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42
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Mah MG, Linster M, Low DHW, Zhuang Y, Jayakumar J, Samsudin F, Wong FY, Bond PJ, Mendenhall IH, Su YCF, Smith GJD. Spike-Independent Infection of Human Coronavirus 229E in Bat Cells. Microbiol Spectr 2023; 11:e0348322. [PMID: 37199653 PMCID: PMC10269751 DOI: 10.1128/spectrum.03483-22] [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: 09/06/2022] [Accepted: 04/17/2023] [Indexed: 05/19/2023] Open
Abstract
Bats are the reservoir for numerous human pathogens, including coronaviruses. Despite many coronaviruses having descended from bat ancestors, little is known about virus-host interactions and broader evolutionary history involving bats. Studies have largely focused on the zoonotic potential of coronaviruses with few infection experiments conducted in bat cells. To determine genetic changes derived from replication in bat cells and possibly identify potential novel evolutionary pathways for zoonotic virus emergence, we serially passaged six human 229E isolates in a newly established Rhinolophus lepidus (horseshoe bat) kidney cell line. Here, we observed extensive deletions within the spike and open reading frame 4 (ORF4) genes of five 229E viruses after passaging in bat cells. As a result, spike protein expression and infectivity of human cells was lost in 5 of 6 viruses, but the capability to infect bat cells was maintained. Only viruses that expressed the spike protein could be neutralized by 229E spike-specific antibodies in human cells, whereas there was no neutralizing effect on viruses that did not express the spike protein inoculated on bat cells. However, one isolate acquired an early stop codon, abrogating spike expression but maintaining infection in bat cells. After passaging this isolate in human cells, spike expression was restored due to acquisition of nucleotide insertions among virus subpopulations. Spike-independent infection of human coronavirus 229E may provide an alternative mechanism for viral maintenance in bats that does not rely on the compatibility of viral surface proteins and known cellular entry receptors. IMPORTANCE Many viruses, including coronaviruses, originated from bats. Yet, we know little about how these viruses switch between hosts and enter human populations. Coronaviruses have succeeded in establishing in humans at least five times, including endemic coronaviruses and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In an approach to identify requirements for host switches, we established a bat cell line and adapted human coronavirus 229E viruses by serial passage. The resulting viruses lost their spike protein but maintained the ability to infect bat cells, but not human cells. Maintenance of 229E viruses in bat cells appears to be independent of a canonical spike receptor match, which in turn might facilitate cross-species transmission in bats.
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Affiliation(s)
- Marcus G. Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Martin Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Dolyce H. W. Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yan Zhuang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jayanthi Jayakumar
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Firdaus Samsudin
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore
| | - Foong Ying Wong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Gavin J. D. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
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Trepte P, Secker C, Kostova S, Maseko SB, Choi SG, Blavier J, Minia I, Ramos ES, Cassonnet P, Golusik S, Zenkner M, Beetz S, Liebich MJ, Scharek N, Schütz A, Sperling M, Lisurek M, Wang Y, Spirohn K, Hao T, Calderwood MA, Hill DE, Landthaler M, Olivet J, Twizere JC, Vidal M, Wanker EE. AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544560. [PMID: 37398436 PMCID: PMC10312674 DOI: 10.1101/2023.06.14.544560] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Protein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays and AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.
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Affiliation(s)
- Philipp Trepte
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- Brain Development and Disease, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030, Vienna, Austria
| | - Christopher Secker
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- Zuse Institute Berlin, Berlin, Germany
| | - Simona Kostova
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Sibusiso B. Maseko
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
| | - Soon Gang Choi
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jeremy Blavier
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
| | - Igor Minia
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125, Berlin, Germany
| | - Eduardo Silva Ramos
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Patricia Cassonnet
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique (CNRS), Université de Paris, Paris, France
| | - Sabrina Golusik
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Martina Zenkner
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Stephanie Beetz
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Mara J. Liebich
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Nadine Scharek
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Anja Schütz
- Protein Production & Characterization, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Marcel Sperling
- Multifunctional Colloids and Coating, Fraunhofer Institute for Applied Polymer Research (IAP), 14476, Potsdam-Golm, Germany
| | - Michael Lisurek
- Structural Chemistry and Computational Biophysics, Leibniz-Institut für Molekulare Pharmakologie (FMP), 13125, Berlin, Germany
| | - Yang Wang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Michael A. Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David E. Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, 13125, Berlin, Germany
| | - Julien Olivet
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
- Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Erich E. Wanker
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
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Bhowal C, Ghosh S, Ghatak D, De R. Pathophysiological involvement of host mitochondria in SARS-CoV-2 infection that causes COVID-19: a comprehensive evidential insight. Mol Cell Biochem 2023; 478:1325-1343. [PMID: 36308668 PMCID: PMC9617539 DOI: 10.1007/s11010-022-04593-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/13/2022] [Indexed: 10/31/2022]
Abstract
SARS-CoV-2 is a positive-strand RNA virus that infects humans through the nasopharyngeal and oral route causing COVID-19. Scientists left no stone unturned to explore a targetable key player in COVID-19 pathogenesis against which therapeutic interventions can be initiated. This article has attempted to review, coordinate and accumulate the most recent observations in support of the hypothesis predicting the altered state of mitochondria concerning mitochondrial redox homeostasis, inflammatory regulations, morphology, bioenergetics and antiviral signalling in SARS-CoV-2 infection. Mitochondria is extremely susceptible to physiological as well as pathological stimuli, including viral infections. Recent studies suggest that SARS-CoV-2 pathogeneses alter mitochondrial integrity, in turn mitochondria modulate cellular response against the infection. SARS-CoV-2 M protein inhibited mitochondrial antiviral signalling (MAVS) protein aggregation in turn hinders innate antiviral response. Viral open reading frames (ORFs) also play an instrumental role in altering mitochondrial regulation of immune response. Notably, ORF-9b and ORF-6 impair MAVS activation. In aged persons, the NLRP3 inflammasome is over-activated due to impaired mitochondrial function, increased mitochondrial reactive oxygen species (mtROS), and/or circulating free mitochondrial DNA, resulting in a hyper-response of classically activated macrophages. This article also tries to understand how mitochondrial fission-fusion dynamics is affected by the virus. This review comprehends the overall mitochondrial attribute in pathogenesis as well as prognosis in patients infected with COVID-19 taking into account pertinent in vitro, pre-clinical and clinical data encompassing subjects with a broad range of severity and morbidity. This endeavour may help in exploring novel non-canonical therapeutic strategies to COVID-19 disease and associated complications.
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Affiliation(s)
- Chandan Bhowal
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Sayak Ghosh
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Debapriya Ghatak
- Indian Association for the Cultivation of Science, Jadavpur, 700032, Kolkata, India
| | - Rudranil De
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India.
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45
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Gupta Y, Savytskyi OV, Coban M, Venugopal A, Pleqi V, Weber CA, Chitale R, Durvasula R, Hopkins C, Kempaiah P, Caulfield TR. Protein structure-based in-silico approaches to drug discovery: Guide to COVID-19 therapeutics. Mol Aspects Med 2023; 91:101151. [PMID: 36371228 PMCID: PMC9613808 DOI: 10.1016/j.mam.2022.101151] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
With more than 5 million fatalities and close to 300 million reported cases, COVID-19 is the first documented pandemic due to a coronavirus that continues to be a major health challenge. Despite being rapid, uncontrollable, and highly infectious in its spread, it also created incentives for technology development and redefined public health needs and research agendas to fast-track innovations to be translated. Breakthroughs in computational biology peaked during the pandemic with renewed attention to making all cutting-edge technology deliver agents to combat the disease. The demand to develop effective treatments yielded surprising collaborations from previously segregated fields of science and technology. The long-standing pharmaceutical industry's aversion to repurposing existing drugs due to a lack of exponential financial gain was overrun by the health crisis and pressures created by front-line researchers and providers. Effective vaccine development even at an unprecedented pace took more than a year to develop and commence trials. Now the emergence of variants and waning protections during the booster shots is resulting in breakthrough infections that continue to strain health care systems. As of now, every protein of SARS-CoV-2 has been structurally characterized and related host pathways have been extensively mapped out. The research community has addressed the druggability of a multitude of possible targets. This has been made possible due to existing technology for virtual computer-assisted drug development as well as new tools and technologies such as artificial intelligence to deliver new leads. Here in this article, we are discussing advances in the drug discovery field related to target-based drug discovery and exploring the implications of known target-specific agents on COVID-19 therapeutic management. The current scenario calls for more personalized medicine efforts and stratifying patient populations early on for their need for different combinations of prognosis-specific therapeutics. We intend to highlight target hotspots and their potential agents, with the ultimate goal of using rational design of new therapeutics to not only end this pandemic but also uncover a generalizable platform for use in future pandemics.
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Affiliation(s)
- Yash Gupta
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Oleksandr V Savytskyi
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; In Vivo Biosystems, Eugene, OR, USA
| | - Matt Coban
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Vasili Pleqi
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Caleb A Weber
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Rohit Chitale
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA; The Council on Strategic Risks, 1025 Connecticut Ave NW, Washington, DC, USA
| | - Ravi Durvasula
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | | | - Prakasha Kempaiah
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of QHS Computational Biology, Mayo Clinic, Jacksonville, FL, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA; Department of Neurosurgery, Mayo Clinic, Jacksonville, FL, USA.
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46
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Keramidas P, Papachristou E, Papi RM, Mantsou A, Choli-Papadopoulou T. Inhibition of PERK Kinase, an Orchestrator of the Unfolded Protein Response (UPR), Significantly Reduces Apoptosis and Inflammation of Lung Epithelial Cells Triggered by SARS-CoV-2 ORF3a Protein. Biomedicines 2023; 11:1585. [PMID: 37371681 DOI: 10.3390/biomedicines11061585] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
SARS-CoV-2 ORF3a accessory protein was found to be involved in virus release, immunomodulation and exhibited a pro-apoptotic character. In order to unravel a potential ORF3a-induced apoptotic and inflammatory death mechanism, lung epithelial cells (A549) were transfected with in vitro synthesized ORF3a mRNA. The protein's dynamic involvement as "stress factor" for the endoplasmic reticulum, causing the activation of PERK kinase and other UPR-involved proteins and therefore the upregulation of their signaling pathway executioners (ATF6, XBP-1s, PERK, phospho eIF2a, ATF4, CHOP, GADD34), has been clearly demonstrated. Furthermore, the overexpression of BAX and BH3-only pro-apoptotic protein PUMA, the upregulation of Bcl-2 family genes (BAX, BAK, BID, BAD), the reduced expression of Bcl-2 in mRNA and protein levels, and lastly, the cleavage of PARP-1 and caspase family members (caspase-3,-8 and -9) indicate that ORF3a displays its apoptotic character through the mitochondrial pathway of apoptosis. Moreover, the upregulation of NFκB, phosphorylation of p65 and IκΒα and the elevated expression of pro-inflammatory cytokines (IL-1b, IL-6, IL-8 and IL-18) in transfected cells with ORF3a mRNA indicate that this protein causes the inflammatory response through NFκB activation and therefore triggers lung injury. An intriguing finding of our study is that upon treatment of the ORF3a-transfected cells with GSK2606414, a selective PERK inhibitor, both complications (apoptosis and inflammatory response) were neutralized, and cell survival was favored, whereas treatment of transfected cells with z-VAD (a pan-caspase inhibitor) despite inhibiting cell death, could not ameliorate the inflammatory response of transfected A549 cells. Given the above, we point out that PERK kinase is a "master tactician" and its activation constitutes the main stimulus for the emergence of ORF3a apoptotic and inflammatory nature and therefore could serve as potential target for developing novel therapeutic approaches against COVID-19.
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Affiliation(s)
- Panagiotis Keramidas
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Eleni Papachristou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Rigini M Papi
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Aglaia Mantsou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Theodora Choli-Papadopoulou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
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47
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Oliveira-Mendes BBR, Alameh M, Ollivier B, Montnach J, Bidère N, Souazé F, Escriou N, Charpentier F, Baró I, De Waard M, Loussouarn G. SARS-CoV-2 E and 3a Proteins Are Inducers of Pannexin Currents. Cells 2023; 12:1474. [PMID: 37296595 PMCID: PMC10252541 DOI: 10.3390/cells12111474] [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: 03/13/2023] [Revised: 05/10/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
Controversial reports have suggested that SARS-CoV E and 3a proteins are plasma membrane viroporins. Here, we aimed at better characterizing the cellular responses induced by these proteins. First, we show that expression of SARS-CoV-2 E or 3a protein in CHO cells gives rise to cells with newly acquired round shapes that detach from the Petri dish. This suggests that cell death is induced upon expression of E or 3a protein. We confirmed this by using flow cytometry. In adhering cells expressing E or 3a protein, the whole-cell currents were not different from those of the control, suggesting that E and 3a proteins are not plasma membrane viroporins. In contrast, recording the currents on detached cells uncovered outwardly rectifying currents much larger than those observed in the control. We illustrate for the first time that carbenoxolone and probenecid block these outwardly rectifying currents; thus, these currents are most probably conducted by pannexin channels that are activated by cell morphology changes and also potentially by cell death. The truncation of C-terminal PDZ binding motifs reduces the proportion of dying cells but does not prevent these outwardly rectifying currents. This suggests distinct pathways for the induction of these cellular events by the two proteins. We conclude that SARS-CoV-2 E and 3a proteins are not viroporins expressed at the plasma membrane.
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Affiliation(s)
| | - Malak Alameh
- L’institut du Thorax, Nantes Université, CNRS, INSERM, F-44000 Nantes, France; (B.B.R.O.-M.); (M.A.)
- Labex Ion Channels, Science and Therapeutics, F-06560 Valbonne, France
| | - Béatrice Ollivier
- L’institut du Thorax, Nantes Université, CNRS, INSERM, F-44000 Nantes, France; (B.B.R.O.-M.); (M.A.)
| | - Jérôme Montnach
- L’institut du Thorax, Nantes Université, CNRS, INSERM, F-44000 Nantes, France; (B.B.R.O.-M.); (M.A.)
| | - Nicolas Bidère
- Team SOAP, CRCI2NA, INSERM, CNRS, Nantes Université, Université d’Angers, F-44000 Nantes, France
- Equipe Labellisée Ligue Contre le Cancer, F-75006 Paris, France
| | | | - Nicolas Escriou
- Institut Pasteur, Université Paris Cité, Département de Santé Globale, F-75015 Paris, France
| | - Flavien Charpentier
- L’institut du Thorax, Nantes Université, CNRS, INSERM, F-44000 Nantes, France; (B.B.R.O.-M.); (M.A.)
| | - Isabelle Baró
- L’institut du Thorax, Nantes Université, CNRS, INSERM, F-44000 Nantes, France; (B.B.R.O.-M.); (M.A.)
| | - Michel De Waard
- L’institut du Thorax, Nantes Université, CNRS, INSERM, F-44000 Nantes, France; (B.B.R.O.-M.); (M.A.)
- Labex Ion Channels, Science and Therapeutics, F-06560 Valbonne, France
| | - Gildas Loussouarn
- L’institut du Thorax, Nantes Université, CNRS, INSERM, F-44000 Nantes, France; (B.B.R.O.-M.); (M.A.)
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48
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Zhu H, Byrnes C, Lee YT, Tuymetova G, Duffy HBD, Bakir JY, Pettit SN, Angina J, Springer DA, Allende ML, Kono M, Proia RL. SARS-CoV-2 ORF3a expression in brain disrupts the autophagy-lysosomal pathway, impairs sphingolipid homeostasis, and drives neuropathogenesis. FASEB J 2023; 37:e22919. [PMID: 37071464 DOI: 10.1096/fj.202300149r] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/10/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes injury to multiple organ systems, including the brain. SARS-CoV-2's neuropathological mechanisms may include systemic inflammation and hypoxia, as well as direct cell damage resulting from viral infections of neurons and glia. How the virus directly causes injury to brain cells, acutely and over the long term, is not well understood. In order to gain insight into this process, we studied the neuropathological effects of open reading frame 3a (ORF3a), a SARS-CoV-2 accessory protein that is a key pathological factor of the virus. Forced ORF3a brain expression in mice caused the rapid onset of neurological impairment, neurodegeneration, and neuroinflammation-key neuropathological features found in coronavirus disease (COVID-19, which is caused by SARS-CoV-2 infection). Furthermore, ORF3a expression blocked autophagy progression in the brain and caused the neuronal accumulation of α-synuclein and glycosphingolipids, all of which are linked to neurodegenerative disease. Studies with ORF3-expressing HeLa cells confirmed that ORF3a disrupted the autophagy-lysosomal pathway and blocked glycosphingolipid degradation, resulting in their accumulation. These findings indicate that, in the event of neuroinvasion by SARS-CoV-2, ORF3a expression in brain cells may drive neuropathogenesis and be an important mediator of both short- and long-term neurological manifestations of COVID-19.
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Affiliation(s)
- Hongling Zhu
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Colleen Byrnes
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Y Terry Lee
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Galina Tuymetova
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Hannah B D Duffy
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Jenna Y Bakir
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Sydney N Pettit
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Jabili Angina
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Danielle A Springer
- Murine Phenotyping Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Maria L Allende
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Mari Kono
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Richard L Proia
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
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49
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Maymand VM, Bavi O, Karami A. Probing the mechanical properties of ORF3a protein, a transmembrane channel of SARS-CoV-2 virus: Molecular dynamics study. Chem Phys 2023; 569:111859. [PMID: 36852417 PMCID: PMC9946729 DOI: 10.1016/j.chemphys.2023.111859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/04/2022] [Accepted: 02/19/2023] [Indexed: 02/24/2023]
Abstract
SARS-CoV-2-encoded accessory protein ORF3a was found to be a conserved coronavirus protein that shows crucial roles in apoptosis in cells as well as in virus release and replications. To complete the knowledge and identify the unknown of this protein, further comprehensive research is needed to clarify the leading role of ORF3a in the functioning of the coronavirus. One of the efficient approaches to determining the functionality of this protein is to investigate the mechanical properties and study its structural dynamics in the presence of physical stimuli. Herein, performing all-atom steered molecular dynamics (SMD) simulations, the mechanical properties of the force-bearing components of the ORF3a channel are calculated in different physiological conditions. As variations occurring in ORF3a may lead to alteration in protein structure and function, the G49V mutation was also simulated to clarify the relationship between the mechanical properties and chemical stability of the protein by comparing the behavior of the wild-type and mutant Orf3a. From a physiological conditions point of view, it was observed that in the solvated system, the presence of water molecules reduces Young's modulus of TM1 by ∼30 %. Our results also show that by substitution of Gly49 with valine, Young's modulus of the whole helix increases from 1.61 ± 0.20 to 2.08 ± 0.15 GPa, which is consistent with the calculated difference in free energy of wild-type and mutant helices. In addition to finding a way to fight against Covid-19 disease, understanding the mechanical behavior of these biological nanochannels can lead to the development of the potential applications of the ORF3a protein channel, such as tunable nanovalves in smart drug delivery systems, nanofilters in the new generation of desalination systems, and promising applications in DNA sequencing.
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Affiliation(s)
| | - Omid Bavi
- Department of Mechanical Engineering, Shiraz University of Technology, Shiraz, Iran
| | - Abbas Karami
- Department of Mechanical Engineering, Shiraz University of Technology, Shiraz, Iran
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Chen TH, Chang CJ, Hung PH. Possible Pathogenesis and Prevention of Long COVID: SARS-CoV-2-Induced Mitochondrial Disorder. Int J Mol Sci 2023; 24:8034. [PMID: 37175745 PMCID: PMC10179190 DOI: 10.3390/ijms24098034] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Patients who have recovered from coronavirus disease 2019 (COVID-19) infection may experience chronic fatigue when exercising, despite no obvious heart or lung abnormalities. The present lack of effective treatments makes managing long COVID a major challenge. One of the underlying mechanisms of long COVID may be mitochondrial dysfunction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections can alter the mitochondria responsible for energy production in cells. This alteration leads to mitochondrial dysfunction which, in turn, increases oxidative stress. Ultimately, this results in a loss of mitochondrial integrity and cell death. Moreover, viral proteins can bind to mitochondrial complexes, disrupting mitochondrial function and causing the immune cells to over-react. This over-reaction leads to inflammation and potentially long COVID symptoms. It is important to note that the roles of mitochondrial damage and inflammatory responses caused by SARS-CoV-2 in the development of long COVID are still being elucidated. Targeting mitochondrial function may provide promising new clinical approaches for long-COVID patients; however, further studies are needed to evaluate the safety and efficacy of such approaches.
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Affiliation(s)
- Tsung-Hsien Chen
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan;
| | - Chia-Jung Chang
- Division of Critical Care Medicine, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan
| | - Peir-Haur Hung
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan;
- Department of Life and Health Science, Chia-Nan University of Pharmacy and Science, Tainan 717301, Taiwan
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