publication . Article . Other literature type . Preprint . 2020

Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site

Umesh Kalathiya; Monikaben Padariya; Marcos Yebenes Mayordomo; Małgorzata Lisowska; Judith Nicholson; Ashita Singh; Maciej Baginski; Robin Fåhraeus; Neil O. Carragher; Kathryn L. Ball; ...
Open Access
  • Published: 14 May 2020 Journal: Journal of Clinical Medicine, volume 9, page 1,473 (eissn: 2077-0383, Copyright policy)
  • Publisher: MDPI AG
  • Country: United Kingdom
Abstract
up&rdquo
Subjects
free text keywords: SARS-CoV-2, coronavirus disease 2019 (COVID-19), spike glycoprotein, variability, molecular docking, molecular dynamics, inhibitors, trimer cavity, binding site, biophysics, COVID-19 ; inhibitors ; molecular dynamics ; molecular docking ; coronavirus disease 2019 ; spike glycoprotein ; variability ; trimer cavity ; SARS-CoV-2 ; binding site, Article, Binding site, Docking (molecular), Drug discovery, Protein subunit, Ligand (biochemistry), Virtual screening, Small molecule, Coronavirus, medicine.disease_cause, medicine, business.industry, business, Cell biology, Biophysics, Glycoprotein, chemistry.chemical_classification, chemistry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Coronavirus disease 2019 (COVID-19), lcsh:Medicine, lcsh:R
88 references, page 1 of 6

Chan, J.F.W.; To, K.K.W.; Tse, H.; Jin, D.Y.; Yuen, K.Y. Interspecies transmission and emergence of novel viruses: lessons from bats and birds. Trends Microbiol. 2013, 21, 544-555.

Cheng, V.C.C.; Lau, S.K.P.; Woo, P.C.Y.; Yuen, K.Y. Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Clin. Microbiol. Rev. 2007, 20, 660-694.

Chan, J.F.W.; Kok, K.H.; Zhu, Z.; Chu, H.; To, K.K.W.; Yuan, S.; Yuen, K.Y. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg. Microbes Infect. 2020, 9, 221-236. [OpenAIRE]

Lau, S.K.P.; Woo, P.C.Y.; Yip, C.C.Y.; Tse, H.; Tsoi, H.W.; Cheng, V.C.C.; Lee, P.; Tang, B.S.; Cheung, C.H.; Lee, R.A. et al. Coronavirus HKU1 and other coronavirus infections in Hong Kong. J. Clin. Microbiol. 2006, 44, 2063-2071.

Shanmugaraj, B.; Siriwattananon, K.; Wangkanont, K.; Phoolcharoen, W. Perspectives on monoclonal antibody therapy as potential therapeutic intervention for coronavirus disease-19 (COVID-19). Asian Pac.

J. Allergy Immunol. 2020, doi: 10.12932/ap-200220-0773 Zhou, H.; Chen, X.; Hu, T.; Li, J.; Song, H.; Liu, Y.; Peihan, W.; Liu, D.; Jing, Y, Edward C. H.; Alice C. et al A novel bat coronavirus reveals natural insertions at the S1/S2 cleavage site of the Spike protein and a possible recombinant origin of HCoV-19. 2020, doi: 10.1101/2020.03.02.974139 Liu, Z, Xiao, X.; Wei, X.; Li, J.; Yang, J.; Tan, H.; Zhu, J.; Zhang, Q.; Wu, J.; Liu, L. Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2. J. Med. Virol. 2020, doi: 10.1002/jmv.25726 Smith, R. D. Responding to global infectious disease outbreaks: Lessons from SARS on the role of risk perception, communication and management. Soc. Sci. Med. 2006, 63, 3113-3123.

10. Woo, P.C.Y.; Lau, S.K.P.; Chu, C.M.; Chan, K.H.; Tsoi, H.W.; Huang, Y.; Beatrice, H.L.W.; Rosana W.S.P.; James J.C.; Wei-kwang, L. et al. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J. Virol. 2004, 79, 884-895.

11. Peiris, J.S.; Lai, S.T.; Poon, L.L.; Guan, Y.; Yam, L.Y.; Lim, W.; Nicholls, J.; Yee, W. K.; Yan, W. W.; Cheung, M.T.; Cheng, V.C.; et al. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet 2003, 361, 1319-1325.

12. Yeung, M.L.; Yao, Y.; Jia, L.; Chan, J.F.; Chan, K.H.; Cheung, K.F.; Chen, H.; Poon, V. K.; Tsang, A.K.; To, K K.; et al. MERS coronavirus induces apoptosis in kidney and lung by upregulating Smad7 and FGF2. Nat. Microbiol. 2016, 1, 16004.

13. Sheahan, T.P.; Sims, A.C.; Zhou, S.; Graham, R.L.; Hill, C.S.; Leist, S.R.; Alexandra, S.; Kenneth, H.D.; Stephanie, A.M.; Maria, L.A.; Andrea, J.P. et al. An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 and multiple endemic, epidemic and bat coronavirus. 2020, doi: 10.1101/2020.03.19.997890

14. David, E.G.; Gwendolyn, M.J.; Mehdi, B.; Jiewei, X.; Kirsten, O.; Matthew, J.; Jeffrey Z G.; Danielle L.S.; Tia A.T.; et al. A SARS-CoV-2-Human protein-protein interaction map reveals drug targets and potential drugrepurposing. 2020, doi: https://doi.org/10.1101/2020.03.22.002386

15. Zhang, L.; Lin, D.; Sun, X.; Curth, U.; Drosten, C.; Sauerhering, L.; Stephan, B.; Katharina, R.; Hilgenfeld, R. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science 2020, doi: 10.1126/science.abb3405

16. Lan, J.; Ge, J.; Yu, J.; Shan, S.; Zhou, H.; Fan, S.; Qi, Z.; Xuanling, S.; Qisheng, W.; Linqi, Z.; Wang, X. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 2020, doi: 10.1038/s41586-020-2180-5

17. Tchesnokov, E.; Feng, J.; Porter, D.; Götte, M. Mechanism of inhibition of Ebola virus RNA-dependent RNA polymerase by remdesivir. Viruses 2019, 11, 326.

18. Wrapp, D.; Wang, N.; Corbett, K.S.; Goldsmith, J.A.; Hsieh, C.L.; Abiona, O.; Graham, B.S.; McLellan, J.S. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 2020, 367, 1260-1263. [OpenAIRE]

88 references, page 1 of 6
Abstract
up&rdquo
Subjects
free text keywords: SARS-CoV-2, coronavirus disease 2019 (COVID-19), spike glycoprotein, variability, molecular docking, molecular dynamics, inhibitors, trimer cavity, binding site, biophysics, COVID-19 ; inhibitors ; molecular dynamics ; molecular docking ; coronavirus disease 2019 ; spike glycoprotein ; variability ; trimer cavity ; SARS-CoV-2 ; binding site, Article, Binding site, Docking (molecular), Drug discovery, Protein subunit, Ligand (biochemistry), Virtual screening, Small molecule, Coronavirus, medicine.disease_cause, medicine, business.industry, business, Cell biology, Biophysics, Glycoprotein, chemistry.chemical_classification, chemistry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Coronavirus disease 2019 (COVID-19), lcsh:Medicine, lcsh:R
88 references, page 1 of 6

Chan, J.F.W.; To, K.K.W.; Tse, H.; Jin, D.Y.; Yuen, K.Y. Interspecies transmission and emergence of novel viruses: lessons from bats and birds. Trends Microbiol. 2013, 21, 544-555.

Cheng, V.C.C.; Lau, S.K.P.; Woo, P.C.Y.; Yuen, K.Y. Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Clin. Microbiol. Rev. 2007, 20, 660-694.

Chan, J.F.W.; Kok, K.H.; Zhu, Z.; Chu, H.; To, K.K.W.; Yuan, S.; Yuen, K.Y. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg. Microbes Infect. 2020, 9, 221-236. [OpenAIRE]

Lau, S.K.P.; Woo, P.C.Y.; Yip, C.C.Y.; Tse, H.; Tsoi, H.W.; Cheng, V.C.C.; Lee, P.; Tang, B.S.; Cheung, C.H.; Lee, R.A. et al. Coronavirus HKU1 and other coronavirus infections in Hong Kong. J. Clin. Microbiol. 2006, 44, 2063-2071.

Shanmugaraj, B.; Siriwattananon, K.; Wangkanont, K.; Phoolcharoen, W. Perspectives on monoclonal antibody therapy as potential therapeutic intervention for coronavirus disease-19 (COVID-19). Asian Pac.

J. Allergy Immunol. 2020, doi: 10.12932/ap-200220-0773 Zhou, H.; Chen, X.; Hu, T.; Li, J.; Song, H.; Liu, Y.; Peihan, W.; Liu, D.; Jing, Y, Edward C. H.; Alice C. et al A novel bat coronavirus reveals natural insertions at the S1/S2 cleavage site of the Spike protein and a possible recombinant origin of HCoV-19. 2020, doi: 10.1101/2020.03.02.974139 Liu, Z, Xiao, X.; Wei, X.; Li, J.; Yang, J.; Tan, H.; Zhu, J.; Zhang, Q.; Wu, J.; Liu, L. Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2. J. Med. Virol. 2020, doi: 10.1002/jmv.25726 Smith, R. D. Responding to global infectious disease outbreaks: Lessons from SARS on the role of risk perception, communication and management. Soc. Sci. Med. 2006, 63, 3113-3123.

10. Woo, P.C.Y.; Lau, S.K.P.; Chu, C.M.; Chan, K.H.; Tsoi, H.W.; Huang, Y.; Beatrice, H.L.W.; Rosana W.S.P.; James J.C.; Wei-kwang, L. et al. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J. Virol. 2004, 79, 884-895.

11. Peiris, J.S.; Lai, S.T.; Poon, L.L.; Guan, Y.; Yam, L.Y.; Lim, W.; Nicholls, J.; Yee, W. K.; Yan, W. W.; Cheung, M.T.; Cheng, V.C.; et al. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet 2003, 361, 1319-1325.

12. Yeung, M.L.; Yao, Y.; Jia, L.; Chan, J.F.; Chan, K.H.; Cheung, K.F.; Chen, H.; Poon, V. K.; Tsang, A.K.; To, K K.; et al. MERS coronavirus induces apoptosis in kidney and lung by upregulating Smad7 and FGF2. Nat. Microbiol. 2016, 1, 16004.

13. Sheahan, T.P.; Sims, A.C.; Zhou, S.; Graham, R.L.; Hill, C.S.; Leist, S.R.; Alexandra, S.; Kenneth, H.D.; Stephanie, A.M.; Maria, L.A.; Andrea, J.P. et al. An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 and multiple endemic, epidemic and bat coronavirus. 2020, doi: 10.1101/2020.03.19.997890

14. David, E.G.; Gwendolyn, M.J.; Mehdi, B.; Jiewei, X.; Kirsten, O.; Matthew, J.; Jeffrey Z G.; Danielle L.S.; Tia A.T.; et al. A SARS-CoV-2-Human protein-protein interaction map reveals drug targets and potential drugrepurposing. 2020, doi: https://doi.org/10.1101/2020.03.22.002386

15. Zhang, L.; Lin, D.; Sun, X.; Curth, U.; Drosten, C.; Sauerhering, L.; Stephan, B.; Katharina, R.; Hilgenfeld, R. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science 2020, doi: 10.1126/science.abb3405

16. Lan, J.; Ge, J.; Yu, J.; Shan, S.; Zhou, H.; Fan, S.; Qi, Z.; Xuanling, S.; Qisheng, W.; Linqi, Z.; Wang, X. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 2020, doi: 10.1038/s41586-020-2180-5

17. Tchesnokov, E.; Feng, J.; Porter, D.; Götte, M. Mechanism of inhibition of Ebola virus RNA-dependent RNA polymerase by remdesivir. Viruses 2019, 11, 326.

18. Wrapp, D.; Wang, N.; Corbett, K.S.; Goldsmith, J.A.; Hsieh, C.L.; Abiona, O.; Graham, B.S.; McLellan, J.S. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 2020, 367, 1260-1263. [OpenAIRE]

88 references, page 1 of 6
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