451
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Pablos I, Machado Y, de Jesus HCR, Mohamud Y, Kappelhoff R, Lindskog C, Vlok M, Bell PA, Butler GS, Grin PM, Cao QT, Nguyen JP, Solis N, Abbina S, Rut W, Vederas JC, Szekely L, Szakos A, Drag M, Kizhakkedathu JN, Mossman K, Hirota JA, Jan E, Luo H, Banerjee A, Overall CM. Mechanistic insights into COVID-19 by global analysis of the SARS-CoV-2 3CL pro substrate degradome. Cell Rep 2021; 37:109892. [PMID: 34672947 PMCID: PMC8501228 DOI: 10.1016/j.celrep.2021.109892] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/10/2021] [Accepted: 10/05/2021] [Indexed: 12/27/2022] Open
Abstract
The main viral protease (3CLpro) is indispensable for SARS-CoV-2 replication. We delineate the human protein substrate landscape of 3CLpro by TAILS substrate-targeted N-terminomics. We identify more than 100 substrates in human lung and kidney cells supported by analyses of SARS-CoV-2-infected cells. Enzyme kinetics and molecular docking simulations of 3CLpro engaging substrates reveal how noncanonical cleavage sites, which diverge from SARS-CoV, guide substrate specificity. Cleaving the interactors of essential effector proteins, effectively stranding them from their binding partners, amplifies the consequences of proteolysis. We show that 3CLpro targets the Hippo pathway, including inactivation of MAP4K5, and key effectors of transcription, mRNA processing, and translation. We demonstrate that Spike glycoprotein directly binds galectin-8, with galectin-8 cleavage disengaging CALCOCO2/NDP52 to decouple antiviral-autophagy. Indeed, in post-mortem COVID-19 lung samples, NDP52 rarely colocalizes with galectin-8, unlike in healthy lungs. The 3CLpro substrate degradome establishes a foundational substrate atlas to accelerate exploration of SARS-CoV-2 pathology and drug design.
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Affiliation(s)
- Isabel Pablos
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yoan Machado
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Hugo C Ramos de Jesus
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yasir Mohamud
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Cecilia Lindskog
- Department of Immunology Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Marli Vlok
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Peter A Bell
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Georgina S Butler
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Peter M Grin
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Quynh T Cao
- Firestone Institute for Respiratory Health - Faculty of Health Sciences, McMaster University, Hamilton, ON L8N 4A6, Canada
| | - Jenny P Nguyen
- Firestone Institute for Respiratory Health - Faculty of Health Sciences, McMaster University, Hamilton, ON L8N 4A6, Canada
| | - Nestor Solis
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Srinivas Abbina
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; The School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Laszlo Szekely
- Department of Pathology and Cytology, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Attila Szakos
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Laboratories, 141 86 Stockholm, Sweden
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; The School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jeremy A Hirota
- Firestone Institute for Respiratory Health - Faculty of Health Sciences, McMaster University, Hamilton, ON L8N 4A6, Canada; Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Honglin Luo
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada; Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
| | - Arinjay Banerjee
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Christopher M Overall
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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452
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Asif M, Saleem M, Yaseen HS, Yehya AH, Saadullah M, Zubair HM, Oon CE, Khaniabadi PM, Khalid SH, Khan IU, Mahrukh. Potential role of marine species-derived bioactive agents in the management of SARS-CoV-2 infection. Future Microbiol 2021; 16:1289-1301. [PMID: 34689597 PMCID: PMC8592065 DOI: 10.2217/fmb-2021-0024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
COVID-19, caused by the SARS-CoV-2 outbreak, has resulted in a massive global health crisis. Bioactive molecules extracted or synthesized using starting material obtained from marine species, including griffithsin, plitidepsin and fingolimod are in clinical trials to evaluate their anti-SARS-CoV-2 and anti-HIV efficacies. The current review highlights the anti-SARS-CoV-2 potential of marine-derived phytochemicals explored using in silico, in vitro and in vivo models. The current literature suggests that these molecules have the potential to bind with various key drug targets of SARS-CoV-2. In addition, many of these agents have anti-inflammatory and immunomodulatory potentials and thus could play a role in the attenuation of COVID-19 complications. Overall, these agents may play a role in the management of COVID-19, but further preclinical and clinical studies are still required to establish their role in the mitigation of the current viral pandemic.
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Affiliation(s)
- Muhammad Asif
- Department of Pharmacology, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, 63100, Punjab, Pakistan
| | - Mohammad Saleem
- Punjab University College of Pharmacy, University of the Punjab, Lahore, 54000, Punjab, Pakistan
| | - Hafiza Sidra Yaseen
- Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Ashwaq Hs Yehya
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, 11800, Malaysia
| | - Malik Saadullah
- Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Hafiz Muhammad Zubair
- Department of Pharmacology, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, 63100, Punjab, Pakistan
| | - Chern E Oon
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, 11800, Malaysia
| | - Pegah Moradi Khaniabadi
- Department of Radiology & Molecular Imaging, College of Medicine & Health Sciences, Sultan Qaboos University, PO. Box 35, 123, Al Khod, Muscat, Oman
| | - Syed Haroon Khalid
- Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Ikram Ullah Khan
- Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Mahrukh
- Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, 38000, Punjab, Pakistan
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453
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6-Thioguanine blocks SARS-CoV-2 replication by inhibition of PLpro. iScience 2021; 24:103213. [PMID: 34632326 PMCID: PMC8487320 DOI: 10.1016/j.isci.2021.103213] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/15/2021] [Accepted: 09/29/2021] [Indexed: 02/08/2023] Open
Abstract
The emergence of SARS-CoV-2 has led to a global health crisis that, in addition to vaccines and immunomodulatory therapies, calls for the identification of antiviral therapeutics. The papain-like protease (PLpro) activity of nsp3 is an attractive drug target as it is essential for viral polyprotein cleavage and for deconjugation of ISG15, an antiviral ubiquitin-like protein. We show here that 6-Thioguanine (6-TG), an orally available and widely available generic drug, inhibits SARS-CoV-2 replication in Vero-E6 cells with an EC50 of approximately 2 μM. 6-TG also inhibited PLpro-catalyzed polyprotein cleavage and de-ISGylation in cells and inhibited proteolytic activity of the purified PLpro domain in vitro. We therefore propose that 6-TG is a direct-acting antiviral that could potentially be repurposed and incorporated into the set of treatment and prevention options for COVID-19.
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454
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Affiliation(s)
- Xuetao Cao
- College of Life Sciences, Nankai University, Tianjin, China. .,Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China.
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455
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Saied EM, El-Maradny YA, Osman AA, Darwish AMG, Abo Nahas HH, Niedbała G, Piekutowska M, Abdel-Rahman MA, Balbool BA, Abdel-Azeem AM. A Comprehensive Review about the Molecular Structure of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Insights into Natural Products against COVID-19. Pharmaceutics 2021; 13:1759. [PMID: 34834174 PMCID: PMC8624722 DOI: 10.3390/pharmaceutics13111759] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
In 2019, the world suffered from the emergence of COVID-19 infection, one of the most difficult pandemics in recent history. Millions of confirmed deaths from this pandemic have been reported worldwide. This disaster was caused by SARS-CoV-2, which is the last discovered member of the family of Coronaviridae. Various studies have shown that natural compounds have effective antiviral properties against coronaviruses by inhibiting multiple viral targets, including spike proteins and viral enzymes. This review presents the classification and a detailed explanation of the SARS-CoV-2 molecular characteristics and structure-function relationships. We present all currently available crystal structures of different SARS-CoV-2 proteins and emphasized on the crystal structure of different virus proteins and the binding modes of their ligands. This review also discusses the various therapeutic approaches for COVID-19 treatment and available vaccinations. In addition, we highlight and compare the existing data about natural compounds extracted from algae, fungi, plants, and scorpion venom that were used as antiviral agents against SARS-CoV-2 infection. Moreover, we discuss the repurposing of select approved therapeutic agents that have been used in the treatment of other viruses.
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Affiliation(s)
- Essa M. Saied
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
- Institute for Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Yousra A. El-Maradny
- Microbiology Department, High Institute of Public Health, Alexandria University, Alexandria 21526, Egypt;
| | - Alaa A. Osman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, New Giza University, Newgiza, km 22 Cairo-Alexandria Desert Road, Cairo 12256, Egypt;
| | - Amira M. G. Darwish
- Food Technology Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA City), Alexandria 21934, Egypt;
| | - Hebatallah H. Abo Nahas
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt; (H.H.A.N.); (M.A.A.-R.)
| | - Gniewko Niedbała
- Department of Biosystems Engineering, Faculty of Environmental and Mechanical Engineering, Poznań University of Life Sciences, Wojska Polskiego 50, 60-627 Poznań, Poland;
| | - Magdalena Piekutowska
- Department of Geoecology and Geoinformation, Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, Partyzantów 27, 76-200 Słupsk, Poland;
| | - Mohamed A. Abdel-Rahman
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt; (H.H.A.N.); (M.A.A.-R.)
| | - Bassem A. Balbool
- Faculty of Biotechnology, October University for Modern Sciences and Arts, Giza 12585, Egypt;
| | - Ahmed M. Abdel-Azeem
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
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456
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Francés-Monerris A, García-Iriepa C, Iriepa I, Hognon C, Miclot T, Barone G, Monari A, Marazzi M. Microscopic interactions between ivermectin and key human and viral proteins involved in SARS-CoV-2 infection. Phys Chem Chem Phys 2021; 23:22957-22971. [PMID: 34636373 DOI: 10.1039/d1cp02967c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The identification of chemical compounds able to bind specific sites of the human/viral proteins involved in the SARS-CoV-2 infection cycle is a prerequisite to design effective antiviral drugs. Here we conduct a molecular dynamics study with the aim to assess the interactions of ivermectin, an antiparasitic drug with broad-spectrum antiviral activity, with the human Angiotensin-Converting Enzyme 2 (ACE2), the viral 3CLpro and PLpro proteases, and the viral SARS Unique Domain (SUD). The drug/target interactions have been characterized in silico by describing the nature of the non-covalent interactions found and by measuring the extent of their time duration along the MD simulation. Results reveal that the ACE2 protein and the ACE2/RBD aggregates form the most persistent interactions with ivermectin, while the binding with the remaining viral proteins is more limited and unspecific.
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Affiliation(s)
- Antonio Francés-Monerris
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France. .,Departament de Química Física, Universitat de València, 46100 Burjassot, Spain.
| | - Cristina García-Iriepa
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares (Madrid), Spain. .,Instituto de Investigación Química "Andrés M. del Río" (IQAR), Universidad de Alcalá, 28871 Alcalá de Henares (Madrid), Spain
| | - Isabel Iriepa
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares (Madrid), Spain. .,Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares (Madrid), Spain
| | - Cécilia Hognon
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France.
| | - Tom Miclot
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France. .,Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceuticche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceuticche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France. .,Université de Paris and CNRS, ITODYS, F-75006, Paris, France
| | - Marco Marazzi
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares (Madrid), Spain. .,Instituto de Investigación Química "Andrés M. del Río" (IQAR), Universidad de Alcalá, 28871 Alcalá de Henares (Madrid), Spain
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457
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Luige O, Bose PP, Stulz R, Steunenberg P, Brun O, Andersson S, Murtola M, Strömberg R. Zn 2+-Dependent peptide nucleic acid-based artificial ribonucleases with unprecedented efficiency and specificity. Chem Commun (Camb) 2021; 57:10911-10914. [PMID: 34590632 DOI: 10.1039/d1cc04383h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present Zn2+-dependent dimethyl-dipyridophenazine PNA conjugates as efficient RNA cleaving artificial enzymes. These PNAzymes display site-specific RNA cleavage with 10 minute half-lives and cleave clinically relevant RNA models.
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Affiliation(s)
- Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Partha Pratim Bose
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Rouven Stulz
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden. .,Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,DMPK, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Peter Steunenberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Omar Brun
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden.
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458
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Burgoyne RA, Fisher AJ, Borthwick LA. The Role of Epithelial Damage in the Pulmonary Immune Response. Cells 2021; 10:cells10102763. [PMID: 34685744 PMCID: PMC8534416 DOI: 10.3390/cells10102763] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 12/14/2022] Open
Abstract
Pulmonary epithelial cells are widely considered to be the first line of defence in the lung and are responsible for coordinating the innate immune response to injury and subsequent repair. Consequently, epithelial cells communicate with multiple cell types including immune cells and fibroblasts to promote acute inflammation and normal wound healing in response to damage. However, aberrant epithelial cell death and damage are hallmarks of pulmonary disease, with necrotic cell death and cellular senescence contributing to disease pathogenesis in numerous respiratory diseases such as idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD) and coronavirus disease (COVID)-19. In this review, we summarise the literature that demonstrates that epithelial damage plays a pivotal role in the dysregulation of the immune response leading to tissue destruction and abnormal remodelling in several chronic diseases. Specifically, we highlight the role of epithelial-derived damage-associated molecular patterns (DAMPs) and senescence in shaping the immune response and assess their contribution to inflammatory and fibrotic signalling pathways in the lung.
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Affiliation(s)
- Rachel Ann Burgoyne
- Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
| | - Andrew John Fisher
- Regenerative Medicine, Stem Cells and Transplantation Theme, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
- Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Lee Anthony Borthwick
- Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
- Fibrofind, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Correspondence: ; Tel.: +44-191-208-3112
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459
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An Update on Innate Immune Responses during SARS-CoV-2 Infection. Viruses 2021; 13:v13102060. [PMID: 34696490 PMCID: PMC8541410 DOI: 10.3390/v13102060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a member of the Coronaviridae family, which is responsible for the COVID-19 pandemic followed by unprecedented global societal and economic disruptive impact. The innate immune system is the body’s first line of defense against invading pathogens and is induced by a variety of cellular receptors that sense viral components. However, various strategies are exploited by SARS-CoV-2 to disrupt the antiviral innate immune responses. Innate immune dysfunction is characterized by the weak generation of type I interferons (IFNs) and the hypersecretion of pro-inflammatory cytokines, leading to mortality and organ injury in patients with COVID-19. This review summarizes the existing understanding of the mutual effects between SARS-CoV-2 and the type I IFN (IFN-α/β) responses, emphasizing the relationship between host innate immune signaling and viral proteases with an insight on tackling potential therapeutic targets.
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460
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Abdurrahman L, Fang X, Zhang Y. Molecular Insights of SARS-CoV-2 Infection and Molecular Treatments. Curr Mol Med 2021; 22:621-639. [PMID: 34645374 DOI: 10.2174/1566524021666211013121831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/15/2021] [Accepted: 07/23/2021] [Indexed: 01/18/2023]
Abstract
The coronavirus disease emerged in December 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome-related coronavirus 2 (SARS-CoV-2) and its rapid global spread has brought an international health emergency and urgent responses for seeking efficient prevention and therapeutic treatment. This has led to imperative needs for illustration of the molecular pathogenesis of SARS-CoV-2, identification of molecular targets or receptors, and development of antiviral drugs, antibodies, and vaccines. In this study, we investigated the current research progress in combating SARS-CoV-2 infection. Based on the published research findings, we first elucidated, at the molecular level, SARS-CoV-2 viral structures, potential viral host-cell-invasion and pathogenic mechanisms, main virus-induced immune responses, and emerging SARS-CoV-2 variants. We then focused on the main virus- and host-based potential targets, summarized and categorized effective inhibitory molecules based on drug development strategies for COVID-19, that can guide efforts for the identification of new drugs and treatment for this problematic disease. Current research and development of antibodies and vaccines were also introduced and discussed. We concluded that the main virus entry route- SARS-CoV-2 spike protein interaction with ACE2 receptors has played a key role in guiding the development of therapeutic treatments against COVID-19, four main therapeutic strategies may be considered in developing molecular therapeutics, and drug repurposing is likely to be an easy, fast and low-cost approach in such a short period of time with urgent need of antiviral drugs. Additionally, the quick development of antibody and vaccine candidates has yielded promising results, but the wide-scale deployment of safe and effective COVID-19 vaccines remains paramount in solving the pandemic crisis. As new variants of the virus begun to emerge, the efficacy of these vaccines and treatments must be closely evaluated. Finally, we discussed the possible challenges of developing molecular therapeutics for COVID-19 and suggested some potential future efforts. Despite the limited availability of literatures, our attempt in this work to provide a relatively comprehensive overview of current SARS-CoV-2 studies can be helpful for quickly acquiring the key information of COVID-19 and further promoting this important research to control and diminish the pandemic.
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Affiliation(s)
- Lama Abdurrahman
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539. United States
| | - Xiaoqian Fang
- Department of Molecular Science, School of Medicine, The University of Texas Rio Grande Valley, Edinburg, Texas 78539. United States
| | - Yonghong Zhang
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539. United States
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461
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Abstract
Coronaviral papain-like proteases (PLpros) are essential enzymes that mediate not only the proteolytic processes of viral polyproteins during virus replication, but also the deubiquitination and deISGylation of cellular proteins that attenuate host innate immune responses. Therefore, PLpros are attractive targets for antiviral drug development. Here we report the crystal structure of the papain-like protease 2 (PLP2) of porcine epidemic diarrhea virus (PEDV) in complex with ubiquitin (Ub). The X-ray structural analyses reveal that PEDV PLP2 interacts with Ub substrate mainly through the Ub core region and C-terminal tail. Mutations of Ub-interacting residues resulted in moderately or completely abolished deubiquitinylating function of PEDV PLP2. In addition, our analyses also indicate that the two residues-extended blocking loop 2 at the S4 subsite contributes to the substrate selectivity and binding affinity of PEDV PLP2. Furthermore, the PEDV PLP2 Glu99 residue, conserved in alpha-CoV PLpros, was found to govern the preference of a positively charged P4 residue of peptidyl substrates. Collectively, our data provided structure-based information for substrate binding and selectivity of PEDV PLP2. These findings may help us gain insights into the deubiquitinating and proteolytic functions of PEDV PLP2 from a structural perspective. Importance Current challenges in CoVs include a comprehensive understanding of mechanistic effects of associated enzymes, including the 3C-like and papain-like proteases. We have previously reported that the PEDV PLP2 exhibits a broader substrate preference, superior DUB function, and inferior peptidase activity. However, the structure basis for these functions remains largely unclear. Here, we show the high-resolution X-ray crystal structure of PEDV PLP2 in complex with Ub. Integrated structural and biochemical analyses revealed: (i) three Ub-core interacting residues are essential for DUB function, (ii) two-residue-elongated blocking loop 2 regulates substrate selectivity, and (iii) a conserved glutamate residue governs the substrate specificity of PEDV PLP2. Collectively, our findings provide not only the structural insights to the catalytic mechanism of PEDV PLP2 but also a model for developing antiviral strategies.
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462
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Alturaiki W, Mubarak A, Al Jurayyan A, Hemida MG. The pivotal roles of the host immune response in the fine-tuning the infection and the development of the vaccines for SARS-CoV-2. Hum Vaccin Immunother 2021; 17:3297-3309. [PMID: 34114940 PMCID: PMC8204314 DOI: 10.1080/21645515.2021.1935172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV2 infection induces various degrees of infections ranging from asymptomatic to severe cases and death. Virus/host interplay contributes substantially to these outcomes. This highlights the potential roles of the host immune system in fighting virus infections. SARS-CoV-2. We highlighted the potential roles of host immune response in the modulation of the outcomes of SARS-CoV infections. The newly emerged SARS-CoV-2 mutants complicated the control and mitigation strategies measures. We are highlighting the current progress of some already deployed vaccines worldwide as well as those still in the pipelines. Recent studies from the large ongoing global vaccination campaign are showing promising results in reducing the hospitality rates as well as the number of severe SARS-CoV-2 infected patients. Careful monitoring of the genetic changes of the virus should be practiced. This is to prepare some highly sensitive diagnostic assays as well as to prepare some homologous vaccines matching the circulating strains in the future.
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Affiliation(s)
- Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, Saudi Arabia
| | - Ayman Mubarak
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abduallah Al Jurayyan
- Immunology and HLA Department, Pathology and Laboratory Medicine, King Fahad Medical City, Riyadh, Al-Ahsa, Saudi Arabia
| | - Maged Gomaa Hemida
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr Ash Shaykh, Egypt
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463
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Precursors of Viral Proteases as Distinct Drug Targets. Viruses 2021; 13:v13101981. [PMID: 34696411 PMCID: PMC8537868 DOI: 10.3390/v13101981] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022] Open
Abstract
Viral proteases are indispensable for successful virion maturation, thus making them a prominent drug target. Their enzyme activity is tightly spatiotemporally regulated by expression in the precursor form with little or no activity, followed by activation via autoprocessing. These cleavage events are frequently triggered upon transportation to a specific compartment inside the host cell. Typically, precursor oligomerization or the presence of a co-factor is needed for activation. A detailed understanding of these mechanisms will allow ligands with non-canonical mechanisms of action to be designed, which would specifically modulate the initial irreversible steps of viral protease autoactivation. Binding sites exclusive to the precursor, including binding sites beyond the protease domain, can be exploited. Both inhibition and up-regulation of the proteolytic activity of viral proteases can be detrimental for the virus. All these possibilities are discussed using examples of medically relevant viruses including herpesviruses, adenoviruses, retroviruses, picornaviruses, caliciviruses, togaviruses, flaviviruses, and coronaviruses.
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464
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Abdalla AE, Xie J, Junaid K, Younas S, Elsaman T, Abosalif KOA, Alameen AAM, Mahjoob MO, Elamir MYM, Ejaz H. Insight into the emerging role of SARS-CoV-2 nonstructural and accessory proteins in modulation of multiple mechanisms of host innate defense. Bosn J Basic Med Sci 2021; 21:515-527. [PMID: 33714258 PMCID: PMC8381213 DOI: 10.17305/bjbms.2020.5543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/04/2021] [Indexed: 11/23/2022] Open
Abstract
Coronavirus disease-19 (COVID-19) is an extremely infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has become a major global health concern. The induction of a coordinated immune response is crucial to the elimination of any pathogenic infection. However, SARS-CoV-2 can modulate the host immune system to favor viral adaptation and persistence within the host. The virus can counteract type I interferon (IFN-I) production, attenuating IFN-I signaling pathway activation and disrupting antigen presentation. Simultaneously, SARS-CoV-2 infection can enhance apoptosis and the production of inflammatory mediators, which ultimately results in increased disease severity. SARS-CoV-2 produces an array of effector molecules, including nonstructural proteins (NSPs) and open-reading frames (ORFs) accessory proteins. We describe the complex molecular interplay of SARS-CoV-2 NSPs and accessory proteins with the host's signaling mediating immune evasion in the current review. In addition, the crucial role played by immunomodulation therapy to address immune evasion is discussed. Thus, the current review can provide new directions for the development of vaccines and specific therapies.
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Affiliation(s)
- Abualgasim Elgaili Abdalla
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Al Jouf, Saudi Arabia
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Omdurman, Sudan
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing, China
| | - Kashaf Junaid
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Al Jouf, Saudi Arabia
| | - Sonia Younas
- Department of Pathology, Tehsil Headquarter Hospital Kamoke, District Gujranwala, Kamoke, Pakistan
| | - Tilal Elsaman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Al Jouf, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Omdurman, Sudan
| | - Khalid Omer Abdalla Abosalif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Al Jouf, Saudi Arabia
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Omdurman, Sudan
| | - Ayman Ali Mohammed Alameen
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Al Jouf, Saudi Arabia
- Department of Chemical Pathology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Mahjoob Osman Mahjoob
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Omdurman, Sudan
| | - Mohammed Yagoub Mohammed Elamir
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Al Jouf, Saudi Arabia
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Omdurman, Sudan
| | - Hasan Ejaz
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Al Jouf, Saudi Arabia
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465
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Ameen F, Mamidala E, Davella R, Vallala S. Rilpivirine inhibits SARS-CoV-2 protein targets: A potential multi-target drug. J Infect Public Health 2021; 14:1454-1460. [PMID: 34326009 PMCID: PMC8294774 DOI: 10.1016/j.jiph.2021.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND COVID-19 disease caused by SARS-CoV-2 is lacking efficient medication although certain medications are used to relief its symptoms. OBJECTIVES We tested an FDA-approved antiviral medication namely rilpivirine to find a drug against SARS-CoV-2. METHODS The inhibition of rilpivirine against multiple SARS-CoV-2 therapeutic targets was studied using in silico method. The binding attraction of the protein-ligand complexes were calculated using molecular docking analysis. RESULTS Docking rilpivirine with main protease (Mpro), papin like protease (PLpro), sprike protein (Spro), human angiotensin converting enzyme-2 (ACE2), and RNA dependent-RNA polymerase (RdRp) yielded binding energies of -8.07, -8.40, -7.55, -9.11, and -8.69 kcal/mol, respectively. The electrostatic interaction is the key force in stabilizing the RdRp-rilpivirine complex, while van der Waals interaction dominates in the ACE2 rilpivirine case. Our findings suggest that rilpivirine can inhibit SARS-CoV-2 replication by targeting not only ACE2, but also RdRp and other targets, and therefore, it can be used to invoke altered mechanisms at the pre-entry and post-entry phases. CONCLUSION As a result of our in silico molecular docking study, we suggest that rilpivirine is a compound that could act as a powerful inhibitor against SARS-CoV-2 targets. Although in vitro and in vivo experiments are needed to verify this prediction we believe that this antiviral drug may be used in preclinical trials to fight against SARS coronavirus.
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Affiliation(s)
- Fuad Ameen
- Department of Botany & Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Estari Mamidala
- Infectious Diseases Research Lab, Department of Zoology, Kakatiya University, Warangal 506 009 TS, India
| | - Rakesh Davella
- Infectious Diseases Research Lab, Department of Zoology, Kakatiya University, Warangal 506 009 TS, India
| | - Shravan Vallala
- Texas Tech University Health Sciences Center, El Paso, TX, USA
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466
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Thery F, Martina L, Asselman C, Zhang Y, Vessely M, Repo H, Sedeyn K, Moschonas GD, Bredow C, Teo QW, Zhang J, Leandro K, Eggermont D, De Sutter D, Boucher K, Hochepied T, Festjens N, Callewaert N, Saelens X, Dermaut B, Knobeloch KP, Beling A, Sanyal S, Radoshevich L, Eyckerman S, Impens F. Ring finger protein 213 assembles into a sensor for ISGylated proteins with antimicrobial activity. Nat Commun 2021; 12:5772. [PMID: 34599178 PMCID: PMC8486878 DOI: 10.1038/s41467-021-26061-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/14/2021] [Indexed: 12/20/2022] Open
Abstract
ISG15 is an interferon-stimulated, ubiquitin-like protein that can conjugate to substrate proteins (ISGylation) to counteract microbial infection, but the underlying mechanisms remain elusive. Here, we use a virus-like particle trapping technology to identify ISG15-binding proteins and discover Ring Finger Protein 213 (RNF213) as an ISG15 interactor and cellular sensor of ISGylated proteins. RNF213 is a poorly characterized, interferon-induced megaprotein that is frequently mutated in Moyamoya disease, a rare cerebrovascular disorder. We report that interferon induces ISGylation and oligomerization of RNF213 on lipid droplets, where it acts as a sensor for ISGylated proteins. We show that RNF213 has broad antimicrobial activity in vitro and in vivo, counteracting infection with Listeria monocytogenes, herpes simplex virus 1, human respiratory syncytial virus and coxsackievirus B3, and we observe a striking co-localization of RNF213 with intracellular bacteria. Together, our findings provide molecular insights into the ISGylation pathway and reveal RNF213 as a key antimicrobial effector.
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Affiliation(s)
- Fabien Thery
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lia Martina
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Caroline Asselman
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Yifeng Zhang
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Madeleine Vessely
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Heidi Repo
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - George D Moschonas
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Clara Bredow
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Biochemistry, Berlin, Germany
| | - Qi Wen Teo
- HKU-Pasteur Research Pole, School of Public Health, University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Jingshu Zhang
- HKU-Pasteur Research Pole, School of Public Health, University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Kevin Leandro
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Denzel Eggermont
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Delphine De Sutter
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Katie Boucher
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, VIB, Ghent, Belgium
| | - Tino Hochepied
- VIB Center for Inflammation Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Nele Festjens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Nico Callewaert
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Bart Dermaut
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Antje Beling
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Biochemistry, Berlin, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK), partner side Berlin, Berlin, Germany
| | - Sumana Sanyal
- HKU-Pasteur Research Pole, School of Public Health, University of Hong Kong, Pok Fu Lam, Hong Kong
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Lilliana Radoshevich
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, USA.
| | - Sven Eyckerman
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- VIB Proteomics Core, VIB, Ghent, Belgium.
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467
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Jafarzadeh A, Jafarzadeh S, Nemati M. Therapeutic potential of ginger against COVID-19: Is there enough evidence? JOURNAL OF TRADITIONAL CHINESE MEDICAL SCIENCES 2021. [PMCID: PMC8492833 DOI: 10.1016/j.jtcms.2021.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In addition to the respiratory system, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strikes other systems, including the digestive, circulatory, urogenital, and even the central nervous system, as its receptor angiotensin-converting enzyme 2 (ACE2) is expressed in various organs, such as lungs, intestine, heart, esophagus, kidneys, bladder, testis, liver, and brain. Different mechanisms, in particular, massive virus replication, extensive apoptosis and necrosis of the lung-related epithelial and endothelial cells, vascular leakage, hyper-inflammatory responses, overproduction of pro-inflammatory mediators, cytokine storm, oxidative stress, downregulation of ACE2, and impairment of the renin-angiotensin system contribute to the COVID-19 pathogenesis. Currently, COVID-19 is a global pandemic with no specific anti-viral treatment. The favorable capabilities of the ginger were indicated in patients suffering from osteoarthritis, neurodegenerative disorders, rheumatoid arthritis, type 2 diabetes, respiratory distress, liver diseases and primary dysmenorrheal. Ginger or its compounds exhibited strong anti-inflammatory and anti-oxidative influences in numerous animal models. This review provides evidence regarding the potential effects of ginger against SARS-CoV-2 infection and highlights its antiviral, anti-inflammatory, antioxidative, and immunomodulatory impacts in an attempt to consider this plant as an alternative therapeutic agent for COVID-19 treatment.
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468
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Patel R, Prajapati J, Rao P, Rawal RM, Saraf M, Goswami D. Repurposing the antibacterial drugs for inhibition of SARS-CoV2-PLpro using molecular docking, MD simulation and binding energy calculation. Mol Divers 2021; 26:2189-2209. [PMID: 34591234 PMCID: PMC8481324 DOI: 10.1007/s11030-021-10325-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/21/2021] [Indexed: 12/23/2022]
Abstract
Papain-like protease (nsp-3; non-structural protein) of novel corona virus is an ideal target for developing drugs as it plays multiple important functions for viral growth and replication. For instance, role of nsp-3 has been recognized in cleavage of viral polyprotein; furthermore, in infected host it weakens the immune system via downregulating the production of type I interferon. This downregulation is promoted by removal of ubiquitin-like interferon-stimulated gene 15 protein (ISG15) from interferon-responsive factor 3 (IRF3) protein. Among known inhibitors of SARS-CoV-PLpro GRL0617 is by far the most effective inhibitor. As PLpro of SARS-CoV2 is having more than 80% similarity with SARS-CoV-PLpro, GRL0617 is reported to be effective even against SARS-CoV2. Owing to this similarity, certain key amino acids remain the same/conserved in both proteins. Among conserved amino acids Tyr268 for SARS-CoV2 and Tyr269 for SARS-CoV produce important hydrophobic interactions with aromatic rings of GRL0617. Here, in this study antibacterial compounds were collected from ZINC database, and they were filtered to select compounds that are having similar structural features as GRL0617. This filtered library of compound was then docked with SARS-CoV and CoV2-PLpro. Five hits were noted that were able to interact with Tyr268 (SARS-CoV2) and Tyr269 (SARS-CoV). Further, best hit 2-(2-((benzofuran-2-carboxamido)methyl)-5-methoxy-1H-indol-1-yl)acetic acid (ZINC44459905) was studied using molecular dynamic simulation where stability of protein–ligand complex as well as stability of produced interactions was noted.
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Affiliation(s)
- Rohit Patel
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Jignesh Prajapati
- Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Priyashi Rao
- Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Rakesh M Rawal
- Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Meenu Saraf
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Dweipayan Goswami
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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469
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Thermodynamics and Kinetic Investigation of Reaction of Acriflavine with L-cysteine in Aqueous Medium. CHEMISTRY AFRICA 2021. [PMCID: PMC8478639 DOI: 10.1007/s42250-021-00280-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The kinetic investigation of reaction of 3,6-diamino-10-methylacridin-10-ium chloride (acriflavine) with l-cysteine in aqueous acidic medium at maximum absorption = 460 nm, ionic strength (I) = 0.1 mol dm−3 and temperature (T) = 307 K has been carried out spectrophotometrically. Using a pseudo first order approach, the rate of the redox reaction resulted to first order with respect to the [acriflavine, (AF)] and [l-cysteine, (CSH)] and second order total. Stoichiometric determination confirms that a mole of the acriflavine is consumed by a mole of l-cysteine at a time for the attainment of product formation. The reaction followed a one-way acid independence path. The adjustment in ionic strength (NaCl) and solvent polarity (water/acetone mixture) of the reaction system showed no reasonable effect and there was a fairly decrease in the reaction rate, respectively. The reaction rate is also characterised by neither catalysis nor inhibition of added ions. The negative magnitude of entropy of activation, \documentclass[12pt]{minimal}
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\begin{document}$$\Delta$$\end{document}ΔS‡, (− 151.39 ± 031 J mol−1 K−1) and positive value of enthalpy of activation, \documentclass[12pt]{minimal}
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\begin{document}$$\Delta$$\end{document}ΔH‡, (+ 31.378 ± 030 kJ mol−1) suggest that the reaction proceeds via an associative pathway and reasonable energy are needed to lower the activation energy for a tangible products formation. Two acridine unit products polymerised afterward forming a dimer as a result of an intramolecular coupling. A determinable intermediate has been observed through a spectroscopic test and confirmed by Michaelis–Menten’s plot. Based on Taube’s inorganic electron transfer reaction, an inner-sphere mechanistic pathway is implicated with a stable intermediate complex formation as shown below;
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470
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Patchett S, Lv Z, Rut W, Békés M, Drag M, Olsen SK, Huang TT. A molecular sensor determines the ubiquitin substrate specificity of SARS-CoV-2 papain-like protease. Cell Rep 2021; 36:109754. [PMID: 34547223 PMCID: PMC8423903 DOI: 10.1016/j.celrep.2021.109754] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/15/2021] [Accepted: 09/02/2021] [Indexed: 11/18/2022] Open
Abstract
The SARS-CoV-2 papain-like protease (PLpro) is a target for antiviral drug development. It is essential for processing viral polyproteins for replication and functions in host immune evasion by cleaving ubiquitin (Ub) and ubiquitin-like protein (Ubl) conjugates. While highly conserved, SARS-CoV-2 and SARS-CoV PLpro have contrasting Ub/Ubl substrate preferences. Using a combination of structural analyses and functional assays, we identify a molecular sensor within the S1 Ub-binding site of PLpro that serves as a key determinant of substrate specificity. Variations within the S1 sensor specifically alter cleavage of Ub substrates but not of the Ubl interferon-stimulated gene 15 protein (ISG15). Significantly, a variant of concern associated with immune evasion carries a mutation in the S1 sensor that enhances PLpro activity on Ub substrates. Collectively, our data identify the S1 sensor region as a potential hotspot of variability that could alter host antiviral immune responses to newly emerging SARS-CoV-2 lineages.
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Affiliation(s)
- Stephanie Patchett
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Zongyang Lv
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Miklos Békés
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Shaun K Olsen
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
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471
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Huff S, Kummetha IR, Tiwari SK, Huante MB, Clark AE, Wang S, Bray W, Smith D, Carlin AF, Endsley M, Rana TM. Discovery and Mechanism of SARS-CoV-2 Main Protease Inhibitors. J Med Chem 2021; 65:2866-2879. [PMID: 34570513 PMCID: PMC8491550 DOI: 10.1021/acs.jmedchem.1c00566] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The emergence of a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents an urgent public health crisis. Without available targeted therapies, treatment options remain limited for COVID-19 patients. Using medicinal chemistry and rational drug design strategies, we identify a 2-phenyl-1,2-benzoselenazol-3-one class of compounds targeting the SARS-CoV-2 main protease (Mpro). FRET-based screening against recombinant SARS-CoV-2 Mpro identified six compounds that inhibit proteolysis with nanomolar IC50 values. Preincubation dilution experiments and molecular docking determined that the inhibition of SARS-CoV-2 Mpro can occur by either covalent or noncovalent mechanisms, and lead E04 was determined to inhibit Mpro competitively. Lead E24 inhibited viral replication with a nanomolar EC50 value (844 nM) in SARS-CoV-2-infected Vero E6 cells and was further confirmed to impair SARS-CoV-2 replication in human lung epithelial cells and human-induced pluripotent stem cell-derived 3D lung organoids. Altogether, these studies provide a structural framework and mechanism of Mpro inhibition that should facilitate the design of future COVID-19 treatments.
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Affiliation(s)
- Sarah Huff
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Indrasena Reddy Kummetha
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Shashi Kant Tiwari
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Matthew B Huante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Alex E Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Shaobo Wang
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - William Bray
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Davey Smith
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Mark Endsley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Tariq M Rana
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States.,Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
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472
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Fukuzawa K, Kato K, Watanabe C, Kawashima Y, Handa Y, Yamamoto A, Watanabe K, Ohyama T, Kamisaka K, Takaya D, Honma T. Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins. J Chem Inf Model 2021; 61:4594-4612. [PMID: 34506132 PMCID: PMC8457332 DOI: 10.1021/acs.jcim.1c00694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Indexed: 01/18/2023]
Abstract
SARS-CoV-2 is the causative agent of coronavirus (known as COVID-19), the virus causing the current pandemic. There are ongoing research studies to develop effective therapeutics and vaccines against COVID-19 using various methods and many results have been published. The structure-based drug design of SARS-CoV-2-related proteins is promising, however, reliable information regarding the structural and intra- and intermolecular interactions is required. We have conducted studies based on the fragment molecular orbital (FMO) method for calculating the electronic structures of protein complexes and analyzing their quantitative molecular interactions. This enables us to extensively analyze the molecular interactions in residues or functional group units acting inside the protein complexes. Such precise interaction data are available in the FMO database (FMODB) (https://drugdesign.riken.jp/FMODB/). Since April 2020, we have performed several FMO calculations on the structures of SARS-CoV-2-related proteins registered in the Protein Data Bank. We have published the results of 681 structures, including three structural proteins and 11 nonstructural proteins, on the COVID-19 special page (as of June 8, 2021). In this paper, we describe the entire COVID-19 special page of the FMODB and discuss the calculation results for various proteins. These data not only aid the interpretation of experimentally determined structures but also the understanding of protein functions, which is useful for rational drug design for COVID-19.
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Affiliation(s)
- Kaori Fukuzawa
- Department of Physical Chemistry, School of Pharmacy
and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara,
Shinagawa-ku, Tokyo 142-8501, Japan
- Department of Biomolecular Engineering, Graduate
School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki,
Aoba-ku, Sendai 980-8579, Japan
| | - Koichiro Kato
- Department of Applied Chemistry, Graduate School of
Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka
819-0395, Japan
- Center for Molecular Systems (CMS),
Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395,
Japan
| | - Chiduru Watanabe
- RIKEN Center for Biosystems Dynamics
Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045,
Japan
- JST PRESTO, 4-1-8, Honcho,
Kawaguchi, Saitama 332-0012, Japan
| | - Yusuke Kawashima
- Department of Physical Chemistry, School of Pharmacy
and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara,
Shinagawa-ku, Tokyo 142-8501, Japan
| | - Yuma Handa
- Department of Physical Chemistry, School of Pharmacy
and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara,
Shinagawa-ku, Tokyo 142-8501, Japan
| | - Ami Yamamoto
- Department of Physical Chemistry, School of Pharmacy
and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara,
Shinagawa-ku, Tokyo 142-8501, Japan
| | - Kazuki Watanabe
- Graduate School of Pharmaceutical Sciences,
Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871,
Japan
- Graduate School of Pharmaceutical Sciences,
Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675,
Japan
| | - Tatsuya Ohyama
- RIKEN Center for Biosystems Dynamics
Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045,
Japan
- Frontier Institute for Biomolecular Engineering
Research (FIBER), Konan University, 7-1-20,
Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kikuko Kamisaka
- RIKEN Center for Biosystems Dynamics
Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045,
Japan
| | - Daisuke Takaya
- RIKEN Center for Biosystems Dynamics
Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045,
Japan
| | - Teruki Honma
- RIKEN Center for Biosystems Dynamics
Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045,
Japan
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473
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Wu Y, Pegan SD, Crich D, Desrochers E, Starling EB, Hansen MC, Booth C, Nicole Mullininx L, Lou L, Chang KY, Xie ZR. Polyphenols as alternative treatments of COVID-19. Comput Struct Biotechnol J 2021; 19:5371-5380. [PMID: 34567475 PMCID: PMC8452152 DOI: 10.1016/j.csbj.2021.09.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/09/2021] [Accepted: 09/18/2021] [Indexed: 01/23/2023] Open
Abstract
Although scientists around the world have put lots of effort into the development of new treatments for COVID-19 since the outbreak, no drugs except Veklury (remdesivir) have been approved by FDA. There is an urgent need to discover some alternative antiviral treatment for COVID-19. Because polyphenols have been shown to possess antiviral activities, here we conducted a large-scale virtual screening for more than 400 polyphenols. Several lead compounds such as Petunidin 3-O-(6″-p-coumaroyl-glucoside) were identified to have promising binding affinities and convincing binding mechanisms. Analyzing the docking results and ADME properties sheds light on the potential efficacy of the top-ranked drug candidates and pinpoints the key residues on the target proteins for the future of drug development.
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Affiliation(s)
- Yifei Wu
- School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens 30602, GA, USA
| | - Scott D Pegan
- Division of Biomedical Sciences., School of Medicine, University of California Riverside, 92521, CA, USA
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens 30602, GA, USA
| | - Ellison Desrochers
- Franklin College of Arts and Sciences, University of Georgia, Athens 30602, GA, USA
| | - Edward B Starling
- Franklin College of Arts and Sciences, University of Georgia, Athens 30602, GA, USA
| | - Madelyn C Hansen
- Franklin College of Arts and Sciences, University of Georgia, Athens 30602, GA, USA
| | - Carson Booth
- Franklin College of Arts and Sciences, University of Georgia, Athens 30602, GA, USA
| | | | - Lei Lou
- School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens 30602, GA, USA
| | - Kuan Y Chang
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung 202, Taiwan, ROC
| | - Zhong-Ru Xie
- School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens 30602, GA, USA
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474
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Sharma HN, Latimore COD, Matthews QL. Biology and Pathogenesis of SARS-CoV-2: Understandings for Therapeutic Developments against COVID-19. Pathogens 2021; 10:pathogens10091218. [PMID: 34578250 PMCID: PMC8470303 DOI: 10.3390/pathogens10091218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 01/18/2023] Open
Abstract
Coronaviruses are positive sense, single-stranded, enveloped, and non-segmented RNA viruses that belong to the Coronaviridae family within the order Nidovirales and suborder Coronavirinae. Two Alphacoronavirus strains: HCoV-229E and HCoV-NL63 and five Betacoronaviruses: HCoV-HKU1, HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2 have so far been recognized as Human Coronaviruses (HCoVs). Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 is currently the greatest concern for humanity. Despite the overflow of research on SARS-CoV-2 and other HCoVs published every week, existing knowledge in this area is insufficient for the complete understanding of the viruses and the diseases caused by them. This review is based on the analysis of 210 published works, and it attempts to cover the basic biology of coronaviruses, including the genetic characteristics, life cycle, and host-pathogen interaction, pathogenesis, the antiviral drugs, and vaccines against HCoVs, especially focusing on SARS-CoV-2. Furthermore, we will briefly discuss the potential link between extracellular vesicles (EVs) and SARS-CoV-2/COVID-19 pathophysiology.
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Affiliation(s)
- Homa Nath Sharma
- Microbiology Program, Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA;
| | | | - Qiana L. Matthews
- Microbiology Program, Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA;
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA;
- Correspondence:
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475
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Alabbas AB, Alamri MA. Analyzing the Effect of Mutations in SARS-CoV2 Papain-Like Protease from Saudi Isolates on Protein Structure and Drug-Protein Binding: Molecular Modelling and Dynamics Studies. Saudi J Biol Sci 2021; 29:526-533. [PMID: 34548835 PMCID: PMC8447498 DOI: 10.1016/j.sjbs.2021.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/31/2021] [Accepted: 09/09/2021] [Indexed: 02/09/2023] Open
Abstract
The continuous and rapid development of the severe acute
respiratory syndrome coronavirus-2 (SARS-CoV-2) virus remains a health concern
especially with the emergence of numerous variants and mutations worldwide. As
with other RNA viruses, SARS-CoV-2 has a genetically high mutation rate. These
mutations have an impact on the virus characteristics, including
transmissibility, antigenicity and development of drug and vaccine resistance.
This work was pursued to identify the differences that exist in the papain-like
protease (PLPro) from 58 Saudi isolates in comparison to the
first reported sequence from Wuhan, China and determine their implications on
protein structure and the inhibitor binding. PLpro is a key
protease enzyme for the host cells invasion and viral proteolytic cleavage,
hence, it emerges as a valuable antiviral therapeutic target. Two mutations were
identified including D108G and A249V and shown to increase the molecular
flexibility of PLPro protein and alter the protein stability,
particularly with D108G mutation. The effect of these mutations on the stability
and dynamic behavior of PLPro structures as well as their
effect on the binding of a known inhibitor; GRL0617 were further investigated by
molecular docking and dynamic simulation.
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Affiliation(s)
- Alhumaidi B Alabbas
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
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476
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Mahajan S, Choudhary S, Kumar P, Tomar S. Antiviral strategies targeting host factors and mechanisms obliging +ssRNA viral pathogens. Bioorg Med Chem 2021; 46:116356. [PMID: 34416512 PMCID: PMC8349405 DOI: 10.1016/j.bmc.2021.116356] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/30/2021] [Accepted: 07/31/2021] [Indexed: 12/21/2022]
Abstract
The ongoing COVID-19 pandemic, periodic recurrence of viral infections, and the emergence of challenging variants has created an urgent need of alternative therapeutic approaches to combat the spread of viral infections, failing to which may pose a greater risk to mankind in future. Resilience against antiviral drugs or fast evolutionary rate of viruses is stressing the scientific community to identify new therapeutic approaches for timely control of disease. Host metabolic pathways are exquisite reservoir of energy to viruses and contribute a diverse array of functions for successful replication and pathogenesis of virus. Targeting the host factors rather than viral enzymes to cease viral infection, has emerged as an alternative antiviral strategy. This approach offers advantage in terms of increased threshold to viral resistance and can provide broad-spectrum antiviral action against different viruses. The article here provides substantial review of literature illuminating the host factors and molecular mechanisms involved in innate/adaptive responses to viral infection, hijacking of signalling pathways by viruses and the intracellular metabolic pathways required for viral replication. Host-targeted drugs acting on the pathways usurped by viruses are also addressed in this study. Host-directed antiviral therapeutics might prove to be a rewarding approach in controlling the unprecedented spread of viral infection, however the probability of cellular side effects or cytotoxicity on host cell should not be ignored at the time of clinical investigations.
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Affiliation(s)
- Supreeti Mahajan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India.
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477
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Cardoso-Lima R, Souza PFN, Guedes MIF, Santos-Oliveira R, Rebelo Alencar LM. SARS-CoV-2 Unrevealed: Ultrastructural and Nanomechanical Analysis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:10762-10769. [PMID: 34351770 PMCID: PMC8370120 DOI: 10.1021/acs.langmuir.1c01488] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/29/2021] [Indexed: 05/28/2023]
Abstract
The ongoing outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) started in late 2019 and spread across the world, infecting millions of people, with over 3.3 million deaths worldwide. To fight back the virus, it is necessary to understand how the main structures work, especially those responsible for the virus infectivity pathogenicity. Here, using the most advanced atomic force microscopy techniques, SARS-CoV-2 viral particles were analyzed, with a special focus on their ultrastructure, adsorption conformation, and nanomechanical behavior. The results uncovered the aspects of the organization and the spatial distribution of the proteins on the surface of the viral particles. It also showed the compliant behavior of the membrane and ability to recover from mechanical injuries. At least three layers composing the membrane and their thickness were measured, protecting the virus from external stress. This study provides new insight into the ultrastructure of SARS-CoV-2 particles at the nanoscale, offering new prospects that could be employed for mapping viral surfaces. The understanding of the viruses' capacity to survive mechanical disruptions at any level and their ability to recover from such injuries can shed a light on the structure-function relationship and help us to find targets for drug action, especially for this virus that, to this day, has no course of treatment approved.
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Affiliation(s)
- Ruana Cardoso-Lima
- Department of Physics, Laboratory of Biophysics and
Nanosystems, Federal University of Maranhão, Campus
Bacanga, São Luís, Maranhão 65080-805,
Brazil
| | | | | | - Ralph Santos-Oliveira
- Laboratory of Nanoradiopharmaceuticals and
Radiopharmacy, Zona Oeste State University, Rio de Janeiro, Rio
de Janeiro 23070200, Brazil
- Brazilian Nuclear Energy Commission,
Nuclear Engineering Institute, Rio de Janeiro, Rio de Janeiro
21941906, Brazil
| | - Luciana M. Rebelo Alencar
- Department of Physics, Laboratory of Biophysics and
Nanosystems, Federal University of Maranhão, Campus
Bacanga, São Luís, Maranhão 65080-805,
Brazil
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478
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Protease cleavage of RNF20 facilitates coronavirus replication via stabilization of SREBP1. Proc Natl Acad Sci U S A 2021; 118:2107108118. [PMID: 34452991 PMCID: PMC8449311 DOI: 10.1073/pnas.2107108118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
COVID-19, caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), has presented a serious risk to global public health. The viral main protease Mpro (also called 3Clpro) encoded by NSP5 is an enzyme essential for viral replication. However, very few host proteins have been experimentally validated as targets of 3Clpro. Here, through bioinformatics analysis of 300 interferon stimulatory genes (ISGs) based on the prediction method NetCorona, we identify RNF20 (Ring Finger Protein 20) as a novel target of 3Clpro. We have also provided evidence that 3Clpro, but not the mutant 3ClproC145A without catalytic activity, cleaves RNF20 at a conserved Gln521 across species, which subsequently prevents SREBP1 from RNF20-mediated degradation and promotes SARS-CoV-2 replication. We show that RNA interference (RNAi)-mediated depletion of either RNF20 or RNF40 significantly enhances viral replication, indicating the antiviral role of RNF20/RNF40 complex against SARS-CoV-2. The involvement of SREBP1 in SARS-CoV-2 infection is evidenced by a decrease of viral replication in the cells with SREBP1 knockdown and inhibitor AM580. Taken together, our findings reveal RNF20 as a novel host target for SARS-CoV-2 main protease and indicate that 3Clpro inhibitors may treat COVID-19 through not only blocking viral polyprotein cleavage but also enhancing host antiviral response.
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479
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McCreary MR, Schnell PM, Rhoda DA. Randomized Double-blind Placebo-controlled Proof-of-concept Trial of Resveratrol for Outpatient Treatment of Mild Coronavirus Disease (COVID-19). RESEARCH SQUARE 2021. [PMID: 34545357 PMCID: PMC8452104 DOI: 10.21203/rs.3.rs-861831/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Resveratrol is a polyphenol that has been well studied and has demonstrated anti-viral and anti-inflammatory properties that might mitigate the effects of COVID-19. Outpatients (N=105) were recruited from central Ohio in late 2020. Participants were randomly assigned to receive placebo or resveratrol. Both groups received a single dose of Vitamin D3 which was used as an adjunct. The primary outcome measure was hospitalization within 21 days of symptom onset; secondary measures were ER visits, incidence of pneumonia and pulmonary embolism. Five patients chose not to participate after randomization. Twenty-one day outcome was determined of all one hundred participants (mean [SD] age 55.6 [8.8] years; 61% female) (or their surrogates). There were no clinically significant adverse events attributed to resveratrol. Outpatients in this phase 2 study treated with resveratrol had a lower incidence compared to placebo of: hospitalization (2% vs. 6%, RR 0.33, 95% CI 0.04-3.10), COVID-related ER visits (8% vs. 14%, RR 0.57, 95% CI 0.18-1.83), and pneumonia (8% vs. 16%, RR 0.5, 95% CI 0.16-1.55). One patient (2%) in each group developed pulmonary embolism (RR 1.00, 95% CI: 0.06-15.55). This underpowered study was limited by small sample size and low incidence of primary adverse events. A larger trial could determine efficacy. TRIAL REGISTRATIONS: ClinicalTrials.gov NCT04400890 26/05/2020; FDA IND #150033 05/05/2020.
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480
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Ghareeb DA, Saleh SR, Seadawy MG, Nofal MS, Abdulmalek SA, Hassan SF, Khedr SM, AbdElwahab MG, Sobhy AA, Abdel-Hamid ASA, Yassin AM, Elmoneam AAA, Masoud AA, Kaddah MMY, El-Zahaby SA, Al-mahallawi AM, El-Gharbawy AM, Zaki A, Seif IK, Kenawy MY, Amin M, Amer K, El Demellawy MA. Nanoparticles of ZnO/Berberine complex contract COVID-19 and respiratory co-bacterial infection in addition to elimination of hydroxychloroquine toxicity. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2021. [DOI: https://doi.org/10.1007/s40005-021-00544-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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481
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Ghareeb DA, Saleh SR, Seadawy MG, Nofal MS, Abdulmalek SA, Hassan SF, Khedr SM, AbdElwahab MG, Sobhy AA, Abdel-Hamid ASA, Yassin AM, Elmoneam AAA, Masoud AA, Kaddah MMY, El-Zahaby SA, Al-Mahallawi AM, El-Gharbawy AM, Zaki A, Seif IK, Kenawy MY, Amin M, Amer K, El Demellawy MA. Nanoparticles of ZnO/Berberine complex contract COVID-19 and respiratory co-bacterial infection in addition to elimination of hydroxychloroquine toxicity. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2021; 51:735-757. [PMID: 34513113 PMCID: PMC8419391 DOI: 10.1007/s40005-021-00544-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/22/2021] [Indexed: 02/07/2023]
Abstract
Purpose A novel coronavirus (COVID-19) that has not been previously identified in humans and has no specific treatment has recently spread. Treatment trials using antiviral and immune-modulating drugs such as hydroxychloroquine (HCQ) were used to control this viral outbreak however several side effects have emerged. Berberine (BER) is an alkaloid that has been reported to reveal some pharmacological properties including antioxidant and antimicrobial activities. Additionally, Zinc oxide nanoparticles (ZnO-NPs) possess potent antioxidant and anti-inflammatory properties. Therefore, this study was undertaken to estimate the efficiency of both BER and synthetic ZnO/BER complex as an anti-COVID-19 therapy. Methods First, the ZnO/BER complex was prepared by the facile mixing method. Then in vitro studies on the two compounds were conducted including VeroE6 toxicity, anti-COVID-19 activity, determination of inhibitory activity towards papain-like proteinase (PL pro) and spike protein- and receptor- binding domain (RBD) as well as assessment of drug toxicity on RBCs. Results The results showed that ZnO/BER complex acts as an anti-COVID-19 by inhibiting spike protein binding with angiotensin-converting enzyme II (ACE II), PL pro activity, spike protein and E protein levels, and expression of both E-gene and RNA dependent RNA polymerase (RdRp) at a concentration lower than that of BER or ZnO-NPs alone. Furthermore, ZnO/BER complex had antioxidant and antimicrobial properties where it prevents the auto oxidation of 2,2-Diphenyl-1-picrylhydrazyl (DPPH) and the culture of lower respiratory system bacteria that affected Covid 19 patients. The ZnO/BER complex prevented as well the HCQ cytotoxic effect on both RBC and WBC (in vitro) and hepatotoxicity, nephrotoxicity and anemia that occurred after HCQ long administration in vivo. Conclusion The ZnO/BER complex can be accounted as promising anti-COVID 19 candidate because it inhibited the virus entry, replication, and assembly. Furthermore, it could be used to treat a second bacterial infection that took place in hospitalized COVID 19 patients. Moreover, ZnO/BER complex was found to eliminate the toxicity of long-term administration of HCQ in vivo.
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Affiliation(s)
- Doaa A Ghareeb
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Samar R Saleh
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | | | - Mohammed S Nofal
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Shaymaa A Abdulmalek
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Salma F Hassan
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Shaimaa M Khedr
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Miral G AbdElwahab
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Ahmed A Sobhy
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Clinical Pharmacy Program, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Ali Saber Ali Abdel-Hamid
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Abdelrahman Mohamed Yassin
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Alshimaa A Abd Elmoneam
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Aliaa A Masoud
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Mohamed M Y Kaddah
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Sally A El-Zahaby
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Pharos University in Alexandria, Alexandria, Egypt
| | - Abdulaziz Mohsen Al-Mahallawi
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo, Egypt
| | - Alaa M El-Gharbawy
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Ahmed Zaki
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Inas K Seif
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Marwa Y Kenawy
- Bio-Screening and Preclinical Trial Lab, Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Fabrication Technology Research Department, Advanced Technology and New Materials Research Institute (ATNMRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria, 21934 Egypt
| | | | - Khaled Amer
- Egypt Center for Research and Regenerative Medicine, Cairo, Egypt
| | - Maha Adel El Demellawy
- Center of Excellence for Drug Preclinical Studies (CE-DPS), Pharmaceutical and Fermentation Industry Development Center, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
- Medical Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research & Technological Applications, New Borg El Arab, Alexandria, Egypt
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482
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Targhetta VP, Amaral MA, Camara NOS. Through DNA sensors and hidden mitochondrial effects of SARS-CoV-2. J Venom Anim Toxins Incl Trop Dis 2021; 27:e20200183. [PMID: 34471404 PMCID: PMC8383803 DOI: 10.1590/1678-9199-jvatitd-2020-0183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/08/2021] [Indexed: 12/23/2022] Open
Abstract
The COVID-19 pandemic brought attention to studies about viral infections and their impact on the cell machinery. SARS-CoV-2, for example, invades the host cells by ACE2 interaction and possibly hijacks the mitochondria. To better understand the disease and to propose novel treatments, crucial aspects of SARS-CoV-2 enrolment with host mitochondria must be studied. The replicative process of the virus leads to consequences in mitochondrial function, and cell metabolism. The hijacking of mitochondria, on the other hand, can drive the extrusion of mitochondrial DNA (mtDNA) to the cytosol. Extracellular mtDNA evoke robust proinflammatory responses once detected, that may act in different pathways, eliciting important immune responses. However, few receptors are validated and are able to detect and respond to mtDNA. In this review, we propose that the mtDNA and its detection might be important in the immune process generated by SARS-CoV-2 and that this mechanism might be important in the lung pathogenesis seen in clinical symptoms. Therefore, investigating the mtDNA receptors and their signaling pathways might provide important clues for therapeutic interventions.
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Affiliation(s)
- Vitor Pedro Targhetta
- Department of Immunology, Institute of Biomedical Sciences (ICB), University of São Paulo (USP), São Paulo, SP, Brazil
| | - Mariana Abrantes Amaral
- Department of Nephrology, Paulista School of Medicine (EPM), Federal University of São Paulo (Unifesp), São Paulo, SP, Brazil
| | - Niels Olsen Saraiva Camara
- Department of Immunology, Institute of Biomedical Sciences (ICB), University of São Paulo (USP), São Paulo, SP, Brazil
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483
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Arwansyah A, Arif AR, Ramli I, Kurniawan I, Sukarti S, Nur Alam M, Illing I, Farid Lewa A, Manguntungi B. Molecular modelling on SARS-CoV-2 papain-like protease: an integrated study with homology modelling, molecular docking, and molecular dynamics simulations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:699-718. [PMID: 34392751 DOI: 10.1080/1062936x.2021.1960601] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
SARS-CoV-2 PLpro was investigated as a therapeutic target for potent antiviral drugs due to its essential role in not only viral replication but also in regulating the inborn immune response. Several computational approaches, including homology modelling, molecular docking, and molecular dynamics (MD) studies, were employed to search for promising drugs in treating SARS-CoV-2. Eighty-one compounds, sub-structurally similar to the antiviral drug, were used as potential inhibitors of PLpro. From our results, three complexes containing the ligands with Pubchem IDs: 153012995, 12149203, and 123608715 showed lower binding energies than the control (Ritonavir), indicating that they may become promising inhibitors for PLpro. MD was performed in a water solvent to validate the stability of the three complexes. All complexes achieved stable structure during the simulation as no significant fluctuations were observed in the validation parameters. Moreover, the binding energy for each complex was estimated using the MM-GBSA method. Complex 1 was the most stable structure based on the lowest binding energy score and its structure remained in a similar cavity with the docket snapshot. Based on our studies, three ligands were assumed to be potential inhibitors. The ligand of complex 1 may become the most promising antiviral drug against SARS-CoV-2 targeting PLpro.
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Affiliation(s)
- A Arwansyah
- Department of Chemistry, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - A R Arif
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia
| | - I Ramli
- Department of Physics, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - I Kurniawan
- School of Computing, Telkom University, Bandung, Indonesia
- Research Center of Human Centric Engineering, Telkom University, Bandung, Indonesia
| | - S Sukarti
- Department of Chemistry, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - M Nur Alam
- Department of Chemistry, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - I Illing
- Department of Chemistry, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - A Farid Lewa
- Department of Nutrition, Poltekkes Kemenkes Palu, Palu, Indonesia
| | - B Manguntungi
- Department of Biotechnology, Faculty of Biotechnology, Sumbawa University of Technology, Sumbawa, Indonesia
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484
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Severa M, Diotti RA, Etna MP, Rizzo F, Fiore S, Ricci D, Iannetta M, Sinigaglia A, Lodi A, Mancini N, Criscuolo E, Clementi M, Andreoni M, Balducci S, Barzon L, Stefanelli P, Clementi N, Coccia EM. Differential plasmacytoid dendritic cell phenotype and type I Interferon response in asymptomatic and severe COVID-19 infection. PLoS Pathog 2021; 17:e1009878. [PMID: 34473805 PMCID: PMC8412261 DOI: 10.1371/journal.ppat.1009878] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/09/2021] [Indexed: 12/25/2022] Open
Abstract
SARS-CoV-2 fine-tunes the interferon (IFN)-induced antiviral responses, which play a key role in preventing coronavirus disease 2019 (COVID-19) progression. Indeed, critically ill patients show an impaired type I IFN response accompanied by elevated inflammatory cytokine and chemokine levels, responsible for cell and tissue damage and associated multi-organ failure. Here, the early interaction between SARS-CoV-2 and immune cells was investigated by interrogating an in vitro human peripheral blood mononuclear cell (PBMC)-based experimental model. We found that, even in absence of a productive viral replication, the virus mediates a vigorous TLR7/8-dependent production of both type I and III IFNs and inflammatory cytokines and chemokines, known to contribute to the cytokine storm observed in COVID-19. Interestingly, we observed how virus-induced type I IFN secreted by PBMC enhances anti-viral response in infected lung epithelial cells, thus, inhibiting viral replication. This type I IFN was released by plasmacytoid dendritic cells (pDC) via an ACE-2-indipendent but Neuropilin-1-dependent mechanism. Viral sensing regulates pDC phenotype by inducing cell surface expression of PD-L1 marker, a feature of type I IFN producing cells. Coherently to what observed in vitro, asymptomatic SARS-CoV-2 infected subjects displayed a similar pDC phenotype associated to a very high serum type I IFN level and induction of anti-viral IFN-stimulated genes in PBMC. Conversely, hospitalized patients with severe COVID-19 display very low frequency of circulating pDC with an inflammatory phenotype and high levels of chemokines and pro-inflammatory cytokines in serum. This study further shed light on the early events resulting from the interaction between SARS-CoV-2 and immune cells occurring in vitro and confirmed ex vivo. These observations can improve our understanding on the contribution of pDC/type I IFN axis in the regulation of the anti-viral state in asymptomatic and severe COVID-19 patients.
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Affiliation(s)
- Martina Severa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Roberta A. Diotti
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
| | - Marilena P. Etna
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Fabiana Rizzo
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Fiore
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Daniela Ricci
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marco Iannetta
- Infectious Disease Clinic, Policlinico Tor Vergata, Rome, Italy
| | | | - Alessandra Lodi
- Infectious Disease Clinic, Policlinico Tor Vergata, Rome, Italy
| | - Nicasio Mancini
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
| | - Elena Criscuolo
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
| | - Massimo Clementi
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
| | | | | | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Nicola Clementi
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
| | - Eliana M. Coccia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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485
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Ku C, Chen I, Lai M. Infection-induced inflammation from specific inborn errors of immunity to COVID-19. FEBS J 2021; 288:5021-5041. [PMID: 33971084 PMCID: PMC8236961 DOI: 10.1111/febs.15961] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/10/2021] [Accepted: 05/07/2021] [Indexed: 01/07/2023]
Abstract
Inborn errors of immunity (IEIs) are a group of genetically defined disorders leading to defective immunity. Some IEIs have been linked to mutations of immune receptors or signaling molecules, resulting in defective signaling of respective cascades essential for combating specific pathogens. However, it remains incompletely understood why in selected IEIs, such as X-linked lymphoproliferative syndrome type 2 (XLP-2), hypo-immune response to specific pathogens results in persistent inflammation. Moreover, mechanisms underlying the generation of anticytokine autoantibodies are mostly unknown. Recently, IEIs have been associated with coronavirus disease 2019 (COVID-19), with a small proportion of patients that contract severe COVID-19 displaying loss-of-function mutations in genes associated with type I interferons (IFNs). Moreover, approximately 10% of patients with severe COVID-19 possess anti-type I IFN-neutralizing autoantibodies. Apart from IEIs that impair immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), SARS-CoV-2 encodes several proteins that suppress early type I IFN production. One primary consequence of the lack of type I IFNs during early SARS-CoV-2 infection is the increased inflammation associated with COVID-19. In XLP-2, resolution of inflammation rescued experimental subjects from infection-induced mortality. Recent studies also indicate that targeting inflammation could alleviate COVID-19. In this review, we discuss infection-induced inflammation in IEIs, using XLP-2 and COVID-19 as examples. We suggest that resolving inflammation may represent an effective therapeutic approach to these diseases.
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Affiliation(s)
- Cheng‐Lung Ku
- Laboratory of Human Immunology and Infectious DiseasesGraduate Institute of Clinical Medical SciencesChang Gung UniversityTaoyuanTaiwan,Department of NephrologyLinkou Chang Gung Memorial HospitalTaoyuanTaiwan
| | - I‐Ting Chen
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Ming‐Zong Lai
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
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486
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Zhang K, Zheludev IN, Hagey RJ, Haslecker R, Hou YJ, Kretsch R, Pintilie GD, Rangan R, Kladwang W, Li S, Wu MTP, Pham EA, Bernardin-Souibgui C, Baric RS, Sheahan TP, D'Souza V, Glenn JS, Chiu W, Das R. Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome. Nat Struct Mol Biol 2021; 28:747-754. [PMID: 34426697 PMCID: PMC8848339 DOI: 10.1038/s41594-021-00653-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023]
Abstract
Drug discovery campaigns against COVID-19 are beginning to target the SARS-CoV-2 RNA genome. The highly conserved frameshift stimulation element (FSE), required for balanced expression of viral proteins, is a particularly attractive SARS-CoV-2 RNA target. Here we present a 6.9 Å resolution cryo-EM structure of the FSE (88 nucleotides, ~28 kDa), validated through an RNA nanostructure tagging method. The tertiary structure presents a topologically complex fold in which the 5' end is threaded through a ring formed inside a three-stem pseudoknot. Guided by this structure, we develop antisense oligonucleotides that impair FSE function in frameshifting assays and knock down SARS-CoV-2 virus replication in A549-ACE2 cells at 100 nM concentration.
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Affiliation(s)
- Kaiming Zhang
- Departments of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ivan N Zheludev
- Department of Biochemistry Stanford University, Stanford, CA, USA
| | - Rachel J Hagey
- Departments of Medicine (Division of Gastroenterology and Hepatology) and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA
| | - Raphael Haslecker
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Grigore D Pintilie
- Departments of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Wipapat Kladwang
- Department of Biochemistry Stanford University, Stanford, CA, USA
| | - Shanshan Li
- Departments of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Marie Teng-Pei Wu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Edward A Pham
- Departments of Medicine (Division of Gastroenterology and Hepatology) and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA
| | - Claire Bernardin-Souibgui
- Departments of Medicine (Division of Gastroenterology and Hepatology) and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Victoria D'Souza
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Jeffrey S Glenn
- Departments of Medicine (Division of Gastroenterology and Hepatology) and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA.
- Palo Alto Veterans Administration, Palo Alto, CA, USA.
| | - Wah Chiu
- Departments of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA.
- Biophysics Program, Stanford University, Stanford, CA, USA.
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
| | - Rhiju Das
- Department of Biochemistry Stanford University, Stanford, CA, USA.
- Biophysics Program, Stanford University, Stanford, CA, USA.
- Department of Physics, Stanford University, Stanford, CA, USA.
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487
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Dodero-Rojas E, Onuchic JN, Whitford PC. Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. eLife 2021; 10:70362. [PMID: 34463614 PMCID: PMC8456623 DOI: 10.7554/elife.70362] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious, and transmission involves a series of processes that may be targeted by vaccines and therapeutics. During transmission, host cell invasion is controlled by a large-scale (200–300 Å) conformational change of the Spike protein. This conformational rearrangement leads to membrane fusion, which creates transmembrane pores through which the viral genome is passed to the host. During Spike-protein-mediated fusion, the fusion peptides must be released from the core of the protein and associate with the host membrane. While infection relies on this transition between the prefusion and postfusion conformations, there has yet to be a biophysical characterization reported for this rearrangement. That is, structures are available for the endpoints, though the intermediate conformational processes have not been described. Interestingly, the Spike protein possesses many post-translational modifications, in the form of branched glycans that flank the surface of the assembly. With the current lack of data on the pre-to-post transition, the precise role of glycans during cell invasion has also remained unclear. To provide an initial mechanistic description of the pre-to-post rearrangement, an all-atom model with simplified energetics was used to perform thousands of simulations in which the protein transitions between the prefusion and postfusion conformations. These simulations indicate that the steric composition of the glycans can induce a pause during the Spike protein conformational change. We additionally show that this glycan-induced delay provides a critical opportunity for the fusion peptides to capture the host cell. In contrast, in the absence of glycans, the viral particle would likely fail to enter the host. This analysis reveals how the glycosylation state can regulate infectivity, while providing a much-needed structural framework for studying the dynamics of this pervasive pathogen.
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Affiliation(s)
- Esteban Dodero-Rojas
- Center for Theoretical Biological Physics, Rice University, Houston, United States
| | - Jose N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, United States.,Department of Physics and Astronomy, Rice University, Houston, United States.,Department of Chemistry, Rice University, Houston, United States.,Department of Biosciences, Rice University, Houston, United States
| | - Paul Charles Whitford
- Center for Theoretical Biological Physics, Northeastern University, Boston, United States.,Department of Physics, Northeastern University, Boston, United States
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488
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Zheng YX, Wang L, Kong WS, Chen H, Wang XN, Meng Q, Zhang HN, Guo SJ, Jiang HW, Tao SC. Nsp2 has the potential to be a drug target revealed by global identification of SARS-CoV-2 Nsp2-interacting proteins. Acta Biochim Biophys Sin (Shanghai) 2021; 53:1134-1141. [PMID: 34159380 DOI: 10.1093/abbs/gmab088] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 01/09/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global health threat since December 2019, and there is still no highly effective drug to control the pandemic. To facilitate drug target identification for drug development, studies on molecular mechanisms, such as SARS-CoV-2 protein interactions, are urgently needed. In this study, we focused on Nsp2, a non-structural protein with largely unknown function and mechanism. The interactome of Nsp2 was revealed through the combination of affinity purification mass spectrometry (AP-MS) and stable isotope labeling by amino acids in cell culture (SILAC), and 84 proteins of high-confidence were identified. Gene ontology analysis demonstrated that Nsp2-interacting proteins are involved in several biological processes such as endosome transport and translation. Network analysis generated two clusters, including ribosome assembly and vesicular transport. Bio-layer interferometry (BLI) assay confirmed the bindings between Nsp2- and 4-interacting proteins, i.e. STAU2 (Staufen2), HNRNPLL, ATP6V1B2, and RAP1GDS1 (SmgGDS), which were randomly selected from the list of 84 proteins. Our findings provide insights into the Nsp2-host interplay and indicate that Nsp2 may play important roles in SARS-CoV-2 infection and serve as a potential drug target for anti-SARS-CoV-2 drug development.
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Affiliation(s)
- Yun-Xiao Zheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei-Sha Kong
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Ning Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qingfeng Meng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Nan Zhang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Juan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - He-Wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
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489
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KOCABAŞ F, USLU M. The current state of validated small molecules inhibiting SARS-CoV-2 nonstructural proteins. Turk J Biol 2021; 45:469-483. [PMID: 34803448 PMCID: PMC8573838 DOI: 10.3906/biy-2106-42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 08/06/2021] [Indexed: 11/03/2022] Open
Abstract
The current COVID-19 outbreak has had a profound influence on public health and daily life. Despite all restrictions and vaccination programs, COVID-19 still can lead to fatality due to a lack of COVID-19-specific treatments. A number of studies have demonstrated the feasibility to develop therapeutics by targeting underlying components of the viral proteome. Here we reviewed recently developed and validated small molecule inhibitors of SARS-CoV-2's nonstructural proteins. We described the validation level of identified compounds specific for SARS-CoV-2 in the presence of in vitro and in vivo supporting data. The mechanisms of pharmacological activity, as well as approaches for developing improved SARS-CoV-2 NSP inhibitors have been emphasized.
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Affiliation(s)
- Fatih KOCABAŞ
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbulTurkey
| | - Merve USLU
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbulTurkey
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490
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Thery F, Eggermont D, Impens F. Proteomics Mapping of the ISGylation Landscape in Innate Immunity. Front Immunol 2021; 12:720765. [PMID: 34447387 PMCID: PMC8383068 DOI: 10.3389/fimmu.2021.720765] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/16/2021] [Indexed: 01/12/2023] Open
Abstract
During infection, pathogen sensing and cytokine signaling by the host induce expression of antimicrobial proteins and specialized post-translational modifications. One such protein is ISG15, a ubiquitin-like protein (UBL) conserved among vertebrates. Similar to ubiquitin, ISG15 covalently conjugates to lysine residues in substrate proteins in a process called ISGylation. Mice deficient for ISGylation or lacking ISG15 are strongly susceptible to many viral pathogens and several intracellular bacterial pathogens. Although ISG15 was the first UBL discovered after ubiquitin, the mechanisms behind its protective activity are poorly understood. Largely, this stems from a lack of knowledge on the ISG15 substrate repertoire. To unravel the antiviral activity of ISG15, early studies used mass spectrometry-based proteomics in combination with ISG15 pulldown. Despite reporting hundreds of ISG15 substrates, these studies were unable to identify the exact sites of modification, impeding a clear understanding of the molecular consequences of protein ISGylation. More recently, a peptide-based enrichment approach revolutionized the study of ubiquitin allowing untargeted discovery of ubiquitin substrates, including knowledge of their exact modification sites. Shared molecular determinants between ISG15 and ubiquitin allowed to take advantage of this technology for proteome-wide mapping of ISG15 substrates and modification sites. In this review, we provide a comprehensive overview of mass spectrometry-based proteomics studies on protein ISGylation. We critically discuss the relevant literature, compare reported substrates and sites and make suggestions for future research.
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Affiliation(s)
- Fabien Thery
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Denzel Eggermont
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,VIB Proteomics Core, VIB, Ghent, Belgium
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491
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Hoch NC. Host ADP-ribosylation and the SARS-CoV-2 macrodomain. Biochem Soc Trans 2021; 49:1711-1721. [PMID: 34351418 PMCID: PMC8421052 DOI: 10.1042/bst20201212] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 11/29/2022]
Abstract
The COVID-19 pandemic has prompted intense research efforts into elucidating mechanisms of coronavirus pathogenesis and to propose antiviral interventions. The interferon (IFN) response is the main antiviral component of human innate immunity and is actively suppressed by several non-structural SARS-CoV-2 proteins, allowing viral replication within human cells. Differences in IFN signalling efficiency and timing have emerged as central determinants of the variability of COVID-19 disease severity between patients, highlighting the need for an improved understanding of host-pathogen interactions that affect the IFN response. ADP-ribosylation is an underexplored post-translational modification catalyzed by ADP-ribosyl transferases collectively termed poly(ADP-ribose) polymerases (PARPs). Several human PARPs are induced by the IFN response and participate in antiviral defences by regulating IFN signalling itself, modulating host processes such as translation and protein trafficking, as well as directly modifying and inhibiting viral target proteins. SARS-CoV-2 and other viruses encode a macrodomain that hydrolyzes ADP-ribose modifications, thus counteracting antiviral PARP activity. This mini-review provides a brief overview of the known targets of IFN-induced ADP-ribosylation and the functions of viral macrodomains, highlighting several open questions in the field.
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Affiliation(s)
- Nicolas C. Hoch
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
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492
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Zhou YW, Xie Y, Tang LS, Pu D, Zhu YJ, Liu JY, Ma XL. Therapeutic targets and interventional strategies in COVID-19: mechanisms and clinical studies. Signal Transduct Target Ther 2021; 6:317. [PMID: 34446699 PMCID: PMC8390046 DOI: 10.1038/s41392-021-00733-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/27/2021] [Accepted: 07/14/2021] [Indexed: 02/06/2023] Open
Abstract
Owing to the limitations of the present efforts on drug discovery against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the lack of the understanding of the biological regulation mechanisms underlying COVID-19, alternative or novel therapeutic targets for COVID-19 treatment are still urgently required. SARS-CoV-2 infection and immunity dysfunction are the two main courses driving the pathogenesis of COVID-19. Both the virus and host factors are potential targets for antiviral therapy. Hence, in this study, the current therapeutic strategies of COVID-19 have been classified into "target virus" and "target host" categories. Repurposing drugs, emerging approaches, and promising potential targets are the implementations of the above two strategies. First, a comprehensive review of the highly acclaimed old drugs was performed according to evidence-based medicine to provide recommendations for clinicians. Additionally, their unavailability in the fight against COVID-19 was analyzed. Next, a profound analysis of the emerging approaches was conducted, particularly all licensed vaccines and monoclonal antibodies (mAbs) enrolled in clinical trials against primary SARS-CoV-2 and mutant strains. Furthermore, the pros and cons of the present licensed vaccines were compared from different perspectives. Finally, the most promising potential targets were reviewed, and the update of the progress of treatments has been summarized based on these reviews.
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Affiliation(s)
- Yu-Wen Zhou
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
- Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yao Xie
- Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
- Department of Dermatovenerology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Lian-Sha Tang
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
- Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Dan Pu
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Ya-Juan Zhu
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
- Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Ji-Yan Liu
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
- Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
| | - Xue-Lei Ma
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
- Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
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493
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Yan F, Gao F. An overview of potential inhibitors targeting non-structural proteins 3 (PL pro and Mac1) and 5 (3CL pro/M pro) of SARS-CoV-2. Comput Struct Biotechnol J 2021; 19:4868-4883. [PMID: 34457214 PMCID: PMC8382591 DOI: 10.1016/j.csbj.2021.08.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 08/02/2021] [Accepted: 08/21/2021] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to develop effective treatments for coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The rapid spread of SARS-CoV-2 has resulted in a global pandemic that has not only affected the daily lives of individuals but also had a significant impact on the global economy and public health. Although extensive research has been conducted to identify inhibitors targeting SARS-CoV-2, there are still no effective treatment strategies to combat COVID-19. SARS-CoV-2 comprises two important proteolytic enzymes, namely, the papain-like proteinase, located within non-structural protein 3 (nsp3), and nsp5, both of which cleave large replicase polypeptides into multiple fragments that are required for viral replication. Moreover, a domain within nsp3, known as the macrodomain (Mac1), also plays an important role in viral replication. Inhibition of their functions should be able to significantly interfere with the replication cycle of the virus, and therefore these key proteins may serve as potential therapeutic targets. The functions of the above viral targets and their corresponding inhibitors have been summarized in the current review. This review provides comprehensive updates of nsp3 and nsp5 inhibitor development and would help advance the discovery of novel anti-viral therapeutics against SARS-CoV-2.
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Affiliation(s)
- Fangfang Yan
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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494
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Naidoo D, Kar P, Roy A, Mutanda T, Bwapwa J, Sen A, Anandraj A. Structural Insight into the Binding of Cyanovirin-N with the Spike Glycoprotein, M pro and PL pro of SARS-CoV-2: Protein-Protein Interactions, Dynamics Simulations and Free Energy Calculations. Molecules 2021; 26:molecules26175114. [PMID: 34500548 PMCID: PMC8434238 DOI: 10.3390/molecules26175114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 02/06/2023] Open
Abstract
The emergence of COVID-19 continues to pose severe threats to global public health. The pandemic has infected over 171 million people and claimed more than 3.5 million lives to date. We investigated the binding potential of antiviral cyanobacterial proteins including cyanovirin-N, scytovirin and phycocyanin with fundamental proteins involved in attachment and replication of SARS-CoV-2. Cyanovirin-N displayed the highest binding energy scores (−16.8 ± 0.02 kcal/mol, −12.3 ± 0.03 kcal/mol and −13.4 ± 0.02 kcal/mol, respectively) with the spike protein, the main protease (Mpro) and the papainlike protease (PLpro) of SARS-CoV-2. Cyanovirin-N was observed to interact with the crucial residues involved in the attachment of the human ACE2 receptor. Analysis of the binding affinities calculated employing the molecular mechanics-Poisson–Boltzmann surface area (MM-PBSA) approach revealed that all forms of energy, except the polar solvation energy, favourably contributed to the interactions of cyanovirin-N with the viral proteins. With particular emphasis on cyanovirin-N, the current work presents evidence for the potential inhibition of SARS-CoV-2 by cyanobacterial proteins, and offers the opportunity for in vitro and in vivo experiments to deploy the cyanobacterial proteins as valuable therapeutics against COVID-19.
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Affiliation(s)
- Devashan Naidoo
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
- Correspondence: (D.N.); (A.R.)
| | - Pallab Kar
- Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri 734013, India; (P.K.); (A.S.)
| | - Ayan Roy
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
- Correspondence: (D.N.); (A.R.)
| | - Taurai Mutanda
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
| | - Joseph Bwapwa
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
| | - Arnab Sen
- Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri 734013, India; (P.K.); (A.S.)
| | - Akash Anandraj
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
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495
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Mslati H, Gentile F, Perez C, Cherkasov A. Comprehensive Consensus Analysis of SARS-CoV-2 Drug Repurposing Campaigns. J Chem Inf Model 2021; 61:3771-3788. [PMID: 34313439 PMCID: PMC8340583 DOI: 10.1021/acs.jcim.1c00384] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 01/18/2023]
Abstract
The current COVID-19 pandemic has elicited extensive repurposing efforts (both small and large scale) to rapidly identify COVID-19 treatments among approved drugs. Herein, we provide a literature review of large-scale SARS-CoV-2 antiviral drug repurposing efforts and highlight a marked lack of consistent potency reporting. This variability indicates the importance of standardizing best practices-including the use of relevant cell lines, viral isolates, and validated screening protocols. We further surveyed available biochemical and virtual screening studies against SARS-CoV-2 targets (Spike, ACE2, RdRp, PLpro, and Mpro) and discuss repurposing candidates exhibiting consistent activity across diverse, triaging assays and predictive models. Moreover, we examine repurposed drugs and their efficacy against COVID-19 and the outcomes of representative repurposed drugs in clinical trials. Finally, we propose a drug repurposing pipeline to encourage the implementation of standard methods to fast-track the discovery of candidates and to ensure reproducible results.
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Affiliation(s)
- Hazem Mslati
- Vancouver Prostate Centre, University of
British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6,
Canada
| | - Francesco Gentile
- Vancouver Prostate Centre, University of
British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6,
Canada
| | - Carl Perez
- Vancouver Prostate Centre, University of
British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6,
Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of
British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6,
Canada
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496
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Arya R, Prashar V, Kumar M. Evaluating Stability and Activity of SARS-CoV-2 PLpro for High-throughput Screening of Inhibitors. Mol Biotechnol 2021; 64:1-8. [PMID: 34420183 PMCID: PMC8380414 DOI: 10.1007/s12033-021-00383-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/16/2021] [Indexed: 12/28/2022]
Abstract
Because of the essential roles of SARS-CoV-2 papain-like protease (PLpro) in the viral polyprotein processing and suppression of host immune responses, it is a crucial target for drug discovery against COVID-19. To develop robust biochemical methodologies for inhibitor screening against PLpro, extensive characterization of recombinant protein is important. Here we report cloning, expression, and purification of the recombinant SARS-CoV-2 PLpro, and explore various parameters affecting its stability and the catalytic activity. We also report the optimum conditions which should be used for high-throughput inhibitor screening using a fluorogenic tetrapeptide substrate.
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Affiliation(s)
- Rimanshee Arya
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.,Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Vishal Prashar
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.
| | - Mukesh Kumar
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, 400085, India. .,Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
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497
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Cho CC, Li SG, Lalonde TJ, Yang KS, Yu G, Qiao Y, Xu S, Ray Liu W. Drug Repurposing for the SARS-CoV-2 Papain-Like Protease. ChemMedChem 2021; 17:e202100455. [PMID: 34423563 PMCID: PMC8653067 DOI: 10.1002/cmdc.202100455] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/17/2021] [Indexed: 12/22/2022]
Abstract
As the pathogen of COVID‐19, SARS‐CoV‐2 encodes two essential cysteine proteases that process the pathogen's two large polypeptide products pp1a and pp1ab in the human cell host to form 15 functionally important, mature nonstructural proteins. One of the two enzymes is papain‐like protease or PLPro. It possesses deubiquitination and deISGylation activities that suppress host innate immune responses toward SARS‐CoV‐2 infection. To repurpose drugs for PLPro, we experimentally screened libraries of 33 deubiquitinase and 37 cysteine protease inhibitors on their inhibition of PLPro. Our results showed that 15 deubiquitinase and 1 cysteine protease inhibitors exhibit strong inhibition of PLPro at 200 μM. More comprehensive characterizations revealed seven inhibitors GRL0617, SJB2‐043, TCID, DUB‐IN‐1, DUB‐IN‐3, PR‐619, and S130 with an IC50 value below 40 μM and four inhibitors GRL0617, SJB2‐043, TCID, and PR‐619 with an IC50 value below 10 μM. Among four inhibitors with an IC50 value below 10 μM, SJB2‐043 is the most unique in that it does not fully inhibit PLPro but has a noteworthy IC50 value of 0.56 μM. SJB2‐043 likely binds to an allosteric site of PLPro to convene its inhibition effect, which needs to be further investigated. As a pilot study, the current work indicates that COVID‐19 drug repurposing by targeting PLPro holds promise, but in‐depth analysis of repurposed drugs is necessary to avoid omitting critical allosteric inhibitors.
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Affiliation(s)
- Chia-Chuan Cho
- The Texas A&M Drug Discovery Laboratory Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Shuhua G Li
- The Texas A&M Drug Discovery Laboratory Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Tyler J Lalonde
- The Texas A&M Drug Discovery Laboratory Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Kai S Yang
- The Texas A&M Drug Discovery Laboratory Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Ge Yu
- The Texas A&M Drug Discovery Laboratory Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Yuchen Qiao
- The Texas A&M Drug Discovery Laboratory Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.,Institute of Biosciences and Technology and Department of Translational Medical Sciences College of Medicine, Texas A&M University, Houston, TX 77030, USA.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.,Department of Molecular and Cellular Medicine College of Medicine, Texas A&M University, College Station, TX 77843, USA
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498
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Muratov EN, Amaro R, Andrade CH, Brown N, Ekins S, Fourches D, Isayev O, Kozakov D, Medina-Franco JL, Merz KM, Oprea TI, Poroikov V, Schneider G, Todd MH, Varnek A, Winkler DA, Zakharov AV, Cherkasov A, Tropsha A. A critical overview of computational approaches employed for COVID-19 drug discovery. Chem Soc Rev 2021; 50:9121-9151. [PMID: 34212944 PMCID: PMC8371861 DOI: 10.1039/d0cs01065k] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Indexed: 01/18/2023]
Abstract
COVID-19 has resulted in huge numbers of infections and deaths worldwide and brought the most severe disruptions to societies and economies since the Great Depression. Massive experimental and computational research effort to understand and characterize the disease and rapidly develop diagnostics, vaccines, and drugs has emerged in response to this devastating pandemic and more than 130 000 COVID-19-related research papers have been published in peer-reviewed journals or deposited in preprint servers. Much of the research effort has focused on the discovery of novel drug candidates or repurposing of existing drugs against COVID-19, and many such projects have been either exclusively computational or computer-aided experimental studies. Herein, we provide an expert overview of the key computational methods and their applications for the discovery of COVID-19 small-molecule therapeutics that have been reported in the research literature. We further outline that, after the first year the COVID-19 pandemic, it appears that drug repurposing has not produced rapid and global solutions. However, several known drugs have been used in the clinic to cure COVID-19 patients, and a few repurposed drugs continue to be considered in clinical trials, along with several novel clinical candidates. We posit that truly impactful computational tools must deliver actionable, experimentally testable hypotheses enabling the discovery of novel drugs and drug combinations, and that open science and rapid sharing of research results are critical to accelerate the development of novel, much needed therapeutics for COVID-19.
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Affiliation(s)
- Eugene N. Muratov
- UNC Eshelman School of Pharmacy, University of North CarolinaChapel HillNCUSA
| | - Rommie Amaro
- University of California in San DiegoSan DiegoCAUSA
| | | | | | - Sean Ekins
- Collaborations PharmaceuticalsRaleighNCUSA
| | - Denis Fourches
- Department of Chemistry, North Carolina State UniversityRaleighNCUSA
| | - Olexandr Isayev
- Department of Chemistry, Carnegie Melon UniversityPittsburghPAUSA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook UniversityStony BrookNYUSA
| | | | - Kenneth M. Merz
- Department of Chemistry, Michigan State UniversityEast LansingMIUSA
| | - Tudor I. Oprea
- Department of Internal Medicine and UNM Comprehensive Cancer Center, University of New Mexico, AlbuquerqueNMUSA
- Department of Rheumatology and Inflammation Research, Gothenburg UniversitySweden
- Novo Nordisk Foundation Center for Protein Research, University of CopenhagenDenmark
| | | | - Gisbert Schneider
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of TechnologyZurichSwitzerland
| | | | - Alexandre Varnek
- Department of Chemistry, University of StrasbourgStrasbourgFrance
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido UniversitySapporoJapan
| | - David A. Winkler
- Monash Institute of Pharmaceutical Sciences, Monash UniversityMelbourneVICAustralia
- School of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe UniversityBundooraAustralia
- School of Pharmacy, University of NottinghamNottinghamUK
| | | | - Artem Cherkasov
- Vancouver Prostate Centre, University of British ColumbiaVancouverBCCanada
| | - Alexander Tropsha
- UNC Eshelman School of Pharmacy, University of North CarolinaChapel HillNCUSA
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499
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Hepatitis C Virus Protease Inhibitors Show Differential Efficacy and Interactions with Remdesivir for Treatment of SARS-CoV-2 In Vitro. Antimicrob Agents Chemother 2021; 65:e0268020. [PMID: 34097489 PMCID: PMC8370243 DOI: 10.1128/aac.02680-20] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Antivirals targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could improve treatment of COVID-19. We evaluated the efficacy of clinically relevant hepatitis C virus (HCV) NS3 protease inhibitors (PIs) against SARS-CoV-2 and their interactions with remdesivir, the only direct-acting antiviral approved for COVID-19 treatment. HCV PIs showed differential potency in short-term treatment assays based on the detection of SARS-CoV-2 spike protein in Vero E6 cells. Linear PIs boceprevir, telaprevir, and narlaprevir had 50% effective concentrations (EC50) of ∼40 μM. Among the macrocyclic PIs, simeprevir had the highest (EC50, 15 μM) and glecaprevir the lowest (EC50, >178 μM) potency, with paritaprevir, grazoprevir, voxilaprevir, vaniprevir, danoprevir, and deldeprevir in between. Acyclic PIs asunaprevir and faldaprevir had EC50s of 72 and 23 μM, respectively. ACH-806, inhibiting the HCV NS4A protease cofactor, had an EC50 of 46 μM. Similar and slightly increased PI potencies were found in human hepatoma Huh7.5 cells and human lung carcinoma A549-hACE2 cells, respectively. Selectivity indexes based on antiviral and cell viability assays were highest for linear PIs. In short-term treatments, combination of macrocyclic but not linear PIs with remdesivir showed synergism in Vero E6 and A549-hACE2 cells. Longer-term treatment of infected Vero E6 and A549-hACE2 cells with 1-fold EC50 PI revealed minor differences in the barrier to SARS-CoV-2 escape. Viral suppression was achieved with 3- to 8-fold EC50 boceprevir or 1-fold EC50 simeprevir or grazoprevir, but not boceprevir, in combination with 0.4- to 0.8-fold EC50 remdesivir; these concentrations did not lead to viral suppression in single treatments. This study could inform the development and application of protease inhibitors for optimized antiviral treatments of COVID-19.
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500
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Cheng L, Zhang X, Chen Y, Wang D, Zhang D, Yan S, Wang H, Xiao M, Liang T, Li H, Xu M, Hou X, Dai J, Wu X, Li M, Lu M, Wu D, Tian R, Zhao J, Zhang Y, Cao W, Wang J, Yan X, Zhou X, Liu Z, Xu Y, He F, Li Y, Yu X, Zhang S. Dynamic landscape mapping of humoral immunity to SARS-CoV-2 identifies non-structural protein antibodies associated with the survival of critical COVID-19 patients. Signal Transduct Target Ther 2021; 6:304. [PMID: 34404759 PMCID: PMC8368053 DOI: 10.1038/s41392-021-00718-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 07/19/2021] [Accepted: 08/01/2021] [Indexed: 12/12/2022] Open
Abstract
A comprehensive analysis of the humoral immune response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential in understanding COVID-19 pathogenesis and developing antibody-based diagnostics and therapy. In this work, we performed a longitudinal analysis of antibody responses to SARS-CoV-2 proteins in 104 serum samples from 49 critical COVID-19 patients using a peptide-based SARS-CoV-2 proteome microarray. Our data show that the binding epitopes of IgM and IgG antibodies differ across SARS-CoV-2 proteins and even within the same protein. Moreover, most IgM and IgG epitopes are located within nonstructural proteins (nsps), which are critical in inactivating the host's innate immune response and enabling SARS-CoV-2 replication, transcription, and polyprotein processing. IgM antibodies are associated with a good prognosis and target nsp3 and nsp5 proteases, whereas IgG antibodies are associated with high mortality and target structural proteins (Nucleocapsid, Spike, ORF3a). The epitopes targeted by antibodies in patients with a high mortality rate were further validated using an independent serum cohort (n = 56) and using global correlation mapping analysis with the clinical variables that are associated with COVID-19 severity. Our data provide fundamental insight into humoral immunity during SARS-CoV-2 infection. SARS-CoV-2 immunogenic epitopes identified in this work could also help direct antibody-based COVID-19 treatment and triage patients.
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Affiliation(s)
- Linlin Cheng
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiaomei Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Yu Chen
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Dan Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Dong Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Songxin Yan
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hongye Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Meng Xiao
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Te Liang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Haolong Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Meng Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Xin Hou
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jiayu Dai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Xian Wu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Mingyuan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Minya Lu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Dong Wu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Ran Tian
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jing Zhao
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yan Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Wei Cao
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jinglan Wang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiaowei Yan
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiang Zhou
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Zhengyin Liu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China.
| | - Yongzhe Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China.
| | - Shuyang Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
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