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Ali MA, Caetano-Anollés G. AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Nucleocapsid Protein Variants. Viruses 2024; 16:1358. [PMID: 39339835 PMCID: PMC11435742 DOI: 10.3390/v16091358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 08/10/2024] [Accepted: 08/21/2024] [Indexed: 09/30/2024] Open
Abstract
The COVID-19 pandemic saw the emergence of various Variants of Concern (VOCs) that took the world by storm, often replacing the ones that preceded them. The characteristic mutant constellations of these VOCs increased viral transmissibility and infectivity. Their origin and evolution remain puzzling. With the help of data mining efforts and the GISAID database, a chronology of 22 haplotypes described viral evolution up until 23 July 2023. Since the three-dimensional atomic structures of proteins corresponding to the identified haplotypes are not available, ab initio methods were here utilized. Regions of intrinsic disorder proved to be important for viral evolution, as evidenced by the targeted change to the nucleocapsid (N) protein at the sequence, structure, and biochemical levels. The linker region of the N-protein, which binds to the RNA genome and self-oligomerizes for efficient genome packaging, was greatly impacted by mutations throughout the pandemic, followed by changes in structure and intrinsic disorder. Remarkably, VOC constellations acted co-operatively to balance the more extreme effects of individual haplotypes. Our strategy of mapping the dynamic evolutionary landscape of genetically linked mutations to the N-protein structure demonstrates the utility of ab initio modeling and deep learning tools for therapeutic intervention.
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Affiliation(s)
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
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2
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Orsini F, Bosica M, Martucci A, De Paola M, Comolli D, Pascente R, Forloni G, Fraser PE, Arancio O, Fioriti L. SARS-CoV-2 Nucleocapsid Protein Induces Tau Pathological Changes That Can Be Counteracted by SUMO2. Int J Mol Sci 2024; 25:7169. [PMID: 39000276 PMCID: PMC11241313 DOI: 10.3390/ijms25137169] [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: 05/31/2024] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
Neurologic manifestations are an immediate consequence of SARS-CoV-2 infection, the etiologic agent of COVID-19, which, however, may also trigger long-term neurological effects. Notably, COVID-19 patients with neurological symptoms show elevated levels of biomarkers associated with brain injury, including Tau proteins linked to Alzheimer's pathology. Studies in brain organoids revealed that SARS-CoV-2 alters the phosphorylation and distribution of Tau in infected neurons, but the mechanisms are currently unknown. We hypothesize that these pathological changes are due to the recruitment of Tau into stress granules (SGs) operated by the nucleocapsid protein (NCAP) of SARS-CoV-2. To test this hypothesis, we investigated whether NCAP interacts with Tau and localizes to SGs in hippocampal neurons in vitro and in vivo. Mechanistically, we tested whether SUMOylation, a posttranslational modification of NCAP and Tau, modulates their distribution in SGs and their pathological interaction. We found that NCAP and Tau colocalize and physically interact. We also found that NCAP induces hyperphosphorylation of Tau and causes cognitive impairment in mice infected with NCAP in their hippocampus. Finally, we found that SUMOylation modulates NCAP SG formation in vitro and cognitive performance in infected mice. Our data demonstrate that NCAP induces Tau pathological changes both in vitro and in vivo. Moreover, we demonstrate that SUMO2 ameliorates NCAP-induced Tau pathology, highlighting the importance of the SUMOylation pathway as a target of intervention against neurotoxic insults, such as Tau oligomers and viral infection.
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Affiliation(s)
- Franca Orsini
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, MI, Italy; (F.O.); (M.B.); (A.M.); (M.D.P.); (D.C.); (R.P.); (G.F.)
| | - Marco Bosica
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, MI, Italy; (F.O.); (M.B.); (A.M.); (M.D.P.); (D.C.); (R.P.); (G.F.)
| | - Annacarla Martucci
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, MI, Italy; (F.O.); (M.B.); (A.M.); (M.D.P.); (D.C.); (R.P.); (G.F.)
| | - Massimiliano De Paola
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, MI, Italy; (F.O.); (M.B.); (A.M.); (M.D.P.); (D.C.); (R.P.); (G.F.)
| | - Davide Comolli
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, MI, Italy; (F.O.); (M.B.); (A.M.); (M.D.P.); (D.C.); (R.P.); (G.F.)
| | - Rosaria Pascente
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, MI, Italy; (F.O.); (M.B.); (A.M.); (M.D.P.); (D.C.); (R.P.); (G.F.)
| | - Gianluigi Forloni
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, MI, Italy; (F.O.); (M.B.); (A.M.); (M.D.P.); (D.C.); (R.P.); (G.F.)
| | - Paul E. Fraser
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 2S8, Canada;
| | - Ottavio Arancio
- Department of Pathology and Cell Biology, Taub Institute for Research of Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY 10032, USA;
| | - Luana Fioriti
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, MI, Italy; (F.O.); (M.B.); (A.M.); (M.D.P.); (D.C.); (R.P.); (G.F.)
- Department of Pathology and Cell Biology, Taub Institute for Research of Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY 10032, USA;
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3
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Song J. Adenosine Triphosphate: The Primordial Molecule That Controls Protein Homeostasis and Shapes the Genome-Proteome Interface. Biomolecules 2024; 14:500. [PMID: 38672516 PMCID: PMC11048592 DOI: 10.3390/biom14040500] [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: 03/29/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Adenosine triphosphate (ATP) acts as the universal energy currency that drives various biological processes, while nucleic acids function to store and transmit genetic information for all living organisms. Liquid-liquid phase separation (LLPS) represents the common principle for the formation of membrane-less organelles (MLOs) composed of proteins rich in intrinsically disordered regions (IDRs) and nucleic acids. Currently, while IDRs are well recognized to facilitate LLPS through dynamic and multivalent interactions, the precise mechanisms by which ATP and nucleic acids affect LLPS still remain elusive. This review summarizes recent NMR results on the LLPS of human FUS, TDP-43, and the viral nucleocapsid (N) protein of SARS-CoV-2, as modulated by ATP and nucleic acids, revealing the following: (1) ATP binds to folded domains overlapping with nucleic-acid-binding interfaces; (2) ATP and nucleic acids interplay to biphasically modulate LLPS by competitively binding to overlapping pockets of folded domains and Arg/Lys within IDRs; (3) ATP energy-independently induces protein folding with the highest efficiency known so far. As ATP likely emerged in the prebiotic monomeric world, while LLPS represents a pivotal mechanism to concentrate and compartmentalize rare molecules for forming primordial cells, ATP appears to control protein homeostasis and shape genome-proteome interfaces throughout the evolutionary trajectory, from prebiotic origins to modern cells.
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Affiliation(s)
- Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore
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4
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Silonov SA, Smirnov EY, Shmidt EA, Kuznetsova IM, Turoverov KK, Fonin AV. Insights into the Cellular Localization and Functional Properties of TSPYL5 Protein. Int J Mol Sci 2023; 25:39. [PMID: 38203210 PMCID: PMC10779080 DOI: 10.3390/ijms25010039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/11/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
In recent years, the role of liquid-liquid phase separation (LLPS) and intrinsically disordered proteins (IDPs) in cellular molecular processes has received increasing attention from researchers. One such intrinsically disordered protein is TSPYL5, considered both as a marker and a potential therapeutic target for various oncological diseases. However, the role of TSPYL5 in intracellular processes remains unknown, and there is no clarity even in its intracellular localization. In this study, we characterized the intracellular localization and exchange dynamics with intracellular contents of TSPYL5 and its parts, utilizing TSPYL5 fusion proteins with EGFP. Our findings reveal that TSPYL5 can be localized in both the cytoplasm and nucleoplasm, including the nucleolus. The nuclear (nucleolar) localization of TSPYL5 is mediated by the nuclear/nucleolar localization sequences (NLS/NoLS) identified in the N-terminal intrinsically disordered region (4-27 aa), while its cytoplasmic localization is regulated by the ordered NAP-like domain (198-382 aa). Furthermore, our results underscore the significant role of the TSPYL5 N-terminal disordered region (1-198 aa) in the exchange dynamics with the nucleoplasm and its potential ability for phase separation. Bioinformatics analysis of the TSPYL5 interactome indicates its potential function as a histone and ribosomal protein chaperone. Taken together, these findings suggest a significant contribution of liquid-liquid phase separation to the processes involving TSPYL5, providing new insights into the role of this protein in the cell's molecular life.
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Affiliation(s)
- Sergey A. Silonov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Russian Academy of Sciences, St. Petersburg 194064, Russia; (E.Y.S.); (E.A.S.); (I.M.K.); (K.K.T.)
| | | | | | | | | | - Alexander V. Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Russian Academy of Sciences, St. Petersburg 194064, Russia; (E.Y.S.); (E.A.S.); (I.M.K.); (K.K.T.)
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5
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Rak A, Isakova-Sivak I, Rudenko L. Overview of Nucleocapsid-Targeting Vaccines against COVID-19. Vaccines (Basel) 2023; 11:1810. [PMID: 38140214 PMCID: PMC10747980 DOI: 10.3390/vaccines11121810] [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: 11/04/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
The new SARS-CoV-2 coronavirus, which emerged in late 2019, is a highly variable causative agent of COVID-19, a contagious respiratory disease with potentially severe complications. Vaccination is considered the most effective measure to prevent the spread and complications of this infection. Spike (S) protein-based vaccines were very successful in preventing COVID-19 caused by the ancestral SARS-CoV-2 strain; however, their efficacy was significantly reduced when coronavirus variants antigenically different from the original strain emerged in circulation. This is due to the high variability of this major viral antigen caused by escape from the immunity caused by the infection or vaccination with spike-targeting vaccines. The nucleocapsid protein (N) is a much more conserved SARS-CoV-2 antigen than the spike protein and has therefore attracted the attention of scientists as a promising target for broad-spectrum vaccine development. Here, we summarized the current data on various N-based COVID-19 vaccines that have been tested in animal challenge models or clinical trials. Despite the high conservatism of the N protein, escape mutations gradually occurring in the N sequence can affect its protective properties. During the three years of the pandemic, at least 12 mutations have arisen in the N sequence, affecting more than 40 known immunogenic T-cell epitopes, so the antigenicity of the N protein of recent SARS-CoV-2 variants may be altered. This fact should be taken into account as a limitation in the development of cross-reactive vaccines based on N-protein.
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Affiliation(s)
- Alexandra Rak
- Department of Virology, Institute of Experimental Medicine, St. Petersburg 197022, Russia; (I.I.-S.); (L.R.)
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6
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Lodola C, Secchi M, Sinigiani V, De Palma A, Rossi R, Perico D, Mauri PL, Maga G. Interaction of SARS-CoV-2 Nucleocapsid Protein and Human RNA Helicases DDX1 and DDX3X Modulates Their Activities on Double-Stranded RNA. Int J Mol Sci 2023; 24:ijms24065784. [PMID: 36982856 PMCID: PMC10058294 DOI: 10.3390/ijms24065784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
The nucleocapsid protein Np of SARS-CoV-2 is involved in the replication, transcription, and packaging of the viral genome, but it also plays a role in the modulation of the host cell innate immunity and inflammation response. Ectopic expression of Np alone was able to induce significant changes in the proteome of human cells. The cellular RNA helicase DDX1 was among the proteins whose levels were increased by Np expression. DDX1 and its related helicase DDX3X were found to physically interact with Np and to increase 2- to 4-fold its affinity for double-stranded RNA in a helicase-independent manner. Conversely, Np inhibited the RNA helicase activity of both proteins. These functional interactions among Np and DDX1 and DDX3X highlight novel possible roles played by these host RNA helicases in the viral life cycle.
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Affiliation(s)
- Camilla Lodola
- Institute of Molecular Genetics IGM CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100 Pavia, PV, Italy
| | - Massimiliano Secchi
- Institute of Molecular Genetics IGM CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100 Pavia, PV, Italy
| | - Virginia Sinigiani
- Institute of Molecular Genetics IGM CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100 Pavia, PV, Italy
| | - Antonella De Palma
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, MI, Italy
| | - Rossana Rossi
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, MI, Italy
| | - Davide Perico
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, MI, Italy
| | - Pier Luigi Mauri
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, MI, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100 Pavia, PV, Italy
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7
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Suramin Disturbs the Association of the N-Terminal Domain of SARS-CoV-2 Nucleocapsid Protein with RNA. Molecules 2023; 28:molecules28062534. [PMID: 36985506 PMCID: PMC10051649 DOI: 10.3390/molecules28062534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Suramin was originally used as an antiparasitic drug in clinics. Here, we demonstrate that suramin can bind to the N-terminal domain of SARS-CoV-2 nucleocapsid protein (N-NTD) and disturb its interaction with RNA. The BLI experiments showed that N-NTD interacts suramin with a dissociate constant (Kd = 2.74 μM) stronger than that of N-NTD with ssRNA-16 (Kd = 8.37 μM). Furthermore, both NMR titration experiments and molecular docking analysis suggested that suramin mainly binds to the positively charged cavity between the finger and the palm subdomains of N-NTD, and residues R88, R92, R93, I94, R95, K102 and A156 are crucial for N-NTD capturing suramin. Besides, NMR dynamics experiments showed that suramin-bound N-NTD adopts a more rigid structure, and the loop between β2-β3 exhibits fast motion on the ps-ns timescale, potentially facilitating suramin binding. Our findings not only reveal the molecular basis of suramin disturbing the association of SARS-CoV-2 N-NTD with RNA but also provide valuable structural information for the development of drugs against SARS-CoV-2.
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8
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Jahirul Islam M, Nawal Islam N, Siddik Alom M, Kabir M, Halim MA. A review on structural, non-structural, and accessory proteins of SARS-CoV-2: Highlighting drug target sites. Immunobiology 2023; 228:152302. [PMID: 36434912 PMCID: PMC9663145 DOI: 10.1016/j.imbio.2022.152302] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 10/30/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is a highly transmittable and pathogenic human coronavirus that first emerged in China in December 2019. The unprecedented outbreak of SARS-CoV-2 devastated human health within a short time leading to a global public health emergency. A detailed understanding of the viral proteins including their structural characteristics and virulence mechanism on human health is very crucial for developing vaccines and therapeutics. To date, over 1800 structures of non-structural, structural, and accessory proteins of SARS-CoV-2 are determined by cryo-electron microscopy, X-ray crystallography, and NMR spectroscopy. Designing therapeutics to target the viral proteins has several benefits since they could be highly specific against the virus while maintaining minimal detrimental effects on humans. However, for ongoing and future research on SARS-CoV-2, summarizing all the viral proteins and their detailed structural information is crucial. In this review, we compile comprehensive information on viral structural, non-structural, and accessory proteins structures with their binding and catalytic sites, different domain and motifs, and potential drug target sites to assist chemists, biologists, and clinicians finding necessary details for fundamental and therapeutic research.
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Affiliation(s)
- Md Jahirul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka 1215, Bangladesh
| | - Nafisa Nawal Islam
- Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Siddik Alom
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Mahmuda Kabir
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, 370 Paulding Avenue NW, Kennesaw, GA 30144, USA
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9
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Henri J, Minder L, Mohanasundaram K, Dilly S, Goupil-Lamy A, Di Primo C, Slama Schwok A. Neuropeptides, New Ligands of SARS-CoV-2 Nucleoprotein, a Potential Link between Replication, Inflammation and Neurotransmission. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228094. [PMID: 36432196 PMCID: PMC9698730 DOI: 10.3390/molecules27228094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]
Abstract
This work identifies new ligands of the nucleoprotein N of SARS-CoV-2 by in silico screening, which used a new model of N, built from an Alphafold model refined by molecular dynamic simulations. The ligands were neuropeptides, such as substance P (1-7) and enkephalin, bound at a large site of the C-terminal or associated with the N-terminal β-sheet. The BA4 and BA5 Omicron variants of N also exhibited a large site as in wt N, and an increased flexibility of the BA5 variant, enabling substance P binding. The binding sites of some ligands deduced from modeling in wt N were assessed by mutation studies in surface plasmon resonance experiments. Dynamic light scattering showed that the ligands impeded RNA binding to N, which likely inhibited replication. We suggest that the physiological role of these neuropeptides in neurotransmission, pain and vasodilation for cholecystokinin and substance P could be altered by binding to N. We speculate that N may link between viral replication and multiple pathways leading to long COVID-19 symptoms. Therefore, N may constitute a "danger hub" that needs to be inhibited, even at high cost for the host. Antivirals targeted to N may therefore reduce the risk of brain fog and stroke, and improve patients' health.
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Affiliation(s)
- Julien Henri
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR-CNRS 7238, Sorbonne Université, F-75005 Paris, France
| | - Laetitia Minder
- Institut Européen de Chimie et Biologie (IECB), CNRS, INSERM UAR 3033, US001, Univ. Bordeaux, F-33000 Bordeaux, France
| | - Kevin Mohanasundaram
- Saint Antoine Hospital, Centre de Recherche Saint Antoine, Sorbonne Université, Biology and Cancer Therapeutics, INSERM U938, F-75231 Paris, France
| | - Sébastien Dilly
- Saint Antoine Hospital, Centre de Recherche Saint Antoine, Sorbonne Université, Biology and Cancer Therapeutics, INSERM U938, F-75231 Paris, France
| | - Anne Goupil-Lamy
- Biovia, Dassault Systèmes, 10 Rue Marcel Dassault, CS40501, CEDEX, F-78946 Vélizy-Villacoublay, France
| | - Carmelo Di Primo
- CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, Univ. Bordeaux, F-33000 Bordeaux, France
| | - Anny Slama Schwok
- Saint Antoine Hospital, Centre de Recherche Saint Antoine, Sorbonne Université, Biology and Cancer Therapeutics, INSERM U938, F-75231 Paris, France
- Correspondence: or
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10
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Focosi D, Franchini M, Casadevall A. On the Need to Determine the Contribution of Anti-Nucleocapsid Antibodies as Potential Contributors to COVID-19 Convalescent Plasma Efficacy. Viruses 2022; 14:2378. [PMID: 36366476 PMCID: PMC9697776 DOI: 10.3390/v14112378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 01/31/2023] Open
Abstract
Historically the therapeutic potential of polyclonal passive immunotherapies in viral diseases has been related to antiviral neutralizing antibodies, but there is also considerable evidence that non-neutralizing antibodies can translate into clinical benefit as well. In the setting of SARS-CoV-2 infection, we review here in vitro and in vivo evidence supporting a contributing role for anti-nucleocapsid antibodies. Retrospective investigation of anti-nucleocapsid antibody levels in randomized clinical trials of COVID-19 convalescent plasma is warranted to better understand whether there is an association with efficacy or lack thereof.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy
| | - Massimo Franchini
- Division of Hematology and Transfusion Medicine, Carlo Poma Hospital, 46100 Mantua, Italy
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21287, USA
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11
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Guseva S, Perez LM, Camacho-Zarco A, Bessa LM, Salvi N, Malki A, Maurin D, Blackledge M. 1H, 13C and 15N Backbone chemical shift assignments of the n-terminal and central intrinsically disordered domains of SARS-CoV-2 nucleoprotein. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:255-260. [PMID: 33730325 PMCID: PMC7967780 DOI: 10.1007/s12104-021-10014-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/07/2021] [Indexed: 05/10/2023]
Abstract
The nucleoprotein (N) from SARS-CoV-2 is an essential cofactor of the viral replication transcription complex and as such represents an important target for viral inhibition. It has also been shown to colocalize to the transcriptase-replicase complex, where many copies of N decorate the viral genome, thereby protecting it from the host immune system. N has also been shown to phase separate upon interaction with viral RNA. N is a 419 amino acid multidomain protein, comprising two folded, RNA-binding and dimerization domains spanning residues 45-175 and 264-365 respectively. The remaining 164 amino acids are predicted to be intrinsically disordered, but there is currently no atomic resolution information describing their behaviour. Here we assign the backbone resonances of the first two intrinsically disordered domains (N1, spanning residues 1-44 and N3, spanning residues 176-263). Our assignment provides the basis for the identification of inhibitors and functional and interaction studies of this essential protein.
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Affiliation(s)
- Serafima Guseva
- University Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | | | | | | | - Nicola Salvi
- University Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | - Anas Malki
- University Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | - Damien Maurin
- University Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
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12
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Ji W. Coronaviruses: What Should We Know About the Characteristics of Viruses? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1318:23-39. [PMID: 33973170 DOI: 10.1007/978-3-030-63761-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The ongoing coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is highly contagious and fatal, posing a direct threat to human health and the global economy. Most strategies to prevent, control, and eradicate COVID-19 are established based on the specific characteristics of the pathogen. The quest for interruption and eradication of COVID-19 has moved research forward in understanding fundamental aspects of the virus genome, proteome, replication mechanisms, and virus-host interactions, which pave the way for the development of effective antiviral drugs and vaccines. This chapter provides an overview of recent progress in human coronavirus taxonomy, molecular features of the SARS-CoV-2 genome and proteome, and virus life cycle.
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Affiliation(s)
- Wei Ji
- Medical school, Liaocheng University, Liaocheng, China. .,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Liaocheng, China.
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13
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Schiavina M, Pontoriero L, Uversky VN, Felli IC, Pierattelli R. The highly flexible disordered regions of the SARS-CoV-2 nucleocapsid N protein within the 1-248 residue construct: sequence-specific resonance assignments through NMR. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:219-227. [PMID: 33660218 PMCID: PMC7928198 DOI: 10.1007/s12104-021-10009-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/15/2021] [Indexed: 05/04/2023]
Abstract
The nucleocapsid protein N from SARS-CoV-2 is one of the most highly expressed proteins by the virus and plays a number of important roles in the transcription and assembly of the virion within the infected host cell. It is expected to be characterized by a highly dynamic and heterogeneous structure as can be inferred by bioinformatics analyses as well as from the data available for the homologous protein from SARS-CoV. The two globular domains of the protein (NTD and CTD) have been investigated while no high-resolution information is available yet for the flexible regions of the protein. We focus here on the 1-248 construct which comprises two disordered fragments (IDR1 and IDR2) in addition to the N-terminal globular domain (NTD) and report the sequence-specific assignment of the two disordered regions, a step forward towards the complete characterization of the whole protein.
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Affiliation(s)
- Marco Schiavina
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, FI, Italy
| | - Letizia Pontoriero
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, FI, Italy
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Isabella C Felli
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, FI, Italy.
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, FI, Italy.
| | - Roberta Pierattelli
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, FI, Italy.
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, FI, Italy.
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14
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Guedes IA, Costa LSC, Dos Santos KB, Karl ALM, Rocha GK, Teixeira IM, Galheigo MM, Medeiros V, Krempser E, Custódio FL, Barbosa HJC, Nicolás MF, Dardenne LE. Drug design and repurposing with DockThor-VS web server focusing on SARS-CoV-2 therapeutic targets and their non-synonym variants. Sci Rep 2021; 11:5543. [PMID: 33692377 PMCID: PMC7946942 DOI: 10.1038/s41598-021-84700-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/16/2021] [Indexed: 02/07/2023] Open
Abstract
The COVID-19 caused by the SARS-CoV-2 virus was declared a pandemic disease in March 2020 by the World Health Organization (WHO). Structure-Based Drug Design strategies based on docking methodologies have been widely used for both new drug development and drug repurposing to find effective treatments against this disease. In this work, we present the developments implemented in the DockThor-VS web server to provide a virtual screening (VS) platform with curated structures of potential therapeutic targets from SARS-CoV-2 incorporating genetic information regarding relevant non-synonymous variations. The web server facilitates repurposing VS experiments providing curated libraries of currently available drugs on the market. At present, DockThor-VS provides ready-for-docking 3D structures for wild type and selected mutations for Nsp3 (papain-like, PLpro domain), Nsp5 (Mpro, 3CLpro), Nsp12 (RdRp), Nsp15 (NendoU), N protein, and Spike. We performed VS experiments of FDA-approved drugs considering the therapeutic targets available at the web server to assess the impact of considering different structures and mutations to identify possible new treatments of SARS-CoV-2 infections. The DockThor-VS is freely available at www.dockthor.lncc.br .
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Affiliation(s)
- Isabella A Guedes
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Leon S C Costa
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Karina B Dos Santos
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Ana L M Karl
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | | | - Iury M Teixeira
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Marcelo M Galheigo
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Vivian Medeiros
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | | | - Fábio L Custódio
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Helio J C Barbosa
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Marisa F Nicolás
- Laboratório de Bioinformática (Labinfo), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil.
| | - Laurent E Dardenne
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil.
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15
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Khan S, Hussain Z, Safdar M, Khan A, Wei DQ. Targeting the N-terminal domain of the RNA-binding protein of the SARS-CoV-2 with high affinity natural compounds to abrogate the protein-RNA interaction: a molecular dynamics study. J Biomol Struct Dyn 2021; 40:6286-6294. [PMID: 33554747 DOI: 10.1080/07391102.2021.1882337] [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] [Indexed: 12/28/2022]
Abstract
The emergence of COVID-19 took the world by shock in December 2019, starting from Wuhan, China and swiftly spreading across the globe. The number of COVID-19 cases continues to rise which is a global burden on the health care system worldwide. Efforts are continuing to come up with a solution either to develop a small molecular inhibitor or vaccine, but still no success. In the fight against SARS-CoV-2, targeting a different protein of the SARS-CoV-2 is the need of the hour to impede and relinquish the current pandemic. Therefore, in this study, computational modelling and simulation approaches are used to target the N-terminal domain of the phosphor-nucleoprotein (RNA binding protein), which is primarily responsible for binding and packing the viral genome to get ribonucleoprotein complex (RNP). Our multi-step drug screening approach shortlisted potential drugs. These top hits were confirmed by re-docking which revealed that the interacting molecules block the key residues i.e. Thr57, His59, Ser105, Arg107, and Arg177 and thus ultimately block the NTD from RNA recognition. Furthermore, the activity of the top four hits was also confirmed by using molecular dynamics simulation and free energy calculation. Our analysis suggests that these top hits possess strong inhibitory properties and should be tested experimentally. In conclusion, we hope these top hits would abrogate the binding of RNA and the NTD of the SARS-CoV-2, which might be helpful to combat COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sohail Khan
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zahid Hussain
- Center for Biotechnology and Microbiology, University of Swat, Mingora, Pakistan
| | - Muhammad Safdar
- Faculty of Pharmacy, Gomal University, Dera Ismail Khan, Pakistan
| | - Abbas Khan
- State Key Lab of Microbial Metabolism, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- State Key Lab of Microbial Metabolism, Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.,Peng Cheng Laboratory, Shenzhen, Guangdong, China
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16
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Wang H, Wu X, Zhang X, Hou X, Liang T, Wang D, Teng F, Dai J, Duan H, Guo S, Li Y, Yu X. SARS-CoV-2 Proteome Microarray for Mapping COVID-19 Antibody Interactions at Amino Acid Resolution. ACS CENTRAL SCIENCE 2020; 6:2238-2249. [PMID: 33372199 PMCID: PMC7586461 DOI: 10.1021/acscentsci.0c00742] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Indexed: 05/07/2023]
Abstract
Comprehensive profiling of humoral antibody response to severe acute respiratory syndrome (SARS) coronavirus-2 (CoV-2) proteins is essential in understanding the host immunity and in developing diagnostic tests and vaccines. To address this concern, we developed a SARS-CoV-2 proteome peptide microarray to analyze antibody interactions at the amino acid resolution. With the array, we demonstrate the feasibility of employing SARS-CoV-1 antibodies to detect the SARS-CoV-2 nucleocapsid phosphoprotein. The first landscape of B-cell epitopes for SARS-CoV-2 IgM and IgG antibodies in the serum of 10 coronavirus disease of 2019 (COVID-19) patients with early infection is also constructed. With array data and structural analysis, a peptide epitope for neutralizing antibodies within the SARS-CoV-2 spike receptor-binding domain's interaction interface with the angiotensin-converting enzyme 2 receptor was predicted. All the results demonstrate the utility of our microarray as a platform to determine the changes of antibody responses in COVID-19 patients and animal models as well as to identify potential targets for diagnosis and treatment.
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Affiliation(s)
- Hongye Wang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xian Wu
- Department
of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union
Medical College, Beijing 100730, China
| | - Xiaomei Zhang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xin Hou
- Department
of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union
Medical College, Beijing 100730, China
| | - Te Liang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Dan Wang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fei Teng
- Department
of Emergency Medicine, Beijing Chao-Yang Hospital, Capital Medical University, & Beijing Key Laboratory of Cardiopulmonary
Cerebral Resuscitation, Beijing 100020, China
| | - Jiayu Dai
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hu Duan
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Shubin Guo
- Department
of Emergency Medicine, Beijing Chao-Yang Hospital, Capital Medical University, & Beijing Key Laboratory of Cardiopulmonary
Cerebral Resuscitation, Beijing 100020, China
| | - Yongzhe Li
- Department
of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union
Medical College, Beijing 100730, China
- (Y.L.)
| | - Xiaobo Yu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
- (X.Y.)
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17
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Littler DR, MacLachlan BJ, Watson GM, Vivian JP, Gully BS. A pocket guide on how to structure SARS-CoV-2 drugs and therapies. Biochem Soc Trans 2020; 48:2625-2641. [PMID: 33258925 PMCID: PMC7752054 DOI: 10.1042/bst20200396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 01/18/2023]
Abstract
The race to identify a successful treatment for COVID19 will be defined by fundamental research into the replication cycle of the SARS-CoV-2 virus. This has identified five distinct stages from which numerous vaccination and clinical trials have emerged alongside an innumerable number of drug discovery studies currently in development for disease intervention. Informing every step of the viral replication cycle has been an unprecedented 'call-to-arms' by the global structural biology community. Of the 20 main SARS-CoV-2 proteins, 13 have been resolved structurally for SARS-CoV-2 with most having a related SARS-CoV and MERS-CoV structural homologue totalling some 300 structures currently available in public repositories. Herein, we review the contribution of structural studies to our understanding of the virus and their role in structure-based development of therapeutics.
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Affiliation(s)
- Dene R. Littler
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Bruce J. MacLachlan
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Gabrielle M. Watson
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Julian P. Vivian
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Benjamin S. Gully
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
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18
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Alothaid H, Aldughaim MSK, El Bakkouri K, AlMashhadi S, Al-Qahtani AA. Similarities between the effect of SARS-CoV-2 and HCV on the cellular level, and the possible role of ion channels in COVID19 progression: a review of potential targets for diagnosis and treatment. Channels (Austin) 2020; 14:403-412. [PMID: 33092458 PMCID: PMC7588196 DOI: 10.1080/19336950.2020.1837439] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has prompted an urgent need to identify effective medicines for the prevention and treatment of the disease. A comparative analysis between SARS-CoV-2 and Hepatitis C Virus (HCV) can expand the available knowledge regarding the virology and potential drug targets against these viruses. Interestingly, comparing HCV with SARS-CoV-2 reveals major similarities between them, ranging from the ion channels that are utilized, to the symptoms that are exhibited by patients. Via this comparative analysis, and from what is known about HCV, the most promising treatments for COVID-19 can focus on the reduction of viral load, treatment of pulmonary system damages, and reduction of inflammation. In particular, the drugs that show most potential in this regard include ritonavir, a combination of peg-IFN, and lumacaftor-ivacaftor. This review anaylses SARS-CoV-2 from the perspective of the role of ion homeostasis and channels in viral pathomechanism. We also highlight other novel treatment approaches that can be used for both treatment and prevention of COVID-19. The relevance of this review is to offer high-quality evidence that can be used as the basis for the identification of potential solutions to the COVID-19 pandemic.
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Affiliation(s)
- Hani Alothaid
- Department of Basic Sciences, Faculty of Applied Medical Sciences, Al-Baha University , Al-Baha, Saudi Arabia
| | | | - Karim El Bakkouri
- Research Center, King Fahad Medical City , Riyadh, Saudi Arabia.,Rapid Test Development Department, SciMed Services and Solutions , Brussels, Belgium
| | - Sufana AlMashhadi
- Research Center, King Fahad Medical City , Riyadh, Saudi Arabia.,McGovern Institute for Brain Research, Massachusetts Institute of Technology , Cambridge, USA
| | - Ahmed A Al-Qahtani
- Department of Infection and Immunity, Research Centre, King Faisal Specialist Hospital & Research Centre , Riyadh, Saudi Arabia.,Department of Microbiology and Immunology, School of Medicine, Alfaisal University , Riyadh, Saudi Arabia
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19
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SARS-CoV-2 nucleocapsid and Nsp3 binding: an in silico study. Arch Microbiol 2020; 203:59-66. [PMID: 32749662 PMCID: PMC7401470 DOI: 10.1007/s00203-020-01998-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/16/2020] [Accepted: 07/23/2020] [Indexed: 12/18/2022]
Abstract
Severe acute respiratory syndrome virus 2 (SARS-CoV-2) belongs to the single-stranded positive-sense RNA family. The virus contains a large genome that encodes four structural proteins, small envelope (E), matrix (M), nucleocapsid phosphoprotein (N), spike (S), and 16 nonstructural proteins (nsp1-16) that together, ensure replication of the virus in the host cell. Among these proteins, the interactions of N and Nsp3 are essential that links the viral genome for processing. The N proteins reside at CoV RNA synthesis sites known as the replication-transcription complexes (RTCs). The N-terminal of N has RNA-binding domain (N-NTD), capturing the RNA genome while the C-terminal domain (N-CTD) anchors the viral Nsp3, a component of RTCs. Although the structural information has been recently released, the residues involved in contacts between N-CTD with Nsp3 are still unknown. To find the residues involved in interactions between two proteins, three-dimensional structures of both proteins were retrieved and docked using HADDOCK. Residues at N-CTD were detected in interaction with L499, R500, K501, V502, P503, T504, D505, N506, Y507, I508, T509, K529, K530K532, S533 of Nsp3 and N-NTD to synthesize SARS-CoV-2 RNA. The interaction between Nsp3 and CTD of N protein may be a potential drug target. The current study provides information for better understanding the interaction between N protein and Nsp3 that could be a possible target for future inhibitors.
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20
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Perdikari TM, Murthy AC, Ryan VH, Watters S, Naik MT, Fawzi NL. SARS-CoV-2 nucleocapsid protein undergoes liquid-liquid phase separation stimulated by RNA and partitions into phases of human ribonucleoproteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.09.141101. [PMID: 32577653 PMCID: PMC7302208 DOI: 10.1101/2020.06.09.141101] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tightly packed complexes of nucleocapsid protein and genomic RNA form the core of viruses and may assemble within viral factories, dynamic compartments formed within the host cells. Here, we examine the possibility that the multivalent RNA-binding nucleocapsid protein (N) from the severe acute respiratory syndrome coronavirus (SARS-CoV-2) compacts RNA via protein-RNA liquid-liquid phase separation (LLPS) and that N interactions with host RNA-binding proteins are mediated by phase separation. To this end, we created a construct expressing recombinant N fused to a N-terminal maltose binding protein tag which helps keep the oligomeric N soluble for purification. Using in vitro phase separation assays, we find that N is assembly-prone and phase separates avidly. Phase separation is modulated by addition of RNA and changes in pH and is disfavored at high concentrations of salt. Furthermore, N enters into in vitro phase separated condensates of full-length human hnRNPs (TDP-43, FUS, and hnRNPA2) and their low complexity domains (LCs). However, N partitioning into the LC of FUS, but not TDP-43 or hnRNPA2, requires cleavage of the solubilizing MBP fusion. Hence, LLPS may be an essential mechanism used for SARS-CoV-2 and other RNA viral genome packing and host protein co-opting, functions necessary for viral replication and hence infectivity.
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Affiliation(s)
| | - Anastasia C Murthy
- Molecular Biology, Cell Biology & Biochemistry Graduate Program, Brown University, Providence, RI, USA
| | - Veronica H Ryan
- Neuroscience Graduate Program, Brown University, Providence, RI, USA
| | - Scott Watters
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA
| | - Mandar T Naik
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA
- Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA
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21
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Ye Q, West AM, Silletti S, Corbett KD. Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.17.100685. [PMID: 32511359 PMCID: PMC7263487 DOI: 10.1101/2020.05.17.100685] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The COVID-2019 pandemic is the most severe acute public health threat of the twenty-first century. To properly address this crisis with both robust testing and novel treatments, we require a deep understanding of the life cycle of the causative agent, the SARS-CoV-2 coronavirus. Here, we examine the architecture and self-assembly properties of the SARS-CoV-2 nucleocapsid protein, which packages viral RNA into new virions. We determined a 1.4 Å resolution crystal structure of this protein's N2b domain, revealing a compact, intertwined dimer similar to that of related coronaviruses including SARS-CoV. While the N2b domain forms a dimer in solution, addition of the C-terminal spacer B/N3 domain mediates formation of a homotetramer. Using hydrogen-deuterium exchange mass spectrometry, we find evidence that at least part of this putatively disordered domain is structured, potentially forming an α-helix that self-associates and cooperates with the N2b domain to mediate tetramer formation. Finally, we map the locations of amino acid substitutions in the N protein from over 38,000 SARS-CoV-2 genome sequences. We find that these substitutions are strongly clustered in the protein's N2a linker domain, and that substitutions within the N1b and N2b domains cluster away from their functional RNA binding and dimerization interfaces. Overall, this work reveals the architecture and self-assembly properties of a key protein in the SARS-CoV-2 life cycle, with implications for both drug design and antibody-based testing.
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Affiliation(s)
- Qiaozhen Ye
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Alan M.V. West
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Steve Silletti
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
| | - Kevin D. Corbett
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA
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