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Wei X, Chan CL, Zhou Y, Tang K, Chen J, Wang S, Chan JFW, Yuan S, Li H, Sun H. Mechanistic insights into bismuth(iii) inhibition of SARS-CoV-2 helicase. Chem Sci 2024; 15:10065-10072. [PMID: 38966375 PMCID: PMC11220592 DOI: 10.1039/d3sc06961c] [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: 01/09/2024] [Accepted: 05/03/2024] [Indexed: 07/06/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 resulted in a global public health crisis. In addition to vaccines, the development of effective therapy is highly desirable. Targeting a protein that plays a critical role in virus replication may allow pan-spectrum antiviral drugs to be developed. Among SARS-CoV-2 proteins, helicase (i.e., non-structural protein 13) is considered as a promising antiviral drug target due to its highly conserved sequence, unique structure and function. Herein, we demonstrate SARS-CoV-2 helicase as a target of bismuth-based antivirals in virus-infected mammalian cells by a metal-tagged antibody approach. To search for more potent bismuth-based antivirals, we further screened a panel of bismuth compounds towards inhibition of ATPase and DNA unwinding activity of nsp13 and identified a highly potent bismuth compound Bi(5-aminotropolonate)3, namely Bi(Tro-NH2)3 with an IC50 of 30 nM for ATPase. We show that bismuth-based compounds inhibited nsp13 unwinding activity via disrupting the binding of ATP and the DNA substrate to viral helicase. Binding of Bi(iii) to nsp13 also abolished the interaction between nsp12 and nsp13 as evidenced by immunofluorescence and co-immunoprecipitation assays. Finally, we validate our in vitro data in SARS-CoV-2 infected mammalian cells. Notably, Bi(6-TG)3 exhibited an EC50 of 1.18 ± 0.09 μM with a selective index of 847 in VeroE6-TMPRSS2 infected cells. This study highlights the important role of helicase for the development of more effective antiviral drugs to combat SARS-CoV-2 infection.
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Affiliation(s)
- Xueying Wei
- Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics on Heath and Environment, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
- Department of Microbiology and State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Chun-Lung Chan
- Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics on Heath and Environment, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Ying Zhou
- Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics on Heath and Environment, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Kaiming Tang
- Department of Microbiology and State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Jingxin Chen
- Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics on Heath and Environment, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Suyu Wang
- Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics on Heath and Environment, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology and State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Shuofeng Yuan
- Department of Microbiology and State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Hongyan Li
- Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics on Heath and Environment, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
| | - Hongzhe Sun
- Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics on Heath and Environment, The University of Hong Kong Pokfulam Hong Kong Special Administrative Region China
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Hassan SS, Bhattacharya T, Nawn D, Jha I, Basu P, Redwan EM, Lundstrom K, Barh D, Andrade BS, Tambuwala MM, Aljabali AA, Hromić-Jahjefendić A, Baetas-da-Cruz W, Serrano-Aroca Á, Uversky VN. SARS-CoV-2 NSP14 governs mutational instability and assists in making new SARS-CoV-2 variants. Comput Biol Med 2024; 170:107899. [PMID: 38232455 DOI: 10.1016/j.compbiomed.2023.107899] [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: 09/26/2023] [Revised: 12/03/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the rapidly evolving RNA virus behind the COVID-19 pandemic, has spawned numerous variants since its 2019 emergence. The multifunctional Nonstructural protein 14 (NSP14) enzyme, possessing exonuclease and messenger RNA (mRNA) capping capabilities, serves as a key player. Notably, single and co-occurring mutations within NSP14 significantly influence replication fidelity and drive variant diversification. This study comprehensively examines 120 co-mutations, 68 unique mutations, and 160 conserved residues across NSP14 homologs, shedding light on their implications for phylogenetic patterns, pathogenicity, and residue interactions. Quantitative physicochemical analysis categorizes 3953 NSP14 variants into three clusters, revealing genetic diversity. This research underscoresthe dynamic nature of SARS-CoV-2 evolution, primarily governed by NSP14 mutations. Understanding these genetic dynamics provides valuable insights for therapeutic and vaccine development.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Tanishta Bhattacharya
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, IISER Berhampur Transit campus (Govt. ITI Building), Engg. School Junction, Berhampur, 760010, Odisha, India.
| | - Debaleena Nawn
- Indian Research Institute for Integrated Medicine (IRIIM), Unsani, Howrah, 711302, West Bengal, India.
| | - Ishana Jha
- Department of Bioinformatics, Pondicherry University, Chinna Kalapet, Kalapet, Puducherry 605014, India.
| | - Pallab Basu
- School of Physics, University of the Witwatersrand, Johannesburg, Braamfontein 2000, 721140, South Africa; Adjunct Faculty, Woxsen School of Sciences, Woxsen University, Telangana, 500 033, 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.
| | | | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, 721172, India; Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil.
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest of Bahia (UESB), Jequié 45083-900, Brazil.
| | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK; College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah, United Arab Emirates.
| | - Alaa A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan.
| | - Altijana Hromić-Jahjefendić
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Hrasnicka cesta 15, 71000 Sarajevo, Bosnia and Herzegovina.
| | - Wagner Baetas-da-Cruz
- Centre for Experimental Surgery, Translational Laboratory in Molecular Physiology, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, c/Guillem de Castro 94, 46001 Valencia, Spain.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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