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Berta B, Tordai H, Lukács GL, Papp B, Enyedi Á, Padányi R, Hegedűs T. SARS-CoV-2 envelope protein alters calcium signaling via SERCA interactions. Sci Rep 2024; 14:21200. [PMID: 39261533 PMCID: PMC11391011 DOI: 10.1038/s41598-024-71144-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 08/26/2024] [Indexed: 09/13/2024] Open
Abstract
The clinical management of severe COVID-19 cases is not yet well resolved. Therefore, it is important to identify and characterize cell signaling pathways involved in virus pathogenesis that can be targeted therapeutically. Envelope (E) protein is a structural protein of the virus, which is known to be highly expressed in the infected host cell and is a key virulence factor; however, its role is poorly characterized. The E protein is a single-pass transmembrane protein that can assemble into a pentamer forming a viroporin, perturbing Ca2+ homeostasis. Because it is structurally similar to regulins such as, for example, phospholamban, that regulate the sarco/endoplasmic reticulum calcium ATPases (SERCA), we investigated whether the SARS-CoV-2 E protein affects the SERCA system as an exoregulin. Using FRET experiments we demonstrate that E protein can form oligomers with regulins, and thus can alter the monomer/multimer regulin ratio and consequently influence their interactions with SERCAs. We also confirm that a direct interaction between E protein and SERCA2b results in a decrease in SERCA-mediated ER Ca2+ reload. Structural modeling of the complexes indicates an overlapping interaction site for E protein and endogenous regulins. Our results reveal novel links in the host-virus interaction network that play an important role in viral pathogenesis and may provide a new therapeutic target for managing severe inflammatory responses induced by SARS-CoV-2.
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Affiliation(s)
- Blanka Berta
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Hedvig Tordai
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Gergely L Lukács
- Department of Physiology, McGill University, Montréal, QC, Canada
| | - Béla Papp
- INSERM UMR U976, Hôpital Saint-Louis, Paris, France
- Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Université de Paris, Paris, France
- CEA, DRF-Institut Francois Jacob, Department of Hemato-Immunology Research, Hôpital Saint-Louis, Paris, France
| | - Ágnes Enyedi
- Department of Transfusiology, Semmelweis University, Budapest, Hungary
| | - Rita Padányi
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
| | - Tamás Hegedűs
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
- HUN-REN-SU Biophysical Virology Research Group, Eötvös Loránd Research Network, Budapest, Hungary.
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Yadav AK, Basavegowda N, Shirin S, Raju S, Sekar R, Somu P, Uthappa UT, Abdi G. Emerging Trends of Gold Nanostructures for Point-of-Care Biosensor-Based Detection of COVID-19. Mol Biotechnol 2024:10.1007/s12033-024-01157-y. [PMID: 38703305 DOI: 10.1007/s12033-024-01157-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/26/2024] [Indexed: 05/06/2024]
Abstract
In 2019, a worldwide pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged. SARS-CoV-2 is the deadly microorganism responsible for coronavirus disease 2019 (COVID-19), which has caused millions of deaths and irreversible health problems worldwide. To restrict the spread of SARS-CoV-2, accurate detection of COVID-19 is essential for the identification and control of infected cases. Although recent detection technologies such as the real-time polymerase chain reaction delivers an accurate diagnosis of SARS-CoV-2, they require a long processing duration, expensive equipment, and highly skilled personnel. Therefore, a rapid diagnosis with accurate results is indispensable to offer effective disease suppression. Nanotechnology is the backbone of current science and technology developments including nanoparticles (NPs) that can biomimic the corona and develop deep interaction with its proteins because of their identical structures on the nanoscale. Various NPs have been extensively applied in numerous medical applications, including implants, biosensors, drug delivery, and bioimaging. Among them, point-of-care biosensors mediated with gold nanoparticles (GNPSs) have received great attention due to their accurate sensing characteristics, which are widely used in the detection of amino acids, enzymes, DNA, and RNA in samples. GNPS have reconstructed the biomedical application of biosensors because of its outstanding physicochemical characteristics. This review provides an overview of emerging trends in GNP-mediated point-of-care biosensor strategies for diagnosing various mutated forms of human coronaviruses that incorporate different transducers and biomarkers. The review also specifically highlights trends in gold nanobiosensors for coronavirus detection, ranging from the initial COVID-19 outbreak to its subsequent evolution into a pandemic.
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Affiliation(s)
- Akhilesh Kumar Yadav
- Department of Environmental Engineering and Management, Chaoyang University of Technology, Taichung, 413310, Taiwan
- Department of Mining Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Nagaraj Basavegowda
- Department of Biotechnology, Yeungnam University, Gyeongsan, 38451, Republic of Korea
| | - Saba Shirin
- Department of Mining Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
- Department of Environmental Science, School of Vocational Studies and Applied Sciences, Gautam Buddha University, Greater Noida, 201312, India
| | - Shiji Raju
- Bioengineering and Nano Medicine Group, Faculty of Medicine and Health Technology, Tampere University, 33720, Tampere, Finland
| | - Rajkumar Sekar
- Department of Chemistry, Karpaga Vinayaga College of Engineering and Technology, GST Road, Chinna Kolambakkam, Chengalpattu, Tamil Nadu, 603308, India
| | - Prathap Somu
- Department of Biotechnology and Chemical Engineering, School of Civil, Biotechnology and Chemical Engineering, Manipal University Jaipur, Dehmi Kalan, Off. Jaipur-Ajmeer Expressway, Jaipur, Rajasthan, 303007, India.
| | - U T Uthappa
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518055, China
- Department of Bioengineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, 602105, India
| | - Gholamreza Abdi
- Department of Biotechnology, Persian Gulf Research Institute, Persian Gulf University, Bushehr, 75169, Iran.
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3
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Pearson GJ, Mears HV, Broncel M, Snijders AP, Bauer DLV, Carlton JG. ER-export and ARFRP1/AP-1-dependent delivery of SARS-CoV-2 Envelope to lysosomes controls late stages of viral replication. SCIENCE ADVANCES 2024; 10:eadl5012. [PMID: 38569033 PMCID: PMC10990277 DOI: 10.1126/sciadv.adl5012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
The β-coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the global COVID-19 pandemic. Coronaviral Envelope (E) proteins are pentameric viroporins that play essential roles in assembly, release, and pathogenesis. We developed a nondisruptive tagging strategy for SARS-CoV-2 E and find that, at steady state, it localizes to the Golgi and to lysosomes. We identify sequences in E, conserved across Coronaviridae, responsible for endoplasmic reticulum-to-Golgi export, and relate this activity to interaction with COP-II via SEC24. Using proximity biotinylation, we identify an ADP ribosylation factor 1/adaptor protein-1 (ARFRP1/AP-1)-dependent pathway allowing Golgi-to-lysosome trafficking of E. We identify sequences in E that bind AP-1, are conserved across β-coronaviruses, and allow E to be trafficked from Golgi to lysosomes. We show that E acts to deacidify lysosomes and, by developing a trans-complementation assay for SARS-CoV-2 structural proteins, that lysosomal delivery of E and its viroporin activity is necessary for efficient viral replication and release.
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Affiliation(s)
- Guy J. Pearson
- Organelle Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- School of Cancer & Pharmaceutical Sciences, King’s College London, Great Maze Pond, London SE1 1UL, UK
| | - Harriet V. Mears
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Malgorzata Broncel
- Proteomic Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P. Snijders
- Proteomic Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David L. V. Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jeremy G. Carlton
- Organelle Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- School of Cancer & Pharmaceutical Sciences, King’s College London, Great Maze Pond, London SE1 1UL, UK
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4
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Cubisino SAM, Milenkovic S, Conti-Nibali S, Musso N, Bonacci P, De Pinto V, Ceccarelli M, Reina S. Electrophysiological properties and structural prediction of the SARS-CoV-2 viroprotein E. Front Mol Biosci 2024; 11:1334819. [PMID: 38606285 PMCID: PMC11007222 DOI: 10.3389/fmolb.2024.1334819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/15/2024] [Indexed: 04/13/2024] Open
Abstract
COVID-19, the infectious disease caused by the most recently discovered coronavirus SARS- CoV-2, has caused millions of sick people and thousands of deaths all over the world. The viral positive-sense single-stranded RNA encodes 31 proteins among which the spike (S) is undoubtedly the best known. Recently, protein E has been reputed as a potential pharmacological target as well. It is essential for the assembly and release of the virions in the cell. Literature describes protein E as a voltage-dependent channel with preference towards monovalent cations whose intracellular expression, though, alters Ca2+ homeostasis and promotes the activation of the proinflammatory cascades. Due to the extremely high sequence identity of SARS-CoV-2 protein E (E-2) with the previously characterized E-1 (i.e., protein E from SARS-CoV) many data obtained for E-1 were simply adapted to the other. Recent solid state NMR structure revealed that the transmembrane domain (TMD) of E-2 self-assembles into a homo-pentamer, albeit the oligomeric status has not been validated with the full-length protein. Prompted by the lack of a common agreement on the proper structural and functional features of E-2, we investigated the specific mechanism/s of pore-gating and the detailed molecular structure of the most cryptic protein of SARS-CoV-2 by means of MD simulations of the E-2 structure and by expressing, refolding and analyzing the electrophysiological activity of the transmembrane moiety of the protein E-2, in its full length. Our results show a clear agreement between experimental and predictive studies and foresee a mechanism of activity based on Ca2+ affinity.
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Affiliation(s)
| | | | - Stefano Conti-Nibali
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Nicolò Musso
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Paolo Bonacci
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- We.MitoBiotech S.R.L, Catania, Italy
| | | | - Simona Reina
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- We.MitoBiotech S.R.L, Catania, Italy
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5
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Xu Z, Wang H, Jiang S, Teng J, Zhou D, Chen Z, Wen C, Xu Z. Brain Pathology in COVID-19: Clinical Manifestations and Potential Mechanisms. Neurosci Bull 2024; 40:383-400. [PMID: 37715924 PMCID: PMC10912108 DOI: 10.1007/s12264-023-01110-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/25/2023] [Indexed: 09/18/2023] Open
Abstract
Neurological manifestations of coronavirus disease 2019 (COVID-19) are less noticeable than the respiratory symptoms, but they may be associated with disability and mortality in COVID-19. Even though Omicron caused less severe disease than Delta, the incidence of neurological manifestations is similar. More than 30% of patients experienced "brain fog", delirium, stroke, and cognitive impairment, and over half of these patients presented abnormal neuroimaging outcomes. In this review, we summarize current advances in the clinical findings of neurological manifestations in COVID-19 patients and compare them with those in patients with influenza infection. We also illustrate the structure and cellular invasion mechanisms of SARS-CoV-2 and describe the pathway for central SARS-CoV-2 invasion. In addition, we discuss direct damage and other pathological conditions caused by SARS-CoV-2, such as an aberrant interferon response, cytokine storm, lymphopenia, and hypercoagulation, to provide treatment ideas. This review may offer new insights into preventing or treating brain damage in COVID-19.
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Affiliation(s)
- Zhixing Xu
- First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Hui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Siya Jiang
- Second School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jiao Teng
- Affiliated Lin'an People's Hospital of Hangzhou Medical College, First People's Hospital of Hangzhou Lin'an District, Lin'an, Hangzhou, 311300, China
| | - Dongxu Zhou
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Zhong Chen
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chengping Wen
- Laboratory of Rheumatology and Institute of TCM Clinical Basic Medicine, College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
| | - Zhenghao Xu
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
- Laboratory of Rheumatology and Institute of TCM Clinical Basic Medicine, College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
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6
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Liao Y, Wang H, Liao H, Sun Y, Tan L, Song C, Qiu X, Ding C. Classification, replication, and transcription of Nidovirales. Front Microbiol 2024; 14:1291761. [PMID: 38328580 PMCID: PMC10847374 DOI: 10.3389/fmicb.2023.1291761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry,as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.
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Affiliation(s)
- Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huiyu Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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7
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Zhang R, Qin H, Prasad R, Fu R, Zhou HX, Cross TA. Dimeric Transmembrane Structure of the SARS-CoV-2 E Protein. Commun Biol 2023; 6:1109. [PMID: 37914906 PMCID: PMC10620413 DOI: 10.1038/s42003-023-05490-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023] Open
Abstract
The SARS-CoV-2 E protein is a transmembrane (TM) protein with its N-terminus exposed on the external surface of the virus. At debate is its oligomeric state, let alone its function. Here, the TM structure of the E protein is characterized by oriented sample and magic angle spinning solid-state NMR in lipid bilayers and refined by molecular dynamics simulations. This protein was previously found to be a pentamer, with a hydrophobic pore that appears to function as an ion channel. We identify only a front-to-front, symmetric helix-helix interface, leading to a dimeric structure that does not support channel activity. The two helices have a tilt angle of only 6°, resulting in an extended interface dominated by Leu and Val sidechains. While residues Val14-Thr35 are almost all buried in the hydrophobic region of the membrane, Asn15 lines a water-filled pocket that potentially serves as a drug-binding site. The E and other viral proteins may adopt different oligomeric states to help perform multiple functions.
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Affiliation(s)
- Rongfu Zhang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA
- National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA
| | - Huajun Qin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA.
- Department of Physics, University of Illinois Chicago, Chicago, IL, 60607, USA.
| | - Timothy A Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA.
- National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA.
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA.
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8
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Medeiros-Silva J, Dregni AJ, Somberg NH, Duan P, Hong M. Atomic structure of the open SARS-CoV-2 E viroporin. SCIENCE ADVANCES 2023; 9:eadi9007. [PMID: 37831764 PMCID: PMC10575589 DOI: 10.1126/sciadv.adi9007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/08/2023] [Indexed: 10/15/2023]
Abstract
The envelope (E) protein of the SARS-CoV-2 virus forms cation-conducting channels in the endoplasmic reticulum Golgi intermediate compartment (ERGIC) of infected cells. The calcium channel activity of E is associated with the inflammatory responses of COVID-19. Using solid-state NMR (ssNMR) spectroscopy, we have determined the open-state structure of E's transmembrane domain (ETM) in lipid bilayers. Compared to the closed state, open ETM has an expansive water-filled amino-terminal chamber capped by key glutamate and threonine residues, a loose phenylalanine aromatic belt in the middle, and a constricted polar carboxyl-terminal pore filled with an arginine and a threonine residue. This structure gives insights into how protons and calcium ions are selected by ETM and how they permeate across the hydrophobic gate of this viroporin.
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Affiliation(s)
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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9
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Javorsky A, Humbert PO, Kvansakul M. Viral manipulation of cell polarity signalling. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119536. [PMID: 37437846 DOI: 10.1016/j.bbamcr.2023.119536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/24/2023] [Accepted: 07/04/2023] [Indexed: 07/14/2023]
Abstract
Cell polarity refers to the asymmetric distribution of biomacromolecules that enable the correct orientation of a cell in a particular direction. It is thus an essential component for appropriate tissue development and function. Viral infections can lead to dysregulation of polarity. This is associated with a poor prognosis due to viral interference with core cell polarity regulatory scaffolding proteins that often feature PDZ (PSD-95, DLG, and ZO-1) domains including Scrib, Dlg, Pals1, PatJ, Par3 and Par6. PDZ domains are also promiscuous, binding to several different partners through their C-terminal region which contain PDZ-binding motifs (PBM). Numerous viruses encode viral effector proteins that target cell polarity regulators for their benefit and include papillomaviruses, flaviviruses and coronaviruses. A better understanding of the mechanisms of action utilised by viral effector proteins to subvert host cell polarity sigalling will provide avenues for future therapeutic intervention, while at the same time enhance our understanding of cell polarity regulation and its role tissue homeostasis.
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Affiliation(s)
- Airah Javorsky
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Patrick O Humbert
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia; Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria 3086, Australia; Department of Biochemistry & Pharmacology, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Marc Kvansakul
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia; Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria 3086, Australia.
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10
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Gullberg RC, Frydman J. Novel Mode of nanoLuciferase Packaging in SARS-CoV-2 Virions and VLPs Provides Versatile Reporters for Virus Production. Viruses 2023; 15:1335. [PMID: 37376634 DOI: 10.3390/v15061335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
SARS-CoV-2 is a positive-strand RNA virus in the Coronaviridae family that is responsible for morbidity and mortality worldwide. To better understand the molecular pathways leading to SARS-CoV-2 virus assembly, we examined a virus-like particle (VLP) system co-expressing all structural proteins together with an mRNA reporter encoding nanoLuciferase (herein nLuc). Surprisingly, the 19 kDa nLuc protein itself was encapsidated into VLPs, providing a better reporter than nLuc mRNA itself. Strikingly, infecting nLuc-expressing cells with the SARS-CoV-2, NL63 or OC43 coronaviruses yielded virions containing packaged nLuc that served to report viral production. In contrast, infection with the flaviviruses, dengue or Zika, did not lead to nLuc packaging and secretion. A panel of reporter protein variants revealed that the packaging is size-limited and requires cytoplasmic expression, indicating that the large virion of coronaviruses can encaspidate a small cytoplasmic reporter protein. Our findings open the way for powerful new approaches to measure coronavirus particle production, egress and viral entry mechanisms.
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Affiliation(s)
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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11
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Su W, Ju J, Gu M, Wang X, Liu S, Yu J, Mu D. SARS-CoV-2 envelope protein triggers depression-like behaviors and dysosmia via TLR2-mediated neuroinflammation in mice. J Neuroinflammation 2023; 20:110. [PMID: 37158916 PMCID: PMC10166055 DOI: 10.1186/s12974-023-02786-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/20/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Depression and dysosmia have been regarded as primary neurological symptoms in COVID-19 patients, the mechanism of which remains unclear. Current studies have demonstrated that the SARS-CoV-2 envelope (E) protein is a pro-inflammatory factor sensed by Toll-like receptor 2 (TLR2), suggesting the pathological feature of E protein is independent of viral infection. In this study, we aim to ascertain the role of E protein in depression, dysosmia and associated neuroinflammation in the central nervous system (CNS). METHODS Depression-like behaviors and olfactory function were observed in both female and male mice receiving intracisternal injection of E protein. Immunohistochemistry was applied in conjunction with RT-PCR to evaluate glial activation, blood-brain barrier status and mediators synthesis in the cortex, hippocampus and olfactory bulb. TLR2 was pharmacologically blocked to determine its role in E protein-related depression-like behaviors and dysosmia in mice. RESULTS Intracisternal injection of E protein evoked depression-like behaviors and dysosmia in both female and male mice. Immunohistochemistry suggested that the E protein upregulated IBA1 and GFAP in the cortex, hippocampus and olfactory bulb, while ZO-1 was downregulated. Moreover, IL-1β, TNF-α, IL-6, CCL2, MMP2 and CSF1 were upregulated in both cortex and hippocampus, whereas IL-1β, IL-6 and CCL2 were upregulated in the olfactory bulb. Furtherly, inhibiting microglia, rather than astrocytes, alleviated depression-like behaviors and dysosmia induced by E protein. Finally, RT-PCR and immunohistochemistry suggested that TLR2 was upregulated in the cortex, hippocampus and olfactory bulb, the blocking of which mitigated depression-like behaviors and dysosmia induced by E protein. CONCLUSIONS Our study demonstrates that envelope protein could directly induce depression-like behaviors, dysosmia, and obvious neuroinflammation in CNS. TLR2 mediated depression-like behaviors and dysosmia induced by envelope protein, which could serve as a promising therapeutic target for neurological manifestation in COVID-19 patients.
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Affiliation(s)
- Wenliang Su
- Department of Anesthesiology, Peking University First Hospital, Beijing, China
| | - Jiahang Ju
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, State Key Laboratory of Brain-Machine Intelligence, Zhejiang University, Hangzhou, 311121 China
| | - Minghui Gu
- Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Xinrui Wang
- Department of Pharmacy, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Shaozhuang Liu
- Department of Urology, Shengjing Hospital of China Medical University, Sanhao Street 36, Shenyang, 110004 Liaoning China
| | - Jiawen Yu
- Department of Anesthesiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dongliang Mu
- Department of Anesthesiology, Peking University First Hospital, Beijing, China
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12
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Zhang R, Qin H, Prasad R, Fu R, Zhou HX, Cross TA. Dimeric Transmembrane Structure of the SARS-CoV-2 E Protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539752. [PMID: 37214926 PMCID: PMC10197518 DOI: 10.1101/2023.05.07.539752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The SARS-CoV-2 E protein is a transmembrane (TM) protein with its N-terminus exposed on the external surface of the virus. Here, the TM structure of the E protein is characterized by oriented sample and magic angle spinning solid-state NMR in lipid bilayers and refined by molecular dynamics simulations. This protein has been found to be a pentamer, with a hydrophobic pore that appears to function as an ion channel. We identified only a symmetric helix-helix interface, leading to a dimeric structure that does not support channel activity. The two helices have a tilt angle of only 6°, resulting in an extended interface dominated by Leu and Val sidechains. While residues Val14-Thr35 are almost all buried in the hydrophobic region of the membrane, Asn15 lines a water-filled pocket that potentially serves as a drug-binding site. The E and other viral proteins may adopt different oligomeric states to help perform multiple functions.
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Affiliation(s)
- Rongfu Zhang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
- National High Magnetic Field Laboratory, Tallahassee, FL 32310
- Contributed equally to this work
| | - Huajun Qin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
- Contributed equally to this work
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL 32310
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607
- Department of Physics, University of Illinois Chicago, Chicago, IL 60607
| | - Timothy A. Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
- National High Magnetic Field Laboratory, Tallahassee, FL 32310
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
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13
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Baliova M, Jahodova I, Jursky F. A Significant Difference in Core PDZ Interactivity of SARS-CoV, SARS-CoV2 and MERS-CoV Protein E Peptide PDZ Motifs In Vitro. Protein J 2023:10.1007/s10930-023-10103-x. [PMID: 36932261 PMCID: PMC10023026 DOI: 10.1007/s10930-023-10103-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2023] [Indexed: 03/19/2023]
Abstract
Small structural E protein of coronaviruses uses its C-terminal PDZ motif to compromise the cellular PDZ interactome. In this work we compared core PDZ interactivity of small (seven amino acids) peptide PDZ motifs, originating from the envelope proteins of recently transmitted coronaviruses SARS-CoV, SARS-CoV2, and MERS-CoV. As the interaction targets we used 23 domains of the largest PDZ proteins MUPP1/MPDZ and PATJ/INAD. Results revealed exceptional affinity and interaction promiscuity of MERS-CoV PDZ motif in vitro, suggesting an increased probability of potential PDZ targets in vivo. We hypothesize that together with its known ability to enter the cells from both apical and basolateral sites, this might further contribute to its elevated disruption of cellular PDZ pathways and higher virulence.
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Affiliation(s)
- Martina Baliova
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska Cesta 21, 845 51 Bratislava, Slovakia
| | - Iveta Jahodova
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska Cesta 21, 845 51 Bratislava, Slovakia
| | - Frantisek Jursky
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska Cesta 21, 845 51 Bratislava, Slovakia
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14
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Khalid T, Hasan A, Fatima JE, Faridi SA, Khan AF, Mir SS. Therapeutic role of mTOR inhibitors in control of SARS-CoV-2 viral replication. Mol Biol Rep 2023; 50:2701-2711. [PMID: 36538171 PMCID: PMC9764303 DOI: 10.1007/s11033-022-08188-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
By the end of 2019, COVID-19 was reported in Wuhan city of China, and through human-human transmission, this virus spread worldwide and became a pandemic. Initial symptoms of the disease include fever, cough, loss of smell, taste, and shortness of breath, but a decrease in the oxygen levels in the body leads, and pneumonia may ultimately lead to the patient's death. However, the symptoms vary from patient to patient. To understand COVID-19 disease pathogenesis, researchers have tried to understand the cellular pathways that could be targeted to suppress viral replication. Thus, this article reviews the markers that could be targeted to inhibit viral replication by inhibiting the translational initiation complex/regulatory kinases and upregulating host autophagic flux that may lead to a reduction in the viral load. The article also highlights that mTOR inhibitors may act as potential inhibitors of viral replication. mTOR inhibitors such as metformin may inhibit the interaction of SARS-CoV-2 Nsp's and ORFs with mTORC1, LARP1, and 4E-BP. They may also increase autophagic flux by decreasing protein degradation via inhibition of Skp2, further promoting viral cell death. These events result in cell cycle arrest at G1 by p27, ultimately causing cell death.
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Affiliation(s)
- Tuba Khalid
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, 226026, Lucknow, India
| | - Adria Hasan
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, 226026, Lucknow, India
- Molecular Cell Biology Laboratory, Integral Information and Research Centre-4 (IIRC-4), Integral University, Kursi Road, 226026, Lucknow, India
| | - Jamal E Fatima
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, 226026, Lucknow, India
| | - Soban Ahmad Faridi
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, 226026, Lucknow, India
| | - Ahamad Faiz Khan
- Department of Bioengineering, Faculty of Engineering, Integral University, Kursi Road, 226026, Lucknow, India
| | - Snober S Mir
- Molecular Cell Biology Laboratory, Integral Information and Research Centre-4 (IIRC-4), Integral University, Kursi Road, 226026, Lucknow, India.
- Department of Biosciences, Faculty of Science, Integral University, Kursi Road, 226026, Lucknow, Uttar Pradesh, India.
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15
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Zhou S, Lv P, Li M, Chen Z, Xin H, Reilly S, Zhang X. SARS-CoV-2 E protein: Pathogenesis and potential therapeutic development. Biomed Pharmacother 2023; 159:114242. [PMID: 36652729 PMCID: PMC9832061 DOI: 10.1016/j.biopha.2023.114242] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating global pandemic, which has seriously affected human health worldwide. The discovery of therapeutic agents is extremely urgent, and the viral structural proteins are particularly important as potential drug targets. SARS-CoV-2 envelope (E) protein is one of the main structural proteins of the virus, which is involved in multiple processes of the virus life cycle and is directly related to pathogenesis process. In this review, we present the amino acid sequence of the E protein and compare it with other two human coronaviruses. We then explored the role of E protein in the viral life cycle and discussed the pathogenic mechanisms that E protein may be involved in. Next, we summarize the potential drugs against E protein discovered in the current studies. Finally, we described the possible effects of E protein mutation on virus and host. This established a knowledge system of E protein to date, aiming to provide theoretical insights for mitigating the current COVID-19 pandemic and potential future coronavirus outbreaks.
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Affiliation(s)
- Shilin Zhou
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Panpan Lv
- Clinical Laboratory, Minhang Hospital, Fudan University, Shanghai, China.
| | - Mingxue Li
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Zihui Chen
- School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Hong Xin
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Svetlana Reilly
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| | - Xuemei Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
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16
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Waisner H, Grieshaber B, Saud R, Henke W, Stephens EB, Kalamvoki M. SARS-CoV-2 Harnesses Host Translational Shutoff and Autophagy To Optimize Virus Yields: the Role of the Envelope (E) Protein. Microbiol Spectr 2023; 11:e0370722. [PMID: 36622177 PMCID: PMC9927098 DOI: 10.1128/spectrum.03707-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/07/2022] [Indexed: 01/10/2023] Open
Abstract
The SARS-CoV-2 virion is composed of four structural proteins: spike (S), nucleocapsid (N), membrane (M), and envelope (E). E spans the membrane a single time and is the smallest, yet most enigmatic of the structural proteins. E is conserved among coronaviruses and has an essential role in virus-mediated pathogenesis. We found that ectopic expression of E had deleterious effects on the host cell as it activated stress responses, leading to LC3 lipidation and phosphorylation of the translation initiation factor eIF2α that resulted in host translational shutoff. During infection E is highly expressed, although only a small fraction is incorporated into virions, suggesting that E activity is regulated and harnessed by the virus to its benefit. Consistently, we found that proteins from heterologous viruses, such as the γ1 34.5 protein of herpes simplex virus 1, prevented deleterious effects of E on the host cell and allowed for E protein accumulation. This observation prompted us to investigate whether other SARS-CoV-2 structural proteins regulate E. We found that the N and M proteins enabled E protein accumulation, whereas S did not. While γ1 34.5 protein prevented deleterious effects of E on the host cells, it had a negative effect on SARS-CoV-2 replication. The negative effect of γ1 34.5 was most likely associated with failure of SARS-CoV-2 to divert the translational machinery and with deregulation of autophagy. Overall, our data suggest that SARS-CoV-2 causes stress responses and subjugates these pathways, including host protein synthesis (phosphorylated eIF2α) and autophagy, to support optimal virus replication. IMPORTANCE In late 2019, a new β-coronavirus, SARS-CoV-2, entered the human population causing a pandemic that has resulted in over 6 million deaths worldwide. Although closely related to SARS-CoV, the mechanisms of SARS-CoV-2 pathogenesis are not fully understood. We found that ectopic expression of the SARS-CoV-2 E protein had detrimental effects on the host cell, causing metabolic alterations, including shutoff of protein synthesis and mobilization of cellular resources through autophagy activation. Coexpression of E with viral proteins known to subvert host antiviral responses such as autophagy and translational inhibition, either from SARS-CoV-2 or from heterologous viruses, increased cell survival and E protein accumulation. However, such factors were found to negatively impact SARS-CoV-2 infection, as autophagy contributes to formation of viral membrane factories and translational control offers an advantage for viral gene expression. Overall, SARS-CoV-2 has evolved mechanisms to harness host functions that are essential for virus replication.
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Affiliation(s)
- Hope Waisner
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Brandon Grieshaber
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Rabina Saud
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Wyatt Henke
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Edward B. Stephens
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Maria Kalamvoki
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
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17
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Nambiar S, Mohan M, Rosin Jose A. Voltammetric Sensors: A Versatile Tool in COVID‐19 Diagnosis and Prognosis. ChemistrySelect 2023. [DOI: 10.1002/slct.202204506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Souparnika Nambiar
- PG and Research Dept. of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala INDIA 682013
| | - Malavika Mohan
- PG and Research Dept. of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala INDIA 682013
| | - Ammu Rosin Jose
- PG and Research Dept. of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala INDIA 682013
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18
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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Choudhury PP, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palu G, Abd El-Aziz TM, Barh D, Uhal BD, Adadi P, Takayama K, Bazan NG, Tambuwala M, Sherchan SP, Lal A, Chauhan G, Baetas-da-Cruz W, Uversky VN. Non-uniform aspects of the SARS-CoV-2 intraspecies evolution reopen question of its origin. Int J Biol Macromol 2022; 222:972-993. [PMID: 36174872 PMCID: PMC9511875 DOI: 10.1016/j.ijbiomac.2022.09.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/04/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022]
Abstract
Several hypotheses have been presented on the origin of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from its identification as the agent causing the current coronavirus disease 19 (COVID-19) pandemic. So far, no solid evidence has been found to support any hypothesis on the origin of this virus, and the issue continue to resurface over and over again. Here we have unfolded a pattern of distribution of several mutations in the SARS-CoV-2 proteins in 24 geo-locations across different continents. The results showed an evenly uneven distribution of the unique protein variants, distinct mutations, unique frequency of common conserved residues, and mutational residues across these 24 geo-locations. Furthermore, ample mutations were identified in the evolutionarily conserved invariant regions in the SARS-CoV-2 proteins across almost all geo-locations studied. This pattern of mutations potentially breaches the law of evolutionary conserved functional units of the beta-coronavirus genus. These mutations may lead to several novel SARS-CoV-2 variants with a high degree of transmissibility and virulence. A thorough investigation on the origin and characteristics of SARS-CoV-2 needs to be conducted in the interest of science and for the preparation of meeting the challenges of potential future pandemics.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Bhulabhai Desai Road, Mumbai 400026, India
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab 21934, Alexandria, Egypt.
| | | | - Pabitra Pal Choudhury
- Indian Statistical Institute, Applied Statistics Unit, 203 B T Road, Kolkata 700108, India
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Cat'olica de Valencia San Vicente Martir, c/Guillem de Castro, 94, 46001 Valencia, Valencia, Spain.
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Faculty of Pharmacy, Irbid 566, Jordan.
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy.
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India; Departamento de Geńetica, Ecologia e Evolucao, Instituto de Cíencias Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 6068507, Japan.
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA 70112, USA.
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | - Samendra P Sherchan
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK.
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, Nuevo León, Mexico.
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Vladimir N Uversky
- Department of Molecular Medicineand USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia.
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19
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Resch MD, Wen K, Mazboudi R, Mulhall Maasz H, Persaud M, Garvey K, Gallardo L, Gottlieb P, Alimova A, Khayat R, Morales J, Bielefeldt-Ohmann H, Bowen RA, Galarza JM. Immunogenicity and Efficacy of Monovalent and Bivalent Formulations of a Virus-Like Particle Vaccine against SARS-CoV-2. Vaccines (Basel) 2022; 10:1997. [PMID: 36560407 PMCID: PMC9782034 DOI: 10.3390/vaccines10121997] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
Virus-like particles (VLPs) offer great potential as a safe and effective vaccine platform against SARS-CoV-2, the causative agent of COVID-19. Here, we show that SARS-CoV-2 VLPs can be generated by expression of the four viral structural proteins in a mammalian expression system. Immunization of mice with a monovalent VLP vaccine elicited a potent humoral response, showing neutralizing activity against multiple variants of SARS-CoV-2. Subsequent immunogenicity and efficacy studies were performed in the Golden Syrian hamster model, which closely resembles the pathology and progression of COVID-19 in humans. Hamsters immunized with a bivalent VLP vaccine were significantly protected from infection with the Beta or Delta variant of SARS-CoV-2. Vaccinated hamsters showed reduced viral load, shedding, replication, and pathology in the respiratory tract. Immunized hamsters also showed variable levels of cross-neutralizing activity against the Omicron variant. Overall, the VLP vaccine elicited robust protective efficacy against SARS-CoV-2. These promising results warrant further study of multivalent VLP vaccines in Phase I clinical trials in humans.
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Affiliation(s)
| | - Ke Wen
- TechnoVax, Inc., 6 Westchester Plaza, Elmsford, NY 10523, USA
| | - Ryan Mazboudi
- TechnoVax, Inc., 6 Westchester Plaza, Elmsford, NY 10523, USA
| | | | - Mirjana Persaud
- TechnoVax, Inc., 6 Westchester Plaza, Elmsford, NY 10523, USA
| | - Kaitlyn Garvey
- TechnoVax, Inc., 6 Westchester Plaza, Elmsford, NY 10523, USA
| | - Leslie Gallardo
- TechnoVax, Inc., 6 Westchester Plaza, Elmsford, NY 10523, USA
| | - Paul Gottlieb
- CUNY School of Medicine, The City College of New York, New York, NY 10031, USA
| | - Aleksandra Alimova
- CUNY School of Medicine, The City College of New York, New York, NY 10031, USA
| | - Reza Khayat
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| | - Jorge Morales
- Microscopy Facility, Division of Science, The City College of New York, New York, NY 10031, USA
| | - Helle Bielefeldt-Ohmann
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Jose M. Galarza
- TechnoVax, Inc., 6 Westchester Plaza, Elmsford, NY 10523, USA
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20
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Dey R, Samadder A, Nandi S. Exploring the Targets of Novel Corona Virus and Docking-based Screening of Potential Natural Inhibitors to Combat COVID-19. Curr Top Med Chem 2022; 22:2410-2434. [PMID: 36281864 DOI: 10.2174/1568026623666221020163831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/07/2022] [Accepted: 09/21/2022] [Indexed: 01/20/2023]
Abstract
There is a need to explore natural compounds against COVID-19 due to their multitargeted actions against various targets of nCoV. They act on multiple sites rather than single targets against several diseases. Thus, there is a possibility that natural resources can be repurposed to combat COVID-19. However, the biochemical mechanisms of these inhibitors were not known. To reveal the mode of anti-nCoV action, structure-based docking plays a major role. The present study is an attempt to explore various potential targets of SARS-CoV-2 and the structure-based screening of various potential natural inhibitors to combat the novel coronavirus.
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Affiliation(s)
- Rishita Dey
- Department of Zoology, Cytogenetics and Molecular Biology Lab., University of Kalyani, Kalyani, Nadia, 741235, India.,Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur, 244713, India
| | - Asmita Samadder
- Department of Zoology, Cytogenetics and Molecular Biology Lab., University of Kalyani, Kalyani, Nadia, 741235, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur, 244713, India
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21
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An integrated computational approach towards the screening of active plant metabolites as potential inhibitors of SARS-CoV-2: an overview. Struct Chem 2022; 34:1073-1104. [PMID: 36212707 PMCID: PMC9526463 DOI: 10.1007/s11224-022-02066-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022]
Abstract
COVID-19 and its causative organism SARS-CoV-2 paralyzed the world and was designated a pandemic by the World Health Organization in March 2020. The worldwide health system is trying to discover an effective therapeutic measure since no clinically authorized medications are present. Screening of plant-derived pharmaceuticals may be a viable technique to fight COVID-19 in this vital situation. This review discusses the potential application of in silico approaches in developing new therapeutic molecules related to preventing SARS-CoV-2 infection. Also, it describes the binding affinity of various phytoconstituents with distinct SARS-CoV-2 target sites. In this perspective, an extensive literature survey was carried out to find the potential phytoconstituents to develop new therapeutic entities to treat COVID-19 in different online academic databases and books. Data retrieved from databases were analyzed and interpreted to conclude that many phytochemicals will bind with the 3-chymotrypsin-like (3CLpro) and papain-like proteases (PLpro), spike glycoprotein, ACE-2, NSP15-endoribonuclease, and E protein targets of SARS-CoV-2 main protease using in silico molecular docking approach. The present investigations reveal that phytoconstituents such as curcumin, apigenin, chrysophanol, and gingerol are significantly binding with spike glycoprotein; laurolistine, acetoside, etc. are bound with Mpro for anti-SARS-CoV-2 therapies. Using virtual applications of in silico studies, the current study constitutes a progressive data analysis on the mechanism of binding efficiency of distinct classes of plant metabolites against the active sites of SARS-CoV-2. Furthermore, the current review also demonstrates the fundamental necessity of the alternative and complementary medicine for future therapeutic uses of phytoconstituents by phytochemists in the fight against COVID-19.
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22
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Poniedziałek B, Hallmann E, Sikora D, Szymański K, Kondratiuk K, Żurawski J, Rzymski P, Brydak L. Relationship between Humoral Response in COVID-19 and Seasonal Influenza Vaccination. Vaccines (Basel) 2022; 10:1621. [PMID: 36298486 PMCID: PMC9610939 DOI: 10.3390/vaccines10101621] [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: 09/05/2022] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 11/17/2022] Open
Abstract
There is evidence that vaccination against seasonal influenza can improve innate immune responses to COVID-19 and decrease disease severity. However, less is known about whether it could also impact the humoral immunity in SARS-CoV-2 infected patients. The present study aimed to compare the SARS-CoV-2 specific humoral responses (IgG antibodies against nucleocapsid; anti-N, receptor binding domain; anti-RBD, subunit S2; anti-S2, and envelope protein; anti-E) between non-hospitalized, COVID-19 unvaccinated, and mild COVID-19 convalescent patients who were and were not vaccinated against influenza during the 2019/2020 epidemic season (n = 489 and n = 292, respectively). The influenza-vaccinated group had significantly higher frequency and titers of anti-N antibodies (75 vs. 66%; mean 559 vs. 520 U/mL) and anti-RBD antibodies (85 vs. 76%; mean 580 vs. 540 U/mL). The prevalence and concentrations of anti-S2 and anti-E antibodies did not differ between groups (40-43%; mean 370-375 U/mL and 1.4-1.7%; mean 261-294 U/mL) and were significantly lower compared to those of anti-RBD and anti-N. In both groups, age, comorbidities, and gender did not affect the prevalence and concentrations of studied antibodies. The results indicate that influenza vaccination can improve serum antibody levels produced in response to SARS-CoV-2 infection.
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Affiliation(s)
- Barbara Poniedziałek
- Department of Environmental Medicine, Poznań University of Medical Sciences, 60-806 Poznan, Poland
| | - Ewelina Hallmann
- Department of Influenza Research, National Influenza Center at the National Institute of Public Health NIH—National Research Institute in Warsaw, Chocimska St. 24, 00-791 Warsaw, Poland
| | - Dominika Sikora
- Department of Environmental Medicine, Poznań University of Medical Sciences, 60-806 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, Fredry St. 10, 61-701 Poznan, Poland
| | - Karol Szymański
- Department of Influenza Research, National Influenza Center at the National Institute of Public Health NIH—National Research Institute in Warsaw, Chocimska St. 24, 00-791 Warsaw, Poland
| | - Katarzyna Kondratiuk
- Department of Influenza Research, National Influenza Center at the National Institute of Public Health NIH—National Research Institute in Warsaw, Chocimska St. 24, 00-791 Warsaw, Poland
| | - Jakub Żurawski
- Department of Immunobiology, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznań University of Medical Sciences, 60-806 Poznan, Poland
- Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), 60-806 Poznan, Poland
| | - Lidia Brydak
- Department of Influenza Research, National Influenza Center at the National Institute of Public Health NIH—National Research Institute in Warsaw, Chocimska St. 24, 00-791 Warsaw, Poland
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23
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Jaron M, Lehky M, Zarà M, Zaydowicz CN, Lak A, Ballmann R, Heine PA, Wenzel EV, Schneider KT, Bertoglio F, Kempter S, Köster RW, Barbieri SS, van den Heuvel J, Hust M, Dübel S, Schubert M. Baculovirus-Free SARS-CoV-2 Virus-like Particle Production in Insect Cells for Rapid Neutralization Assessment. Viruses 2022. [PMID: 36298643 DOI: 10.3390/v14102087/s1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Virus-like particles (VLPs) resemble authentic virus while not containing any genomic information. Here, we present a fast and powerful method for the production of SARS-CoV-2 VLP in insect cells and the application of these VLPs to evaluate the inhibition capacity of monoclonal antibodies and sera of vaccinated donors. Our method avoids the baculovirus-based approaches commonly used in insect cells by employing direct plasmid transfection to co-express SARS-CoV-2 envelope, membrane, and spike protein that self-assemble into VLPs. After optimization of the expression plasmids and vector ratios, VLPs with an ~145 nm diameter and the typical "Corona" aura were obtained, as confirmed by nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM). Fusion of the membrane protein to GFP allowed direct quantification of binding inhibition to angiotensin II-converting enzyme 2 (ACE2) on cells by therapeutic antibody candidates or sera from vaccinated individuals. Neither VLP purification nor fluorescent labeling by secondary antibodies are required to perform these flow cytometric assays.
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Affiliation(s)
- Marcel Jaron
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Michael Lehky
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Marta Zarà
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Chris Nicole Zaydowicz
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Aidin Lak
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering, Technische Universität Braunschweig, Hans-Sommer-Straße 66, 38106 Braunschweig, Germany
| | - Rico Ballmann
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Philip Alexander Heine
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | | | - Kai-Thomas Schneider
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Federico Bertoglio
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Susanne Kempter
- Department of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Reinhard Wolfgang Köster
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Silvia Stella Barbieri
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Joop van den Heuvel
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Stefan Dübel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Maren Schubert
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
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24
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Jaron M, Lehky M, Zarà M, Zaydowicz CN, Lak A, Ballmann R, Heine PA, Wenzel EV, Schneider KT, Bertoglio F, Kempter S, Köster RW, Barbieri SS, van den Heuvel J, Hust M, Dübel S, Schubert M. Baculovirus-Free SARS-CoV-2 Virus-like Particle Production in Insect Cells for Rapid Neutralization Assessment. Viruses 2022; 14:v14102087. [PMID: 36298643 PMCID: PMC9606917 DOI: 10.3390/v14102087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/16/2022] Open
Abstract
Virus-like particles (VLPs) resemble authentic virus while not containing any genomic information. Here, we present a fast and powerful method for the production of SARS-CoV-2 VLP in insect cells and the application of these VLPs to evaluate the inhibition capacity of monoclonal antibodies and sera of vaccinated donors. Our method avoids the baculovirus-based approaches commonly used in insect cells by employing direct plasmid transfection to co-express SARS-CoV-2 envelope, membrane, and spike protein that self-assemble into VLPs. After optimization of the expression plasmids and vector ratios, VLPs with an ~145 nm diameter and the typical “Corona” aura were obtained, as confirmed by nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM). Fusion of the membrane protein to GFP allowed direct quantification of binding inhibition to angiotensin II-converting enzyme 2 (ACE2) on cells by therapeutic antibody candidates or sera from vaccinated individuals. Neither VLP purification nor fluorescent labeling by secondary antibodies are required to perform these flow cytometric assays.
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Affiliation(s)
- Marcel Jaron
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Michael Lehky
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Marta Zarà
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Chris Nicole Zaydowicz
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Aidin Lak
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering, Technische Universität Braunschweig, Hans-Sommer-Straße 66, 38106 Braunschweig, Germany
| | - Rico Ballmann
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Philip Alexander Heine
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | | | - Kai-Thomas Schneider
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Federico Bertoglio
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Susanne Kempter
- Department of Physics, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Reinhard Wolfgang Köster
- Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Silvia Stella Barbieri
- Unit of Brain-Heart Axis, IRCCS Monzino Cardiology Center, Via C. Parea 4, 20138 Milano, Italy
| | - Joop van den Heuvel
- Recombinant Protein Expression Platform, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Stefan Dübel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Maren Schubert
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
- Correspondence:
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25
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Manan A, Pirzada RH, Haseeb M, Choi S. Toll-like Receptor Mediation in SARS-CoV-2: A Therapeutic Approach. Int J Mol Sci 2022; 23:10716. [PMID: 36142620 PMCID: PMC9502216 DOI: 10.3390/ijms231810716] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 01/18/2023] Open
Abstract
The innate immune system facilitates defense mechanisms against pathogen invasion and cell damage. Toll-like receptors (TLRs) assist in the activation of the innate immune system by binding to pathogenic ligands. This leads to the generation of intracellular signaling cascades including the biosynthesis of molecular mediators. TLRs on cell membranes are adept at recognizing viral components. Viruses can modulate the innate immune response with the help of proteins and RNAs that downregulate or upregulate the expression of various TLRs. In the case of COVID-19, molecular modulators such as type 1 interferons interfere with signaling pathways in the host cells, leading to an inflammatory response. Coronaviruses are responsible for an enhanced immune signature of inflammatory chemokines and cytokines. TLRs have been employed as therapeutic agents in viral infections as numerous antiviral Food and Drug Administration-approved drugs are TLR agonists. This review highlights the therapeutic approaches associated with SARS-CoV-2 and the TLRs involved in COVID-19 infection.
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Affiliation(s)
- Abdul Manan
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | | | - Muhammad Haseeb
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
- S&K Therapeutics, Ajou University Campus Plaza 418, 199 Worldcup-ro, Yeongtong-gu, Suwon 16502, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
- S&K Therapeutics, Ajou University Campus Plaza 418, 199 Worldcup-ro, Yeongtong-gu, Suwon 16502, Korea
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26
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Warsame C, Valerini D, Llavori I, Barber AH, Goel S. Modal analysis of novel coronavirus (SARS COV-2) using finite element methodology. J Mech Behav Biomed Mater 2022; 135:105406. [PMID: 36075162 PMCID: PMC9391233 DOI: 10.1016/j.jmbbm.2022.105406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/11/2022] [Accepted: 07/26/2022] [Indexed: 11/28/2022]
Abstract
Many new engineering and scientific innovations have been proposed to date to passivate the novel coronavirus (SARS CoV-2), with the aim of curing the related disease that is now recognised as COVID-19. Currently, vaccine development remains the most reliable solution available. Efforts to provide solutions as alternatives to vaccinations are growing and include established control of behaviours such as self-isolation, social distancing, employing facial masks and use of antimicrobial surfaces. The work here proposes a novel engineering method employing the concept of resonant frequencies to denature SARS CoV-2. Specifically, “modal analysis” is used to computationally analyse the Eigenvalues and Eigenvectors i.e. frequencies and mode shapes to denature COVID-19. An average virion dimension of 63 nm with spike proteins number 6, 7 and 8 were examined, which revealed a natural frequency of a single virus in the range of 88–125 MHz. The information derived about the natural frequency of the virus through this study will open newer ways to exploit medical solutions to combat future pandemics.
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27
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Samandar F, Amiri Tehranizadeh Z, Saberi MR, Chamani J. 1,2,3,4,6-Pentagalloyl glucose of Pistacia lentiscus can inhibit the replication and transcription processes and viral pathogenesis of SARS-COV-2. Mol Cell Probes 2022; 65:101847. [PMID: 35843391 PMCID: PMC9281425 DOI: 10.1016/j.mcp.2022.101847] [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: 04/16/2022] [Revised: 07/09/2022] [Accepted: 07/09/2022] [Indexed: 11/30/2022]
Abstract
SARS-COV-2 stands as the source of the most catastrophic pandemic of this century, known as COVID-19. In this regard, we explored the effects of five Pistacia sp. active ingredients on the most crucial targets of SARS-COV-2, including 3CLpro, PLpro, RdRp, helicase, NSP15, and E protein. The results of molecular docking determined 1,2,3,4,6-pentagalloyl glucose (PG) as the most effective compound of Pistacia sp, which also confirmed its excellent binding affinities and stable interactions with helicase (−10.76 kcal/mol), RdRp (−10.19 kcal/mol), E protein (−9.51 kcal/mol), and 3CLpro (−9.47 kcal/mol). Furthermore, MD simulation was conducted to investigate the stability of all complexes throughout a 100 ns. In contrast to PLpro and NSP15, the analyses of Lennard-Jones potential, RMSDas, PCA, and SASA verified the ability of PG in forming stable and adequate interactions with RdRp, helicase, 3CLpro, and E protein due to standing as an effective inhibitor among the six targets, these data proposed the capability of PG, the most important compound of Pistacia sp., in inducing antiviral, anti-inflammatory, and antioxidant impacts on RdRp, helicase, 3CLpro, and E protein. Therefore, the possibility of inhibiting the replication and transcription processes and viral pathogenesis of SARS-COV-2 may be facilitated through the application of PG.
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Affiliation(s)
- Farzaneh Samandar
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran.
| | - Zeinab Amiri Tehranizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohammad Reza Saberi
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran.
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28
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Sharma A, Virmani T, Pathak V, Sharma A, Pathak K, Kumar G, Pathak D. Artificial Intelligence-Based Data-Driven Strategy to Accelerate Research, Development, and Clinical Trials of COVID Vaccine. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7205241. [PMID: 35845955 PMCID: PMC9279074 DOI: 10.1155/2022/7205241] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022]
Abstract
The global COVID-19 (coronavirus disease 2019) pandemic, which was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in a significant loss of human life around the world. The SARS-CoV-2 has caused significant problems to medical systems and healthcare facilities due to its unexpected global expansion. Despite all of the efforts, developing effective treatments, diagnostic techniques, and vaccinations for this unique virus is a top priority and takes a long time. However, the foremost step in vaccine development is to identify possible antigens for a vaccine. The traditional method was time taking, but after the breakthrough technology of reverse vaccinology (RV) was introduced in 2000, it drastically lowers the time needed to detect antigens ranging from 5-15 years to 1-2 years. The different RV tools work based on machine learning (ML) and artificial intelligence (AI). Models based on AI and ML have shown promising solutions in accelerating the discovery and optimization of new antivirals or effective vaccine candidates. In the present scenario, AI has been extensively used for drug and vaccine research against SARS-COV-2 therapy discovery. This is more useful for the identification of potential existing drugs with inhibitory human coronavirus by using different datasets. The AI tools and computational approaches have led to speedy research and the development of a vaccine to fight against the coronavirus. Therefore, this paper suggests the role of artificial intelligence in the field of clinical trials of vaccines and clinical practices using different tools.
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Affiliation(s)
- Ashwani Sharma
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Tarun Virmani
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Vipluv Pathak
- GL Bajaj Institute of Technology and Management, Greater Noida, Uttar Pradesh, India
| | | | - Kamla Pathak
- Uttar Pradesh University of Medical Sciences, Etawah, Uttar Pradesh 206001, India
| | - Girish Kumar
- School of Pharmaceutical Sciences, MVN University, Haryana 121102, India
| | - Devender Pathak
- Rajiv Academy for Pharmacy, NH. #2, Mathura Delhi Road P.O, Chhatikara, Mathura, Uttar Pradesh 281001, India
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29
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Zeng S, Li Y, Zhu W, Luo Z, Wu K, Li X, Fang Y, Qin Y, Chen W, Li Z, Zou L, Liu X, Yi L, Fan S. The Advances of Broad-Spectrum and Hot Anti-Coronavirus Drugs. Microorganisms 2022; 10:microorganisms10071294. [PMID: 35889013 PMCID: PMC9317368 DOI: 10.3390/microorganisms10071294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 02/01/2023] Open
Abstract
Coronaviruses, mainly including severe acute respiratory syndrome virus, severe acute respiratory syndrome coronavirus 2, Middle East respiratory syndrome virus, human coronavirus OC43, chicken infectious bronchitis virus, porcine infectious gastroenteritis virus, porcine epidemic diarrhea virus, and murine hepatitis virus, can cause severe diseases in humans and livestock. The severe acute respiratory syndrome coronavirus 2 is infecting millions of human beings with high morbidity and mortality worldwide, and the multiplicity of swine epidemic diarrhea coronavirus in swine suggests that coronaviruses seriously jeopardize the safety of public health and that therapeutic intervention is urgently needed. Currently, the most effective methods of prevention and control for coronaviruses are vaccine immunization and pharmacotherapy. However, the emergence of mutated viruses reduces the effectiveness of vaccines. In addition, vaccine developments often lag behind, making it difficult to put them into use early in the outbreak. Therefore, it is meaningful to screen safe, cheap, and broad-spectrum antiviral agents for coronaviruses. This review systematically summarizes the mechanisms and state of anti-human and porcine coronavirus drugs, in order to provide theoretical support for the development of anti-coronavirus drugs and other antivirals.
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Affiliation(s)
- Sen Zeng
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yuwan Li
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wenhui Zhu
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zipeng Luo
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Keke Wu
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Xiaowen Li
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Yiqi Fang
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yuwei Qin
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Zhaoyao Li
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Linke Zou
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xiaodi Liu
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Correspondence: (L.Y.); (S.F.); Fax: +86-20-8528-0245 (S.F.)
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (S.Z.); (Y.L.); (W.Z.); (Z.L.); (K.W.); (X.L.); (Y.F.); (Y.Q.); (W.C.); (Z.L.); (L.Z.); (X.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Correspondence: (L.Y.); (S.F.); Fax: +86-20-8528-0245 (S.F.)
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30
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Sokolinskaya EL, Putlyaeva LV, Gorshkova AA, Lukyanov KA. Intermembrane oligomerization of SARS-CoV-2 M-protein: possible role in viral budding. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2022. [DOI: 10.24075/brsmu.2022.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Despite the extensive research spurred by the catastrophic effects of COVID-19 pandemic, precise molecular mechanisms of some stages in SARS-CoV-2 life cycle remain elusive. One of such stages is the detachment of viral particles during budding. Using confocal fluorescence microscopy, we observed formation of specific structures by endoplasmic reticulum in human cells expressing SARS-CoV-2 M-protein, implicating oligomerization of M-protein across parallel membranes. In our opinion, such intermembrane oligomerization may provide a driving force for pinching off the viral particles during SARS-CoV-2 budding.
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Affiliation(s)
- EL Sokolinskaya
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - LV Putlyaeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - AA Gorshkova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - KA Lukyanov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
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31
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Madanagopal P, Muthukumar H, Thiruvengadam K. Computational study and design of effective siRNAs to silence structural proteins associated genes of Indian SARS-CoV-2 strains. Comput Biol Chem 2022; 98:107687. [PMID: 35537364 PMCID: PMC9052778 DOI: 10.1016/j.compbiolchem.2022.107687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 01/26/2023]
Abstract
SARS-CoV-2 is a highly transmissible and pathogenic coronavirus that first emerged in late 2019 and has since triggered a pandemic of acute respiratory disease named COVID-19 which poses a significant threat to all public health institutions in the absence of specific antiviral treatment. Since the outbreak began in March 2020, India has reported 4.77 lakh Coronavirus deaths, according to the World Health Organization (WHO). The innate RNA interference (RNAi) pathway, on the other hand, allows for the development of nucleic acid-based antiviral drugs in which complementary small interfering RNAs (siRNAs) mediate the post-transcriptional gene silencing (PTGS) of target mRNA. Therefore, in this current study, the potential of RNAi was harnessed to construct siRNA molecules that target the consensus regions of specific structural proteins associated genes of SARS-CoV-2, such as the envelope protein gene (E), membrane protein gene (M), nucleocapsid phosphoprotein gene (N), and surface glycoprotein gene (S) which are important for the viral pathogenesis. Conserved sequences of 811 SARS-CoV-2 strains from around India were collected to design 21 nucleotides long siRNA duplex based on various computational algorithms and parameters targeting E, M, N and S genes. The proposed siRNA molecules possessed sufficient nucleotide-based and other features for effective gene silencing and BLAST results revealed that siRNAs' targets have no significant matches across the whole human genome. Hence, siRNAs were found to have no off-target effects on the genome, ruling out the possibility of off-target silencing. Finally, out of 157 computationally identified siRNAs, only 4 effective siRNA molecules were selected for each target gene which is proposed to exert the best action based on GC content, free energy of folding, free energy of binding, melting temperature, heat capacity and molecular docking analysis with Human AGO2 protein. Our engineered siRNA candidates could be used as a genome-level therapeutic treatment against various sequenced SARS-CoV-2 strains in India. However, future applications will necessitate additional validations in vitro and in vivo animal models.
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Patial S, Kumar A, Raizada P, Le QV, Nguyen VH, Selvasembian R, Singh P, Thakur S, Hussain CM. Potential of graphene based photocatalyst for antiviral activity with emphasis on COVID-19: A review. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2022; 10:107527. [PMID: 35280853 PMCID: PMC8902865 DOI: 10.1016/j.jece.2022.107527] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/18/2022] [Accepted: 03/06/2022] [Indexed: 05/13/2023]
Abstract
Coronavirus disease-2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been one of the most challenging worldwide epidemics of recent times. Semiconducting materials (photocatalysts) could prove effectual solar-light-driven technology on account of variant reactive oxidative species (ROS), including superoxide (•O2 - ) and hydroxyl (•OH) radicals either by degradation of proteins, DNA, RNA, or preventing cell development by terminating cellular membrane. Graphene-based materials have been exquisitely explored for antiviral applications due to their extraordinary physicochemical features including large specific surface area, robust mechanical strength, tunable structural features, and high electrical conductivity. Considering that, the present study highlights a perspective on the potentials of graphene based materials for photocatalytic antiviral activity. The interaction of virus with the surface of graphene based nanomaterials and the consequent physical, as well as ROS induced inactivation process, has been highlighted and discussed. It is highly anticipated that the present review article emphasizing mechanistic antiviral insights could accelerate further research in this field.
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Affiliation(s)
- Shilpa Patial
- School of Advanced Chemical Sciences, Faculty of Basic Sciences, Shoolini University, Solan, Himachal Pradesh 173229, India
| | - Abhinandan Kumar
- School of Advanced Chemical Sciences, Faculty of Basic Sciences, Shoolini University, Solan, Himachal Pradesh 173229, India
| | - Pankaj Raizada
- School of Advanced Chemical Sciences, Faculty of Basic Sciences, Shoolini University, Solan, Himachal Pradesh 173229, India
| | - Quyet Van Le
- Department of Materials Science and Engineering, Korea University, 145, Anam-ro Seongbuk-gu, Seoul, 02841, South Korea
| | - Van-Huy Nguyen
- School of Advanced Chemical Sciences, Faculty of Basic Sciences, Shoolini University, Solan, Himachal Pradesh 173229, India
| | - Rangabhashiyam Selvasembian
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613401, Tamilnadu, India
| | - Pardeep Singh
- School of Advanced Chemical Sciences, Faculty of Basic Sciences, Shoolini University, Solan, Himachal Pradesh 173229, India
| | - Sourbh Thakur
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Chaudhery Mustansar Hussain
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
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Zamhuri SA, Soon CF, Nordin AN, Ab Rahim R, Sultana N, Khan MA, Lim GP, Tee KS. A review on the contamination of SARS-CoV-2 in water bodies: Transmission route, virus recovery and recent biosensor detection techniques. SENSING AND BIO-SENSING RESEARCH 2022; 36:100482. [PMID: 35251937 PMCID: PMC8889793 DOI: 10.1016/j.sbsr.2022.100482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 12/11/2022] Open
Abstract
The discovery of SARS-CoV-2 virus in the water bodies has been reported, and the risk of virus transmission to human via the water route due to poor wastewater management cannot be disregarded. The main source of the virus in water bodies is the sewage network systems which connects to the surface water. Wastewater-based epidemiology has been applied as an early surveillance tool to sense SARS-CoV-2 virus in the sewage network. This review discussed possible transmission routes of the SARS-CoV-2 virus and the challenges of the existing method in detecting the virus in wastewater. One significant challenge for the detection of the virus is that the high virus loading is diluted by the sheer volume of the wastewater. Hence, virus preconcentration from water samples prior to the application of virus assay is essential to accurately detect traceable virus loading. The preparation time, materials and conditions, virus type, recovery percentage, and various virus recovery techniques are comprehensively discussed in this review. The practicability of molecular methods such as Polymer-Chain-Reaction (PCR) for the detection of SARS-CoV-2 in wastewater will be revealed. The conventional virus detection techniques have several shortcomings and the potential of biosensors as an alternative is also considered. Biosensing techniques have also been proposed as an alternative to PCR and have reported detection limits of 10 pg/μl. This review serves to guide the reader on the future designs and development of highly sensitive, robust and, cost effective SARS-CoV-2 lab-on-a-chip biosensors for use in complex wastewater.
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Affiliation(s)
- Siti Adibah Zamhuri
- Microelectronics and Nanotechnology-Shamsuddin Research Centre, Universiti Tun Hussein Onn Malaysia, 86400, Parit Raja, Batu Pahat, Johor, Malaysia
| | - Chin Fhong Soon
- Microelectronics and Nanotechnology-Shamsuddin Research Centre, Universiti Tun Hussein Onn Malaysia, 86400, Parit Raja, Batu Pahat, Johor, Malaysia
- Faculty of Electrical and Electronic Engineering, Universiti Tun Hussein Onn Malaysia, 86400, Parit Raja, Batu Pahat, Johor, Malaysia
| | - Anis Nurashikin Nordin
- Department of Electrical and Computer Engineering, Kulliyah of Engineering, International University of Islam Malaysia, 53100, Jalan Gombak, Kuala Lumpur, Malaysia
| | - Rosminazuin Ab Rahim
- Department of Electrical and Computer Engineering, Kulliyah of Engineering, International University of Islam Malaysia, 53100, Jalan Gombak, Kuala Lumpur, Malaysia
| | | | - Muhammad Arif Khan
- Microelectronics and Nanotechnology-Shamsuddin Research Centre, Universiti Tun Hussein Onn Malaysia, 86400, Parit Raja, Batu Pahat, Johor, Malaysia
| | - Gim Pao Lim
- Microelectronics and Nanotechnology-Shamsuddin Research Centre, Universiti Tun Hussein Onn Malaysia, 86400, Parit Raja, Batu Pahat, Johor, Malaysia
| | - Kian Sek Tee
- Faculty of Electrical and Electronic Engineering, Universiti Tun Hussein Onn Malaysia, 86400, Parit Raja, Batu Pahat, Johor, Malaysia
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SARS-CoV-2 Envelope (E) Protein Binds and Activates TLR2 Pathway: A Novel Molecular Target for COVID-19 Interventions. Viruses 2022; 14:v14050999. [PMID: 35632741 PMCID: PMC9146335 DOI: 10.3390/v14050999] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022] Open
Abstract
This paper presents a molecular characterization of the interaction between the SARS-CoV-2 envelope (E) protein and TLR2. We demonstrated that the E protein, both as a recombinant soluble protein and as a native membrane protein associated with SARS-CoV-2 viral particles, interacts physically with the TLR2 receptor in a specific and dose-dependent manner. Furthermore, we showed that the specific interaction with the TLR2 pathway activates the NF-κB transcription factor and stimulates the production of the CXCL8 inflammatory chemokine. In agreement with the importance of NF-κB in the TLR signaling pathway, we showed that the chemical inhibition of this transcription factor leads to significant inhibition of CXCL8 production, while the blockade of the P38 and ERK1/2 MAP kinases only results in partial CXCL8 inhibition. Overall, our findings propose the envelope (E) protein as a novel molecular target for COVID-19 interventions: either (i) by exploring the therapeutic effect of anti-E blocking/neutralizing antibodies in symptomatic COVID-19 patients, or (ii) as a promising non-spike SARS-CoV-2 antigen candidate for inclusion in the development of next-generation prophylactic vaccines against COVID-19 infection and disease.
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Kuzmin A, Orekhov P, Astashkin R, Gordeliy V, Gushchin I. Structure and dynamics of the SARS-CoV-2 envelope protein monomer. Proteins 2022; 90:1102-1114. [PMID: 35119706 DOI: 10.1002/prot.26317] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/09/2022] [Accepted: 01/31/2022] [Indexed: 12/11/2022]
Abstract
Coronaviruses, especially severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), present an ongoing threat to human wellbeing. Consequently, elucidation of molecular determinants of their function and interaction with the host is an important task. Whereas some of the coronaviral proteins are extensively characterized, others remain understudied. Here, we use molecular dynamics simulations to analyze the structure and dynamics of the SARS-CoV-2 envelope (E) protein (a viroporin) in the monomeric form. The protein consists of the hydrophobic α-helical transmembrane domain (TMD) and amphiphilic α-helices H2 and H3, connected by flexible linkers. We show that TMD has a preferable orientation in the membrane, while H2 and H3 reside at the membrane surface. Orientation of H2 is strongly influenced by palmitoylation of cysteines Cys40, Cys43, and Cys44. Glycosylation of Asn66 affects the orientation of H3. We also observe that the monomeric E protein both generates and senses the membrane curvature, preferably localizing with the C-terminus at the convex regions of the membrane; the protein in the pentameric form displays these properties as well. Localization to curved regions may be favorable for assembly of the E protein oligomers, whereas induction of curvature may facilitate the budding of the viral particles. The presented results may be helpful for a better understanding of the function of the coronaviral E protein and viroporins in general, and for overcoming the ongoing SARS-CoV-2 pandemic.
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Affiliation(s)
- Alexander Kuzmin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Roman Astashkin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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Sullivan E, Sung PY, Wu W, Berry N, Kempster S, Ferguson D, Almond N, Jones IM, Roy P. SARS-CoV-2 Virus-like Particles Produced by a Single Recombinant Baculovirus Generate Anti-S Antibody and Protect against Variant Challenge. Viruses 2022; 14:914. [PMID: 35632656 PMCID: PMC9143203 DOI: 10.3390/v14050914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 01/27/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19), caused by infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has highlighted the need for the rapid generation of efficient vaccines for emerging disease. Virus-like particles, VLPs, are an established vaccine technology that produces virus-like mimics, based on expression of the structural proteins of a target virus. SARS-CoV-2 is a coronavirus where the basis of VLP formation has been shown to be the co-expression of the spike, membrane and envelope structural proteins. Here we describe the generation of SARS-CoV-2 VLPs by the co-expression of the salient structural proteins in insect cells using the established baculovirus expression system. VLPs were heterologous ~100 nm diameter enveloped particles with a distinct fringe that reacted strongly with SARS-CoV-2 convalescent sera. In a Syrian hamster challenge model, non-adjuvanted VLPs induced neutralizing antibodies to the VLP-associated Wuhan S protein and reduced virus shedding and protected against disease associated weight loss following a virulent challenge with SARS-CoV-2 (B.1.1.7 variant). Immunized animals showed reduced lung pathology and lower challenge virus replication than the non-immunized controls. Our data suggest SARS-CoV-2 VLPs offer an efficient vaccine that mitigates against virus load and prevents severe disease.
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Affiliation(s)
- Edward Sullivan
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (E.S.); (P.-Y.S.); (W.W.)
| | - Po-Yu Sung
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (E.S.); (P.-Y.S.); (W.W.)
| | - Weining Wu
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (E.S.); (P.-Y.S.); (W.W.)
| | - Neil Berry
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control, Potters Bar EN6 3QG, UK; (N.B.); (S.K.); (D.F.); (N.A.)
| | - Sarah Kempster
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control, Potters Bar EN6 3QG, UK; (N.B.); (S.K.); (D.F.); (N.A.)
| | - Deborah Ferguson
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control, Potters Bar EN6 3QG, UK; (N.B.); (S.K.); (D.F.); (N.A.)
| | - Neil Almond
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control, Potters Bar EN6 3QG, UK; (N.B.); (S.K.); (D.F.); (N.A.)
| | - Ian M. Jones
- School of Biological Sciences, University of Reading, Reading RG6 6AH, UK;
| | - Polly Roy
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (E.S.); (P.-Y.S.); (W.W.)
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Medeiros-Silva J, Somberg NH, Wang HK, McKay MJ, Mandala VS, Dregni AJ, Hong M. pH- and Calcium-Dependent Aromatic Network in the SARS-CoV-2 Envelope Protein. J Am Chem Soc 2022; 144:6839-6850. [PMID: 35380805 DOI: 10.1021/jacs.2c00973] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The envelope (E) protein of the SARS-CoV-2 virus is a membrane-bound viroporin that conducts cations across the endoplasmic reticulum Golgi intermediate compartment (ERGIC) membrane of the host cell to cause virus pathogenicity. The structure of the closed state of the E transmembrane (TM) domain, ETM, was recently determined using solid-state NMR spectroscopy. However, how the channel pore opens to mediate cation transport is unclear. Here, we use 13C and 19F solid-state NMR spectroscopy to investigate the conformation and dynamics of ETM at acidic pH and in the presence of calcium ions, which mimic the ERGIC and lysosomal environment experienced by the E protein in the cell. Acidic pH and calcium ions increased the conformational disorder of the N- and C-terminal residues and also increased the water accessibility of the protein, indicating that the pore lumen has become more spacious. ETM contains three regularly spaced phenylalanine (Phe) residues in the center of the peptide. 19F NMR spectra of para-fluorinated Phe20 and Phe26 indicate that both residues exhibit two sidechain conformations, which coexist within each channel. These two Phe conformations differ in their water accessibility, lipid contact, and dynamics. Channel opening by acidic pH and Ca2+ increases the population of the dynamic lipid-facing conformation. These results suggest an intricate aromatic network that regulates the opening of the ETM channel pore. This aromatic network may be a target for E inhibitors against SARS-CoV-2 and related coronaviruses.
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Affiliation(s)
- João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Noah H Somberg
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Harrison K Wang
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Matthew J McKay
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Aurelio J Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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Kirar M, Singh H, Sehrawat N. Virtual screening and molecular dynamics simulation study of plant protease inhibitors against SARS-CoV-2 envelope protein. INFORMATICS IN MEDICINE UNLOCKED 2022; 30:100909. [PMID: 35311063 PMCID: PMC8919766 DOI: 10.1016/j.imu.2022.100909] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/06/2022] [Accepted: 03/06/2022] [Indexed: 11/02/2022] Open
Abstract
Due to the outbreak of a new strain of pandemic coronavirus, there is a huge loss of economy and health. In 2021, some vaccines are recommended as emergency licensed vaccines to protect against the virus, and efforts are continuously ongoing to evaluate the vaccine safety measures for licensed vaccines. Recently, there was an increase in the cases of a new variant of coronavirus (omicron). Envelope protein plays an important role in virus packaging and assembly. If viral assembly is blocked, there is less chance of spreading the infection to another cell.In the present study, the plant protease inhibitors (PPIs) were screened against the envelope protein of SARS CoV 2. The structures were downloaded from the protein data bank. The plant protease inhibitors cystatin-I, Eravatmin, squash, Kunitz, Bowman-Birk, Alpha-amylase inhibitors, and potato serine protease inhibitors were screened and out of them Kunitz, alpha-amylase, and squash protease inhibitors have shown maximum binding energy. The molecular dynamics simulation was performed for docked complexes showing the lowest binding energy by NMA (normal mode analysis) to visualize the motion and stability of complexes. These plant-based protease inhibitors are a good target to fight against the new emerging strain of coronavirus because plant extracted compounds are natural and there is fewer side effect than synthetic compounds.
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Affiliation(s)
- Manisha Kirar
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Hitesh Singh
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Neelam Sehrawat
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, India
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Savina K, Sreekumar R, Soonu VK, Variyar EJ. Various vaccine platforms in the field of COVID-19. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2022; 11:35. [PMID: 35284578 PMCID: PMC8899459 DOI: 10.1186/s43088-022-00215-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/15/2022] [Indexed: 12/16/2022] Open
Abstract
Background With the emergence of Corona virus Disease-2019, a novel worldwide health disaster is threatening the population. The WHO declared COVID-19 as a pandemic in December 2019, when it first surfaced in Hunan seafood market in Wuhan, South China, and quickly spread far and wide. Different corona virus variants are currently causing concern all across the world. Main body It has become critical for our scientists to develop a viable method to prevent infection or the pandemic from spreading globally. Antiviral medicines, oxygen therapy, and immune system stimulation are all used to treat the condition. SARS-CoV-2 undergoes mutation and due to evolutionary pressures, different mutant strains caused various symptoms in different geographical regions and the epidemic is spreading and becoming more fragile, posing a greater risk of mortality. Vaccines are tools to increase our immunity as a precaution, and increasing the global immunization rate can help improve the situation. Recent developments in the field of vaccine platforms are discussed here. Short conclusion Vaccines are of highest priority to control and eradicate the viral infectious disease COVID-19 more than any other protective solutions. A number of mutations have occurred and some variants such as alpha, beta, gamma, and delta, and it has now progressed to the new version Omicron, which is a variant of concern. Booster doses are anticipated to function as a barrier to the capacity of the most recent known variety, and more research is needed to determine how effective they will be. This page discusses various technologies employed in the field of COVID-19 vaccine, as well as potential barriers and recent developments in this field.
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da Silva Torres MK, Bichara CDA, de Almeida MDNDS, Vallinoto MC, Queiroz MAF, Vallinoto IMVC, dos Santos EJM, de Carvalho CAM, Vallinoto ACR. The Complexity of SARS-CoV-2 Infection and the COVID-19 Pandemic. Front Microbiol 2022; 13:789882. [PMID: 35222327 PMCID: PMC8870622 DOI: 10.3389/fmicb.2022.789882] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to the death of millions of people worldwide and thousands more infected individuals developed sequelae due to the disease of the new coronavirus of 2019 (COVID-19). The development of several studies has contributed to the knowledge about the evolution of SARS-CoV2 infection and the disease to more severe forms. Despite this information being debated in the scientific literature, many mechanisms still need to be better understood in order to control the spread of the virus and treat clinical cases of COVID-19. In this article, we carried out an extensive literature review in order to bring together, in a single article, the biological, social, genetic, diagnostic, therapeutic, immunization, and even socioeconomic aspects that impact the SAR-CoV-2 pandemic. This information gathered in this article will enable a broad and consistent reading of the main aspects related to the current pandemic.
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Affiliation(s)
- Maria Karoliny da Silva Torres
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
| | - Carlos David Araújo Bichara
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
| | - Maria de Nazaré do Socorro de Almeida
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
- Laboratory of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Mariana Cayres Vallinoto
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- University Center of the State of Pará, Belém, Brazil
| | - Maria Alice Freitas Queiroz
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
| | | | - Eduardo José Melo dos Santos
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
- Laboratory of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | - Antonio Carlos R. Vallinoto
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
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Duma Z, Chuturgoon AA, Ramsuran V, Edward V, Naidoo P, Mpaka-Mbatha MN, Bhengu KN, Nembe N, Pillay R, Singh R, Mkhize-Kwitshana ZL. The challenges of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing in low-middle income countries and possible cost-effective measures in resource-limited settings. Global Health 2022; 18:5. [PMID: 35065670 PMCID: PMC8783193 DOI: 10.1186/s12992-022-00796-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/03/2022] [Indexed: 02/06/2023] Open
Abstract
Diagnostic testing for the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection remains a challenge around the world, especially in low-middle-income countries (LMICs) with poor socio-economic backgrounds. From the beginning of the pandemic in December 2019 to August 2021, a total of approximately 3.4 billion tests were performed globally. The majority of these tests were restricted to high income countries. Reagents for diagnostic testing became a premium, LMICs either cannot afford or find manufacturers unwilling to supply them with expensive analytical reagents and equipment. From March to December 2020 obtaining testing kits for SARS-CoV-2 testing was a challenge. As the number of SARS-CoV-2 infection cases increases globally, large-scale testing still remains a challenge in LMICs. The aim of this review paper is to compare the total number and frequencies of SARS-CoV-2 testing in LMICs and high-income countries (HICs) using publicly available data from Worldometer COVID-19, as well as discussing possible interventions and cost-effective measures to increase testing capability in LMICs. In summary, HICs conducted more SARS-CoV-2 testing (USA: 192%, Australia: 146%, Switzerland: 124% and Canada: 113%) compared to middle-income countries (MICs) (Vietnam: 43%, South Africa: 29%, Brazil: 27% and Venezuela: 12%) and low-income countries (LICs) (Bangladesh: 6%, Uganda: 4% and Nigeria: 1%). Some of the cost-effective solutions to counteract the aforementioned problems includes using saliva instead of oropharyngeal or nasopharyngeal swabs, sample pooling, and testing high-priority groups to increase the number of mass testing in LMICs.
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Affiliation(s)
- Zamathombeni Duma
- Department of Medical Microbiology, School of Laboratory Medicine & Medical Sciences, Howard College, University of KwaZulu-Natal, Glenwood, Durban, 4041, South Africa.
- Division of Research Capacity Development, South African Medical Research Council (SAMRC), Tygerberg, Cape Town, 7505, South Africa.
| | - Anil A Chuturgoon
- Department of Medical Biochemistry, School of Laboratory Medicine & Medical Sciences, Howard College, University of KwaZulu-Natal, Glenwood, Durban, 4041, South Africa
| | - Veron Ramsuran
- Department of Medical Microbiology, School of Laboratory Medicine & Medical Sciences, Howard College, University of KwaZulu-Natal, Glenwood, Durban, 4041, South Africa
| | - Vinodh Edward
- The Aurum Institute, Parktown, Johannesburg, 2194, South Africa
| | - Pragalathan Naidoo
- Department of Medical Microbiology, School of Laboratory Medicine & Medical Sciences, Howard College, University of KwaZulu-Natal, Glenwood, Durban, 4041, South Africa
- Division of Research Capacity Development, South African Medical Research Council (SAMRC), Tygerberg, Cape Town, 7505, South Africa
| | - Miranda N Mpaka-Mbatha
- Department of Medical Microbiology, School of Laboratory Medicine & Medical Sciences, Howard College, University of KwaZulu-Natal, Glenwood, Durban, 4041, South Africa
- Division of Research Capacity Development, South African Medical Research Council (SAMRC), Tygerberg, Cape Town, 7505, South Africa
- Department of Biomedical Sciences, Mangosuthu University of Technology, Umlazi, Durban, 4031, South Africa
| | - Khethiwe N Bhengu
- Department of Medical Microbiology, School of Laboratory Medicine & Medical Sciences, Howard College, University of KwaZulu-Natal, Glenwood, Durban, 4041, South Africa
- Division of Research Capacity Development, South African Medical Research Council (SAMRC), Tygerberg, Cape Town, 7505, South Africa
- Department of Biomedical Sciences, Mangosuthu University of Technology, Umlazi, Durban, 4031, South Africa
| | - Nomzamo Nembe
- Department of Medical Microbiology, School of Laboratory Medicine & Medical Sciences, Howard College, University of KwaZulu-Natal, Glenwood, Durban, 4041, South Africa
- Division of Research Capacity Development, South African Medical Research Council (SAMRC), Tygerberg, Cape Town, 7505, South Africa
| | - Roxanne Pillay
- Department of Medical Microbiology, School of Laboratory Medicine & Medical Sciences, Howard College, University of KwaZulu-Natal, Glenwood, Durban, 4041, South Africa
- Division of Research Capacity Development, South African Medical Research Council (SAMRC), Tygerberg, Cape Town, 7505, South Africa
- Department of Biomedical Sciences, Mangosuthu University of Technology, Umlazi, Durban, 4031, South Africa
| | - Ravesh Singh
- Department of Medical Microbiology, School of Laboratory Medicine & Medical Sciences, Howard College, University of KwaZulu-Natal, Glenwood, Durban, 4041, South Africa
| | - Zilungile L Mkhize-Kwitshana
- Department of Medical Microbiology, School of Laboratory Medicine & Medical Sciences, Howard College, University of KwaZulu-Natal, Glenwood, Durban, 4041, South Africa
- Division of Research Capacity Development, South African Medical Research Council (SAMRC), Tygerberg, Cape Town, 7505, South Africa
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Drobysh M, Ramanaviciene A, Viter R, Chen CF, Samukaite-Bubniene U, Ratautaite V, Ramanavicius A. Biosensors for the Determination of SARS-CoV-2 Virus and Diagnosis of COVID-19 Infection. Int J Mol Sci 2022; 23:666. [PMID: 35054850 PMCID: PMC8776074 DOI: 10.3390/ijms23020666] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/29/2021] [Accepted: 01/03/2022] [Indexed: 02/04/2023] Open
Abstract
Monitoring and tracking infection is required in order to reduce the spread of the coronavirus disease 2019 (COVID-19), induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To achieve this goal, the development and deployment of quick, accurate, and sensitive diagnostic methods are necessary. The determination of the SARS-CoV-2 virus is performed by biosensing devices, which vary according to detection methods and the biomarkers which are inducing/providing an analytical signal. RNA hybridisation, antigen-antibody affinity interaction, and a variety of other biological reactions are commonly used to generate analytical signals that can be precisely detected using electrochemical, electrochemiluminescence, optical, and other methodologies and transducers. Electrochemical biosensors, in particular, correspond to the current trend of bioanalytical process acceleration and simplification. Immunosensors are based on the determination of antigen-antibody interaction, which on some occasions can be determined in a label-free mode with sufficient sensitivity.
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Affiliation(s)
- Maryia Drobysh
- State Research Institute Center for Physical and Technological Sciences, Sauletekio Ave. 3, LT-10257 Vilnius, Lithuania; (M.D.); (U.S.-B.); (V.R.)
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania;
| | - Almira Ramanaviciene
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania;
| | - Roman Viter
- Center for Collective Use of Scientific Equipment, Sumy State University, Sanatornaya Str. 31, 40018 Sumy, Ukraine
- Institute of Atomic Physics and Spectroscopy, University of Latvia, Jelgavas Street 3, LV-1004 Riga, Latvia
| | - Chien-Fu Chen
- Institute of Applied Mechanics, National Taiwan University 1, Sec. 4, Roosevelt Rd., Da’an Dist., Taipei 106, Taiwan;
| | - Urte Samukaite-Bubniene
- State Research Institute Center for Physical and Technological Sciences, Sauletekio Ave. 3, LT-10257 Vilnius, Lithuania; (M.D.); (U.S.-B.); (V.R.)
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania;
| | - Vilma Ratautaite
- State Research Institute Center for Physical and Technological Sciences, Sauletekio Ave. 3, LT-10257 Vilnius, Lithuania; (M.D.); (U.S.-B.); (V.R.)
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania;
| | - Arunas Ramanavicius
- State Research Institute Center for Physical and Technological Sciences, Sauletekio Ave. 3, LT-10257 Vilnius, Lithuania; (M.D.); (U.S.-B.); (V.R.)
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania;
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Kiryanov SA, Levina TA, Konopleva MV, Suslov AP. Identification of Hotspot Mutations in the N Gene of SARS-CoV-2 in Russian Clinical Samples That May Affect the Detection by Reverse Transcription-PCR. Diagnostics (Basel) 2022; 12:diagnostics12010147. [PMID: 35054314 PMCID: PMC8774456 DOI: 10.3390/diagnostics12010147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/28/2021] [Accepted: 01/04/2022] [Indexed: 12/27/2022] Open
Abstract
Sensitive and reliable diagnostic test systems based on real-time PCR are of great importance in the fight against the ongoing SARS-CoV-2 pandemic. The genetic variability of the SARS-CoV-2 virus leads to the accumulation of mutations, some of which may affect the sensitivity of modern PCR assays. The aim of this study was to search in Russian clinical samples for new mutations in SARS-CoV-2 gene N that can affect the detection by RT-PCR. In this study, the polymorphisms in the regions of the target gene N causing failed or poor detection of the target N in the RT-PCR assay on 12 selected samples were detected. Sequencing the entire N and E genes in these samples along with other 195 samples that were positive for both target regions was performed. Here, we identified a number of nonsynonymous mutations and one novel deletion in the N gene that affected the ability to detect a target in the N gene as well a few mutations in the E gene of SARS-CoV-2 that did not affect detection. Sequencing revealed that majority of the mutations in the N gene were located in the variable region between positions 193 and 235 aa, inside and nearby the phosphorylated serine-rich region of the protein N. This study highlights the importance of the further characterization of the genetic variability and evolution of gene N, the most common target for detecting SARS-CoV-2. The use of at least two targets for detecting SARS-CoV-2, including one for the E gene, will be necessary for reliable diagnostics.
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Affiliation(s)
- Sergei A. Kiryanov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (T.A.L.); (M.V.K.); (A.P.S.)
- Correspondence:
| | - Tatiana A. Levina
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (T.A.L.); (M.V.K.); (A.P.S.)
- OOO “DNA-Technology”, 117587 Moscow, Russia
| | - Maria V. Konopleva
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (T.A.L.); (M.V.K.); (A.P.S.)
| | - Anatoly P. Suslov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (T.A.L.); (M.V.K.); (A.P.S.)
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Roy A, Menon T. Evaluation of bioactive compounds from Boswellia serrata against SARS-CoV-2. VEGETOS (BAREILLY, INDIA) 2022; 35:404-414. [PMID: 34803247 PMCID: PMC8595075 DOI: 10.1007/s42535-021-00318-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 04/21/2023]
Abstract
With the COVID-19 pandemic still wreaking havoc worldwide, new variants being discovered every month in some parts of the globe due to the mutating nature of the virus. There is no specific solution for this highly transmissible disease. In search of a lead molecule for the discovery and development of drug, extensive research is being conducted throughout the world. Many synthetic drugs are already in clinical trials and some are utilized for the treatment of this viral infection. Apart from synthetic drugs, phytocompounds from plants act as a potential drug candidate which can inhibit the growth of virus and thus able to prevent the viral infection. In this study, 26 ligands (bioactive compounds) from Boswellia serrata (an important medicinal plant) were tested against SARS-CoV-2 by using computational method. Selected ligands were shortlisted using Lipinski's rule and then subjected to molecular docking against one of the main proteins of SARS-CoV-2, i.e., Mpro. Out of these compounds, Euphane, Ursane, α-Amyrin, Phytosterols, and 2,3-Dihydroxyurs-12-en-28-oic acid were potential to inhibit the Mpro activity with binding energies of - 10.47 kcal/mol, - 10.41 kcal/mol, - 9.99 kcal/mol, - 9.94 kcal/mol and - 9.72 kcal/mol respectively. A comparative study was performed using the best five ligands against four possible drug targets of SARS-CoV-2. It was found that Euphane showed highest negative binding energy against all the four crucial targets of SARS-CoV-2. Further, in-vitro experimentation is required to validate the use of Euphane as a potent drug against SARS-CoV-2.
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Affiliation(s)
- Arpita Roy
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Tarunya Menon
- Department of Biotechnology, Delhi Technological University, Delhi, India
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Essentials of COVID-19 and treatment approaches. DATA SCIENCE FOR COVID-19 2022. [PMCID: PMC8988944 DOI: 10.1016/b978-0-323-90769-9.00026-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The coronavirus family is as old as the 1930s when it first showed symptoms in chicken. The virus thereafter kept evolving and it has significantly taken over a large percentage of people worldwide in the form of this new pandemic. As of the present day, there is no treatment available for coronavirus disease 2019 (COVID-19) (caused by the severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]), although supportive therapy and preventive measures have shown a tremendous control rate among certain patients. Drugs like remdesivir, camostat, nafamostat, ritonavir/lopinavir, several monoclonal antibodies, and CPs are in their early phases of trials. There are approved by the WHO under an emergency use authorization program. Favipiravir has entered its phase 3 clinical trial and is supported by evidence to show no or less adverse effects in patients infected with SARS-CoV-2. Vaccine development is accelerating its pace, and vaccines will probably become available by the end of the year 2020.
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Ahmadi K, Zahedifard F, Mafakher L, Einakian MA, Ghaedi T, Kavousipour S, Faezi S, Karmostaji A, Sharifi-Sarasiabi K, Gouklani H, Hassaniazad M. Active site-based analysis of structural proteins for drug targets in different human Coronaviruses. Chem Biol Drug Des 2021; 99:585-602. [PMID: 34914204 DOI: 10.1111/cbdd.14004] [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: 08/05/2021] [Revised: 11/03/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
Seven types of Coronaviruses (CoVs) have been identified that can cause infection in humans, including HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV, HCoV-MERS, and SARS-CoV-2. In this study, we investigated the genetic structure, the homology of the structural protein sequences, as well as the investigation of the active site of structural proteins. The active site of structural proteins was determined based on the previous studies, and the homology of their amino acid sequences and structure was compared. Multiple sequence alignment of Spike protein of HCoVs showed that the receptor-binding domain of SARS-CoV-2, SARS-CoV, and MERS-CoV was located at a similar site to the S1 subunit. The binding motif of PDZ (postsynaptic density- 95/discs large/zona occludens-1) of the envelope protein, was conserved in SARS-CoV and SARS-CoV-2 according to multiple sequence alignment but showed different changes in the other HCoVs. Overall, Spike protein showed the most variation in its active sites, but the other structural proteins were highly conserved. In this study, for the first time, the active site of all structural proteins of HCoVs as a drug target was investigated. The binding site of these proteins can be suitable targets for drugs or vaccines among HCoVs.
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Affiliation(s)
- Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Farnaz Zahedifard
- Drug discovery and Evaluation unit, Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ladan Mafakher
- Thalassemia & Hemoglobinopathy Research center, Health research institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Ali Einakian
- Food Health Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Tayebeh Ghaedi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Soudabeh Kavousipour
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Sobhan Faezi
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Afsaneh Karmostaji
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Khojasteh Sharifi-Sarasiabi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hamed Gouklani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mehdi Hassaniazad
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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The Potential of Mesenchymal Stem Cells for the Treatment of Cytokine Storm due to COVID-19. BIOMED RESEARCH INTERNATIONAL 2021; 2021:3178796. [PMID: 34840969 PMCID: PMC8626179 DOI: 10.1155/2021/3178796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/24/2021] [Accepted: 10/29/2021] [Indexed: 12/15/2022]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has seriously affected public health and social stability. The main route of the transmission is droplet transmission, where the oral cavity is the most important entry point to the body. Due to both the direct harmful effects of SARS-CoV-2 and disordered immune responses, some COVID-19 patients may progress to acute respiratory distress syndrome or even multiple organ failure. Genetic variants of SARS-CoV-2 have been emerging and circulating around the world. Currently, there is no internationally approved precise treatment for COVID-19. Mesenchymal stem cells (MSCs) can traffic and migrate towards the affected tissue, regulate both the innate and acquired immune systems, and participate in the process of healing. Here, we will discuss and investigate the mechanisms of immune disorder in COVID-19 and the therapeutic activity of MSCs, in particular human gingiva mesenchymal stem cells.
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Gül Ş. In silico drug repositioning against human NRP1 to block SARS-CoV-2 host entry. Turk J Biol 2021; 45:442-458. [PMID: 34803446 PMCID: PMC8573850 DOI: 10.3906/biy-2012-52] [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: 12/17/2020] [Accepted: 05/08/2021] [Indexed: 12/21/2022] Open
Abstract
Despite COVID-19 turned into a pandemic, no approved drug for the treatment or globally available vaccine is out yet. In such a global emergency, drug repurposing approach that bypasses a costly and long-time demanding drug discovery process is an effective way in search of finding drugs for the COVID-19 treatment. Recent studies showed that SARS-CoV-2 uses neuropilin-1 (NRP1) for host entry. Here we took advantage of structural information of the NRP1 in complex with C-terminal of spike (S) protein of SARS-CoV-2 to identify drugs that may inhibit NRP1 and S protein interaction. U.S. Food and Drug Administration (FDA) approved drugs were screened using docking simulations. Among top drugs, well-tolerated drugs were selected for further analysis. Molecular dynamics (MD) simulations of drugs-NRP1 complexes were run for 100 ns to assess the persistency of binding. MM/GBSA calculations from MD simulations showed that eltrombopag, glimepiride, sitagliptin, dutasteride, and ergotamine stably and strongly bind to NRP1. In silico Alanine scanning analysis revealed that Tyr297, Trp301, and Tyr353 amino acids of NRP1 are critical for drug binding. Validating the effect of drugs analyzed in this paper by experimental studies and clinical trials will expedite the drug discovery process for COVID-19.
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Affiliation(s)
- Şeref Gül
- Department of Chemical and Biological Engineering, Koç University, İstanbul Turkey.,Biotechnology Division, Department of Biology, Faculty of Science, İstanbul University, İstanbul Turkey
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Computational and in vitro experimental analyses of the anti-COVID-19 potential of Mortaparib and MortaparibPlus. Biosci Rep 2021; 41:229940. [PMID: 34647577 PMCID: PMC8527209 DOI: 10.1042/bsr20212156] [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: 09/08/2021] [Revised: 09/16/2021] [Accepted: 10/04/2021] [Indexed: 11/17/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has become a global health emergency. Although new vaccines have been generated and being implicated, discovery and application of novel preventive and control measures are warranted. We aimed to identify compounds that may possess the potential to either block the entry of virus to host cells or attenuate its replication upon infection. Using host cell surface receptor expression (angiotensin-converting enzyme 2 (ACE2) and Transmembrane protease serine 2 (TMPRSS2)) analysis as an assay, we earlier screened several synthetic and natural compounds and identified candidates that showed ability to down-regulate their expression. Here, we report experimental and computational analyses of two small molecules, Mortaparib and MortaparibPlus that were initially identified as dual novel inhibitors of mortalin and PARP-1, for their activity against SARS-CoV-2. In silico analyses showed that MortaparibPlus, but not Mortaparib, stably binds into the catalytic pocket of TMPRSS2. In vitro analysis of control and treated cells revealed that MortaparibPlus caused down-regulation of ACE2 and TMPRSS2; Mortaparib did not show any effect. Furthermore, computational analysis on SARS-CoV-2 main protease (Mpro) that also predicted the inhibitory activity of MortaparibPlus. However, cell-based antiviral drug screening assay showed 30-60% viral inhibition in cells treated with non-toxic doses of either MortaparibPlus or Mortaparib. The data suggest that these two closely related compounds possess multimodal anti-COVID-19 activities. Whereas MortaparibPlus works through direct interactions/effects on the host cell surface receptors (ACE2 and TMPRSS2) and the virus protein (Mpro), Mortaparib involves independent mechanisms, elucidation of which warrants further studies.
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50
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Bracquemond D, Muriaux D. Betacoronavirus Assembly: Clues and Perspectives for Elucidating SARS-CoV-2 Particle Formation and Egress. mBio 2021; 12:e0237121. [PMID: 34579570 PMCID: PMC8546641 DOI: 10.1128/mbio.02371-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In 2019, a new pandemic virus belonging to the betacoronavirus family emerged, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This new coronavirus appeared in Wuhan, China, and is responsible for severe respiratory pneumonia in humans, namely, coronavirus disease 2019 (COVID-19). Having infected almost 200 million people worldwide and caused more than 4.1 million deaths as of today, this new disease has raised a significant number of questions about its molecular mechanism of replication and, in particular, how infectious viral particles are produced. Although viral entry is well characterized, the full assembly steps of SARS-CoV-2 have still not been fully described. Coronaviruses, including SARS-CoV-2, have four main structural proteins, namely, the spike glycoprotein (S), the membrane glycoprotein (M), the envelope protein (E), and the nucleocapsid protein (N). All these proteins have key roles in the process of coronavirus assembly and budding. In this review, we gathered the current knowledge about betacoronavirus structural proteins involved in viral particle assembly, membrane curvature and scission, and then egress in order to suggest and question a coherent model for SARS-CoV-2 particle production and release.
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Affiliation(s)
- David Bracquemond
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS UMR9004, Montpellier, France
| | - Delphine Muriaux
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS UMR9004, Montpellier, France
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