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In silico identification of SARS-CoV-2 cell entry inhibitors from selected natural antivirals

Şimşek et al., Journal of Molecular Graphics and Modelling, doi:10.1016/j.jmgm.2021.108038
Sep 2021  
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Quercetin for COVID-19
24th treatment shown to reduce risk in July 2021
*, now known with p = 0.0031 from 11 studies.
No treatment is 100% effective. Protocols combine complementary and synergistic treatments. * >10% efficacy in meta analysis with ≥3 clinical studies.
3,800+ studies for 60+ treatments.
In Silico study identifying quercetin derivatives as SARS-CoV-2 spike protein, ACE2, and neuropilin inhibitors.
In Silico studies predict inhibition of SARS-CoV-2, or minimization of side effects, with quercetin or metabolites via binding to the spike Note A, Alavi, Azmi (B), Chandran, Kandeil, Mandal, Moschovou, Nguyen, Pan, Thapa (B), Şimşek, Mpro Note B, Akinwumi, Alanzi, Ibeh, Kandeil, Mandal, Moschovou, Nguyen, Qin, Rehman, Sekiou (B), Singh, Thapa (B), Wang, Zhang, RNA-dependent RNA polymerase Note C, Corbo, PLpro Note D, Ibeh, Zhang, ACE2 Note E, Chandran, Ibeh, Qin, Thapa (B), Şimşek, Alkafaas, TMPRSS2 Note F, Chandran, helicase Note G, Alanzi, Singh (B), endoribonuclease Note H, Alavi, cathepsin L Note I, Ahmed, Wnt-3 Note J, Chandran, FZD Note K, Chandran, LRP6 Note L, Chandran, ezrin Note M, Chellasamy, ADRP Note N, Nguyen, NRP1 Note O, Şimşek, PTGS2 Note P, Qin, HSP90AA1 Note Q, Qin, matrix metalloproteinase 9 Note R, Sai Ramesh, IL-6 Note S, Yang, Yang (B), IL-10 Note T, Yang, VEGFA Note U, Yang (B), and RELA Note V, Yang (B) proteins. In Vitro studies demonstrate efficacy in Calu-3 Note W, DiGuilio, A549 Note X, Yang, HEK293-ACE2+ Note Y, Singh (C), Huh-7 Note Z, Pan, Caco-2 Note AA, Roy, Vero E6 Note AB, Kandeil, El-Megharbel, Roy, mTEC Note AC, Wu, and RAW264.7 Note AD, Wu cells. Animal studies demonstrate efficacy in K18-hACE2 mice Note AE, Aguado, db/db mice Note AF, Wu, Wu (B), BALB/c mice Note AG, Shaker, and rats El-Megharbel (B). Quercetin reduced proinflammatory cytokines and protected lung and kidney tissue against LPS-induced damage in mice Shaker.
Şimşek et al., 29 Sep 2021, peer-reviewed, 3 authors.
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
This PaperQuercetinAll
In silico identification of SARS-CoV-2 cell entry inhibitors from selected natural antivirals
Yusuf Şimşek, Sahra Setenay Baran, Belma Aslım
Journal of Molecular Graphics and Modelling, doi:10.1016/j.jmgm.2021.108038
The aim of this study is to identify potential drug-like molecules against SARS-CoV-2 virus among the natural antiviral compounds published in the Encyclopedia of Traditional Chinese Medicine. To test inhibition capability of these compounds first, we docked them with Spike protein, angiotensin-converting enzyme 2 (ACE2) (PDB ID: 6M0J) and neuropilin 1 (NRP1) (PDB ID: 7JJC) receptors, and found significant docking scores with extra precision up to -11 kcal/mol. Then, their stability in the binding pockets were further evaluated with molecular dynamics simulation. Eight natural antiviral compounds were identified as potential inhibitors against SARS-CoV-2 cell entry after 200 ns molecular dynamics simulations. We found CMP-3, CMP-4, CMP-5, CMP-6 and CMP-8 are strong binders for the spike protein, CMP-1, CMP-2, CMP-4, CMP-5 and CMP-7 are strong binders for the neuropilin receptor, and CMP-5 is a strong binder for the ACE2. Quercetin derivatives (CMP-4, CMP-5, CMP-6 and CMP-7) were found highly stable in the active domain of NRP1, ACE2 and Spike protein. Especially, CMP-5 showed an inhibitory activity for all targets. These natural antivirals may be potential drug candidates for the prevention of SARS-CoV-2 infection.
Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Appendix A. Supplementary data Supplementary data to this article can be found online at https://doi. org/10.1016/j.jmgm.2021.108038.
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