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Structure-based virtual identification of natural inhibitors of SARS-CoV-2 and its Delta and Omicron variant proteins

Alanzi et al., Future Virology, doi:10.2217/fvl-2022-0184
Jun 2023  
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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.
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3,800+ studies for 60+ treatments.
In Silico study showing the flavonoid quercetin and its derivative quercetin-3-acetyl-glucoside exhibit potential inhibitory activity against SARS-CoV-2 main protease, helicase, and spike proteins. Related flavonoids like rutin and kaempferol also demonstrated strong predicted binding.
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, rats El-Megharbel (B), and db/db mice Note AF, Wu, Wu (B).
Alanzi et al., 1 Jun 2023, peer-reviewed, 3 authors. Contact: (corresponding author), (corresponding author),
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
This PaperQuercetinAll
Structure-based virtual identification of natural inhibitors of SARS-CoV-2 and its Delta and Omicron variant proteins
Abdullah R Alanzi, Mohammad K Parvez, Mohammed S Al-Dosari
Future Virology, doi:10.2217/fvl-2022-0184
Aim: Structure-based identification of natural compounds against SARS-CoV-2, Delta and Omicron target proteins. Materials & methods: Several known antiviral natural compounds were subjected to molecular docking and MD simulation against SARS-CoV-2 Mpro, Helicase and Spike, including Delta and Omicron Spikes. Results: Of the docked ligands, 20 selected for each complex exhibited overall good binding affinities (-7.79 to -5.06 kcal/mol) with acceptable physiochemistry following Lipinski's rule. Finally, two best ligands from each complex upon simulation showed structural stability and compactness. Conclusion: Quercetin-3-acetyl-glucoside, Rutin, Kaempferol, Catechin, Orientin, Obetrioside and Neridienone A were identified as potential inhibitors of SARS-CoV-2 Mpro, Helicase and Spike, while Orientin and Obetrioside also showed good binding affinities with Omicron Spike. Catechin and Neridienone A formed stable complexes with Delta Spike. Plain language summary: Mutant strains of SARS-CoV-2 called 'variants of concern' (VOCs) are linked to a good ability to infect, re-infect and spread among people. They are also linked to poor ability to fight the disease and reduced effectiveness of vaccines. Delta and Omicron are important VOCs because they are difficult to control and treat. Specific resistance to some drugs used to treat COVID-19 poses a further challenge. Therefore, discovering natural or plant-derived drugs with no known resistance would be valuable to the treatment of COVID-19. In this study, we screen and identify seven plantderived compounds that may be useful to treating COVID-19 -we identify Quercetin-3-acetyl-glucoside, Rutin, Kaempferol, Catechin, Orientin, Obetrioside and Neridienone A as potential candidates. Orientin, Obetrioside, Catechin and Neridienone A are identified as candidates against Delta and Omicron for the first time.
Financial & competing interests disclosure The authors acknowledge the Researchers Supporting Project (no. RSP2023R379), King Saud University, Riyadh, Saudi Arabia for funding this work. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.
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