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Valadan R, Alizadeh-Navaei R, Lagzian M, Saeedi M, Roozbeh F, Hedayatizadeh-Omran A, Amanlou M. Repurposing naproxen as a potential nucleocapsid antagonist of beta-coronaviruses: targeting a conserved protein in the search for a broad-spectrum treatment option. J Biomol Struct Dyn 2024:1-16. [PMID: 38407203 DOI: 10.1080/07391102.2024.2321245] [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: 06/06/2023] [Accepted: 02/14/2024] [Indexed: 02/27/2024]
Abstract
Ongoing mutations in the coronavirus family, especially beta-coronaviruses, raise new concerns about the possibility of new unexpected outbreaks. Therefore, it is crucial to explore new alternative treatments to reduce the impact of potential future strains until new vaccines can be developed. A promising approach to combat the virus is to target its conserved parts such as the nucleocapsid, especially via repurposing of existing drugs. The possibility of this approach is explored here to find a potential anti-nucleocapsid compound to target these viruses. 3D models of the N- and C-terminal domains (CTDs) of the nucleocapsid consensus sequence were constructed. Each domain was then screened against an FDA-approved drug database, and the most promising candidate was selected for further analysis. A 100 ns molecular dynamics (MD) simulation was conducted to analyze the final candidate in more detail. Naproxen was selected and found to interact with the N-terminal domain via conserved salt bridges and hydrogen bonds which are completely conserved among all Coronaviridae members. MD analysis also revealed that all relevant coordinates of naproxen with N terminal domain were kept during 100 ns of simulation time. This study also provides insights into the specific interaction of naproxen with conserved RNA binding pocket of the nucleocapsid that could interfere with the packaging of the viral genome into capsid and virus assembly. Additionally, the in-vitro binding assay demonstrated direct interaction between naproxen and recombinant nucleocapsid protein, further supporting the computational predictions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Reza Valadan
- Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Molecular and Cell Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Reza Alizadeh-Navaei
- Gastrointestinal Cancer Research Center, Non-Communicable Disease Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Milad Lagzian
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Majid Saeedi
- Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
- Pharmaceutical Sciences Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Fatemeh Roozbeh
- Infectious Specialist, Mazandaran University of Medical Sciences, Sari, Iran
| | - Akbar Hedayatizadeh-Omran
- Gastrointestinal Cancer Research Center, Non-Communicable Disease Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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Lee E, Redzic JS, Saviola AJ, Li X, Ebmeier CC, Kutateladze T, Hansen KC, Zhao R, Ahn N, Sluchanko NN, Eisenmesser E. Molecular insight into the specific interactions of the SARS-Coronavirus-2 nucleocapsid with RNA and host protein. Protein Sci 2023; 32:e4603. [PMID: 36807437 PMCID: PMC10019451 DOI: 10.1002/pro.4603] [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: 12/20/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) nucleocapsid protein is the most abundantly expressed viral protein during infection where it targets both RNA and host proteins. However, identifying how a single viral protein interacts with so many different targets remains a challenge, providing the impetus here for identifying the interaction sites through multiple methods. Through a combination of nuclear magnetic resonance (NMR), electron microscopy, and biochemical methods, we have characterized nucleocapsid interactions with RNA and with three host proteins, which include human cyclophilin-A, Pin1, and 14-3-3τ. Regarding RNA interactions, the nucleocapsid protein N-terminal folded domain preferentially interacts with smaller RNA fragments relative to the C-terminal region, suggesting an initial RNA engagement is largely dictated by this N-terminal region followed by weaker interactions to the C-terminal region. The nucleocapsid protein forms 10 nm ribonuclear complexes with larger RNA fragments that include 200 and 354 nucleic acids, revealing its potential diversity in sequestering different viral genomic regions during viral packaging. Regarding host protein interactions, while the nucleocapsid targets all three host proteins through its serine-arginine-rich region, unstructured termini of the nucleocapsid protein also engage host cyclophilin-A and host 14-3-3τ. Considering these host proteins play roles in innate immunity, the SARS-CoV-2 nucleocapsid protein may block the host response by competing interactions. Finally, phosphorylation of the nucleocapsid protein quenches an inherent dynamic exchange process within its serine-arginine-rich region. Our studies identify many of the diverse interactions that may be important for SARS-CoV-2 pathology during infection.
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Affiliation(s)
- Eunjeong Lee
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Jasmina S. Redzic
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Anthony J. Saviola
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | | | - Tatiana Kutateladze
- Department of PharmacologySchool of Medicine, University of Colorado DenverAuroraColoradoUSA
| | - Kirk Charles Hansen
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Natalie Ahn
- Department of BiochemistryUniversity of Colorado BoulderBoulderColoradoUSA
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of SciencesMoscowRussia
| | - Elan Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
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Chechetkin VR, Lobzin VV. Evolving ribonucleocapsid assembly/packaging signals in the genomes of the human and animal coronaviruses: targeting, transmission and evolution. J Biomol Struct Dyn 2022; 40:11239-11263. [PMID: 34338591 DOI: 10.1080/07391102.2021.1958061] [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] [Indexed: 10/20/2022]
Abstract
A world-wide COVID-19 pandemic intensified strongly the studies of molecular mechanisms related to the coronaviruses. The origin of coronaviruses and the risks of human-to-human, animal-to-human and human-to-animal transmission of coronaviral infections can be understood only on a broader evolutionary level by detailed comparative studies. In this paper, we studied ribonucleocapsid assembly-packaging signals (RNAPS) in the genomes of all seven known pathogenic human coronaviruses, SARS-CoV, SARS-CoV-2, MERS-CoV, HCoV-OC43, HCoV-HKU1, HCoV-229E and HCoV-NL63 and compared them with RNAPS in the genomes of the related animal coronaviruses including SARS-Bat-CoV, MERS-Camel-CoV, MHV, Bat-CoV MOP1, TGEV and one of camel alphacoronaviruses. RNAPS in the genomes of coronaviruses were evolved due to weakly specific interactions between genomic RNA and N proteins in helical nucleocapsids. Combining transitional genome mapping and Jaccard correlation coefficients allows us to perform the analysis directly in terms of underlying motifs distributed over the genome. In all coronaviruses, RNAPS were distributed quasi-periodically over the genome with the period about 54 nt biased to 57 nt and to 51 nt for the genomes longer and shorter than that of SARS-CoV, respectively. The comparison with the experimentally verified packaging signals for MERS-CoV, MHV and TGEV proved that the distribution of particular motifs is strongly correlated with the packaging signals. We also found that many motifs were highly conserved in both characters and positioning on the genomes throughout the lineages that make them promising therapeutic targets. The mechanisms of encapsidation can affect the recombination and co-infection as well.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vladimir R Chechetkin
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia
| | - Vasily V Lobzin
- School of Physics, University of Sydney, Sydney, NSW, Australia
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Saville JW, Berezuk AM, Srivastava SS, Subramaniam S. Three-Dimensional Visualization of Viral Structure, Entry, and Replication Underlying the Spread of SARS-CoV-2. Chem Rev 2022; 122:14066-14084. [PMID: 35863749 PMCID: PMC9344915 DOI: 10.1021/acs.chemrev.1c01062] [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] [Indexed: 11/23/2022]
Abstract
![]()
The global spread
of SARS-CoV-2 has proceeded at an unprecedented
rate. Remarkably, characterization of the virus using modern tools
in structural biology has also progressed at exceptional speed. Advances
in electron-based imaging techniques, combined with decades of foundational
studies on related viruses, have enabled the research community to
rapidly investigate structural aspects of the novel coronavirus from
the level of individual viral proteins to imaging the whole virus
in a native context. Here, we provide a detailed review of the structural
biology and pathobiology of SARS-CoV-2 as it relates to all facets
of the viral life cycle, including cell entry, replication, and three-dimensional
(3D) packaging based on insights obtained from X-ray crystallography,
cryo-electron tomography, and single-particle cryo-electron microscopy.
The structural comparison between SARS-CoV-2 and the related earlier
viruses SARS-CoV and MERS-CoV is a common thread throughout this review.
We conclude by highlighting some of the outstanding unanswered structural
questions and underscore areas that are under rapid current development
such as the design of effective therapeutics that block viral infection.
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Affiliation(s)
- James W Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Alison M Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Shanti S Srivastava
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3.,Gandeeva Therapeutics Inc., Vancouver, British Columbia, Canada, V5C 6N5
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O’Leary VB, Dolly OJ, Höschl C, Černa M, Ovsepian SV. Unpacking Pandora From Its Box: Deciphering the Molecular Basis of the SARS-CoV-2 Coronavirus. Int J Mol Sci 2020; 22:ijms22010386. [PMID: 33396557 PMCID: PMC7795774 DOI: 10.3390/ijms22010386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/25/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
An enigmatic localized pneumonia escalated into a worldwide COVID-19 pandemic from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This review aims to consolidate the extensive biological minutiae of SARS-CoV-2 which requires decipherment. Having one of the largest RNA viral genomes, the single strand contains the genes ORF1ab, S, E, M, N and ten open reading frames. Highlighting unique features such as stem-loop formation, slippery frameshifting sequences and ribosomal mimicry, SARS-CoV-2 represents a formidable cellular invader. Hijacking the hosts translational engine, it produces two polyprotein repositories (pp1a and pp1ab), armed with self-cleavage capacity for production of sixteen non-structural proteins. Novel glycosylation sites on the spike trimer reveal unique SARS-CoV-2 features for shielding and cellular internalization. Affording complexity for superior fitness and camouflage, SARS-CoV-2 challenges diagnosis and vaccine vigilance. This review serves the scientific community seeking in-depth molecular details when designing drugs to curb transmission of this biological armament.
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Affiliation(s)
- Valerie Bríd O’Leary
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruska 87, Vinohrady, 10000 Prague, Czech Republic;
- Department of Experimental Neurobiology, National Institute of Mental Health, Research Programme 1, Topolova 748, 25067 Klecany, Czech Republic; (C.H.); (S.V.O.)
- Correspondence:
| | - Oliver James Dolly
- International Centre for Neurotherapeutics, Dublin City University, Collins Avenue, Dublin 9, Ireland;
| | - Cyril Höschl
- Department of Experimental Neurobiology, National Institute of Mental Health, Research Programme 1, Topolova 748, 25067 Klecany, Czech Republic; (C.H.); (S.V.O.)
- Department of Psychiatry and Medical Psychology, Third Faculty of Medicine, Charles University, Ruska 87, Vinohrady, 10000 Prague, Czech Republic
| | - Marie Černa
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruska 87, Vinohrady, 10000 Prague, Czech Republic;
| | - Saak Victor Ovsepian
- Department of Experimental Neurobiology, National Institute of Mental Health, Research Programme 1, Topolova 748, 25067 Klecany, Czech Republic; (C.H.); (S.V.O.)
- International Centre for Neurotherapeutics, Dublin City University, Collins Avenue, Dublin 9, Ireland;
- Department of Psychiatry and Medical Psychology, Third Faculty of Medicine, Charles University, Ruska 87, Vinohrady, 10000 Prague, Czech Republic
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