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Susceptibility of spike glycoprotein and RNA-dependent RNA polymerase of SARS-CoV-2 to mutation: in silico structural dynamics study Cover

Susceptibility of spike glycoprotein and RNA-dependent RNA polymerase of SARS-CoV-2 to mutation: in silico structural dynamics study

Open Access
|Dec 2021

References

  1. World Health Organization. Coronavirus Disease (COVID-19) Dashboard [Internet]. Geneva: WHO; 2020 [updated 2021 Dec 02; cited 2021 Dec 03]. Available from: https://covid19.who.int.
  2. European Centre for Disease Prevention and Control. Risk related to spread of new SARS-CoV-2 variants of concern in the EU/EEA. Stockholm: ECDC; 2020. 26 p.
  3. Centers for Disease Control and Prevention. Science brief: Emerging SARS-CoV-2 variants [Internet]. USA: CDC; 2020 [updated 2021 Jan 28; cited 2021 Jul 30]. Available from: https://www.cdc.gov/coronavirus/2019-ncov/science/science-briefs/scientific-brief-emerging-variants.html.
  4. Dawood AA. Mutated COVID-19 may foretell a great risk for mankind in the future. NMNI 2020;35:100673; DOI:10.1016/j.nmni.2020.100673.
  5. Maison DP, Ching LL, Shikuma CM, Nerurkar VR. Genetic characteristics and phylogeny of 969-bp S gene sequence of SARS-CoV-2 from Hawai’i Reveals the worldwide emerging P681H mutation. Hawaii J Health Soc Welf. 2021;80(3):52–61.
  6. Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, Cheng Z, Yu T, Xia J, Wei Y, Wu W, Xie X, Yin W, Li H, Liu M, Xiao Y, Gao H, Guo L, Xie J, Wang G, Jiang R, Gao Z, Jin Q, Wang J, Cao B. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020;395(10223):497–506. DOI: 10.1016/S0140-6736(20)30183-5.
  7. Khateeb J, Li Y, Zhang H. Emerging SARS-CoV-2 variants of concern and potential intervention approaches. Crit Care. 2021;25:244; DOI:10.1186/s13054-021-03662-x.
  8. Latif AA, Mullen JL, Alkuzweny M, Tsueng G, Cano M, Haag E, Zhou J, Zeller M, Hufbauer E, Matteson N, Wu C, Andersen KG, Su AI, Gangavarapu K, Hughes LD. B.1.351 Lineage Report. [Internet]. USA: outbreak. info; 2021 [updated 2021 Nov 30; cited 2021 Dec 03]. Available from: https://outbreak.info/situation-reports?pango=B.1.351.
  9. Di Giacomo S, Mercatelli D, Rakhimov A, Giorgi FM. Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. J. Med Virol. 2021;93:5638–5643; DOI:10.1002/jmv.27062.
  10. Fatoki TH, Ibraheem O, Ogunyemi IO, Akinmoladun AC, Ugboko HU, Adeseko CJ, Awofisayo OA, Olusegun SJ, Enibukun JM. Network analysis, sequence and structure dynamics of key proteins of coronavirus and human host, and molecular docking of selected phytochemicals of nine medicinal plants. J Biomol Struct Dyn. 2021;39(16):6195–6217; DOI:10.1080/07391102.2020.1794971.
  11. Hossain MU, Bhattacharjee A, Emon MTH, Chowdhury ZM, Ahammad I, Mosaib MG, Moniruzzaman M, Rahman MH, Islam MN, Ahmed I, Amin MR, Rashed A, Das KC, Keya CA, Salimullah M. Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. J Genet Eng Biotechnol. 2021;19(1):52; DOI:10.1186/s43141-021-00152-z.
  12. Rezaei S, Sefidbakht Y, Uskoković V. Comparative molecular dynamics study of the receptor-binding domains in SARS-CoV-2 and SARS-CoV and the effects of mutations on the binding affinity. J Biomol Struct Dyn. 2020:1–20; DOI:10.1080/07391102.2020.1860829.
  13. Kuriata A, Gierut AM, Oleniecki T, Ciemny MP, Kolinski A, Kurcinski M, Kmiecik S. CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures. Nucleic Acids Res. 2018;46(W1):W338–W343; DOI:10.1093/nar/gky356.
  14. Ikram A, Naz A, Awan FM, Rauff B, Obaid A, Hakim MS, Malik A, The impact of mutations on the structural and functional properties of SARS-CoV-2 proteins: A comprehensive bioinformatics analysis. bioRxiv [Preprint] 2021; DOI:10.1101/2021.03.01.433340.
  15. Holm L. Using Dali for Protein Structure Comparison. Methods Mol Biol. 2020;2112:29–42; DOI:10.1007/978-1-0716-0270-6_3.
  16. Xu J, Zhao S, Teng T, Abdalla AE, Zhu W, Xie L, Wang Y and Guo X, Systematic comparison of two animal-to-human transmitted human coronaviruses: SARS-CoV-2 and SARS-CoV. Viruses. 2020;12:244; DOI:10.3390/v12020244.
  17. Tchesnokova V, Kulasekara H, Larson L, Bowers V, Rechkina E, Kisiela D, Sledneva Y, Choudhury D, Maslova I, Deng K, Kutumbaka K, Geng H, Fowler C, Greene D, Ralston J, Samadpour M, Sokurenko E. Acquisition of the L452R mutation in the ACE2-binding interface of spike protein triggers recent massive expansion of SARS-CoV-2 variants. J Clin Microbiol. 2021;59(11):e0092121; DOI:10.1128/JCM.00921-21.
  18. Hodcroft EB, Zuber M, Nadeau S, Vaughan TG, Crawford KHD, Althaus CL, Reichmuth ML, Bowen JE, Walls AC, Corti D, Bloom JD, Veesler D, Mateo D, Hernando A, Comas I, González-Candelas F; SeqCOVID-SPAIN consortium, Stadler T, Neher RA. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature, 2021;595(7869):707–712; DOI:10.1038/s41586-021-03677-y.
  19. Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E, Storici P, Masciovecchio C, Angeletti S, Ciccozzi M, Gallo RC, Zella D, Ippodrino R. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med. 2020;18(1):179; DOI:10.1186/s12967-020-02344-6.
  20. Adeoye AO, Oso BJ, Olaoye IF, Tijjani H, Adebayo AI. Repurposing of chloroquine and some clinically approved antiviral drugs as effective therapeutics to prevent cellular entry and replication of coronavirus. J Biomol Struct Dyn. 2021;39(10):3469–3479; DOI:10.1080/07391102.2020.1765876.
  21. Centers for Disease and Control Prevention. SARS-CoV-2 Variant Classifications and Definitions [Internet]. USA: CDC; 2020 [updated 2021 Dec 01; cited 2021 Dec 03]. Available from: https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html.
  22. Schmidt F, Weisblum Y, Rutkowska M, Poston D, Da Silva J, Zhang F, Bednarski E, Cho A, Schaefer-Babajew DJ, Gaebler C, Caskey M, Nussenzweig MC, Hatziioannou T, Bieniasz PD. High genetic barrier to SARS-CoV-2 polyclonal neutralizing antibody escape. Nature. 2021:1–9; DOI:10.1038/s41586-021-04005-0.
  23. Janik E, Niemcewicz M, Podogrocki M, Majsterek I, Bijak M. The emerging concern and interest SARS-CoV-2 variants. Pathogens. 2021;10:633; DOI:10.3390/pathogens10060633.
Language: English
Page range: 148 - 152
Submitted on: Oct 2, 2021
Accepted on: Nov 18, 2021
Published on: Dec 30, 2021
Published by: Foundation for Cell Biology and Molecular Biology
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year

© 2021 Toluwase Hezekiah Fatoki, Jude Akinyelu, Oluwafijimi Yomi Adetuyi, Temitope Olawale Jeje, Uchechukwu Nebo, Jesupemi Mercy Fatoki, Tolulope Mercy Kupolati, published by Foundation for Cell Biology and Molecular Biology
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.