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Evaluation of therapeutic potentials of some bioactive compounds in selected African plants targeting main protease (Mpro) in SARS-CoV-2: a molecular docking study

Akinwumi et al., Egyptian Journal of Medical Human Genetics, doi:10.1186/s43042-023-00456-4
Dec 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.
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. c19early.org
In Silico study showing potential antiviral benefits of quercetin, catechin, epicatechin, vitexin, kaempferol, gamma-sitosterol, and kaur-16-ene against the SARS-CoV-2 main protease (Mpro). Molecular docking analysis showed that these compounds bind more strongly to Mpro than the control drug Remdesivir, inhibiting Mpro's activity. The compounds exhibited suitable drug-likeness and ADMET properties.
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, RNA-dependent RNA polymerase Note C, Corbo, PLpro Note D, Ibeh, 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).
Akinwumi et al., 11 Dec 2023, peer-reviewed, 4 authors. Contact: akinwumiishola5000@gmail.com.
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
This PaperQuercetinAll
Evaluation of therapeutic potentials of some bioactive compounds in selected African plants targeting main protease (Mpro) in SARS-CoV-2: a molecular docking study
Ishola Abeeb Akinwumi, Barakat Olamide Ishola, Oluwatosin Maryam Adeyemo, Adefolarin Phebean Owojuyigbe
Egyptian Journal of Medical Human Genetics, doi:10.1186/s43042-023-00456-4
Background Coronavirus disease 2019 is an infectious disease brought on by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a global treat in early 2020. Despite worldwide research proving different medications used to treat COVID-19, the infection still affects the human race; we need to continue researching the virus to protect humanity and reduce the complications that some medications might cause. This study focuses on finding another promising therapeutic compound against SARS-CoV-2. Twenty-four (24) bioactive compounds were selected from the following African plants' Adansonia digitata L, Aframomum melegueta K. Schum, Ageratum conyzoides (L.) L, and Boswellia dalzielii, and Remdesivir was used as the control medication. The PubChem web server acquired the 3D structures of bioactive compounds in the plant and the control medication. The SARS-CoV-2 main protease (M pro ) crystal structure was obtained using the Protein Data Bank (PDB). Using the SwissADME web server, the bioactive compounds' drug-likeness was assessed, and AutoDock was employed for the molecular docking with the M pro . The Proteins Plus and Protein-Ligand Interaction Profiler web servers were used to analyse the docked complexes. Furthermore, the admetSAR website was utilized to predict the ligands' absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. Results Based on the drug-likeness screening, Rutin violated more than one of the Lipinski rules of five, while Remdesivir violated two. Molecular docking analysis results indicated that Catechin, Epicatechin, Vitexin, Quercetin, Kaempferol, Gamma-Sitosterol, and Kaur-16-ene exhibited a stronger binding affinity with M pro , with binding scores of -7.1, -7.1, -8.0, -7.3, -7.2, -6.8, and -6.5 kcal/mol, respectively, compared to Remdesivir's binding score of -6.3 kcal/mol. Consequently, binding scores of bioactive compounds suggest their potential biological activity against the SARS-CoV-2 main protease. Additionally, these bioactive compounds exhibited favourable ADMET properties. Vitexin also has a plasma protein binding below 90%, a promising medication distribution feature. Conclusions This study shows that Catechin, Epicatechin, Vitexin, Quercetin, Kaempferol, Gamma-Sitosterol, and Kaur-16-ene have better binding affinities with M pro than Remdesivir. Molecular dynamics simulation in vitro and in vivo investigation is required to support this study.
Class Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare that they have no competing interests. Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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