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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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Emelyanova EV. Micromycete Responses to Acetone: Electrochemical Express Evaluation of Acetone Metabolism. Appl Biochem Biotechnol 2023; 195:6359-6368. [PMID: 36867387 DOI: 10.1007/s12010-023-04408-x] [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] [Accepted: 02/17/2023] [Indexed: 03/04/2023]
Abstract
The biosensor method has not yet been applied to study the fungus-acetone interaction. The first electrochemical (amperometric) study of Fusarium oxysporum f. sp. vasinfectum cells' responses to acetone was performed to evaluate the initial stages of the metabolism of acetone in the cells of the micromycete. Using a laboratory model of a membrane microbial sensor based on the micromycete cells, it was found that the fungus had constitutive enzyme systems that were involved in acetone transport into fungal cells. The research showed that uninduced by acetone cells had degradative activity against acetone. A positive cooperativity of acetone binding with enzymes initiating acetone degradation was revealed. Oxygen concentration affected the activation of cell enzymes initiating acetone degradation, but the cells' activity in the presence of acetone maintained even at low oxygen concentration. Kinetic parameters (the maximum rate of the cells' response to substrate and the half-saturation constant) of the processes causing the fungal cells' response to acetone were calculated. The results demonstrated the convenience of the biosensor method for assessing the potential of the micromycete as a substrate-degrading culture. In the future, the mechanism of response to acetone for microbial cells will be studied.
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Affiliation(s)
- Elena V Emelyanova
- Laboratory of Biosensors, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Moscow Region, Pushchino, 142290, Russian Federation.
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Krivoshey AV, Efremov AA, Matveishina EK, Panova VV, Vrzheshch PV. Simulation of the Level of Prostaglandins in Open Systems under the Action of Nonsteroidal Anti-Inflammatory Drugs. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021050289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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