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Isolation and In Silico Inhibitory Potential against SARS-CoV-2 RNA Polymerase of the Rare Kaempferol 3--(6″--acetyl)-Glucoside from . | LitMetric

AI Article Synopsis

  • - The research focused on the phytochemical constituents of Jaub. & Spach (from the Polygonaceae family), leading to the first-time isolation of a rare flavonol glycoside called kaempferol 3--(6″--acetyl)-glucoside (K3G-A).
  • - K3G-A was analyzed for its potential to inhibit SARS-CoV-2, showing high structural similarity to the antiviral drug remdesivir, and further studies confirmed its effective binding to the virus's RNA-dependent RNA polymerase (RdRp).
  • - The safety and drug-likeness of K3G-A were established through in silico ADMET and toxicity evaluations, alongside the identification of two additional metabolites

Article Abstract

The phytochemical constituents of Jaub. & Spach (Family Polygonaceae) were studied for the first time. The study resulted in the isolation of the rare flavonol glycoside, kaempferol 3--(6″--acetyl)-glucoside,(K3G-A). The potential inhibitive activity of K3G-A toward SARS-CoV-2 was investigated utilizing several in silico approaches. First, molecular fingerprints and structural similarity experiments were carried out for K3G-A against nine co-crystallized ligands of nine proteins of SARS-CoV-2 to reveal if there is a structural similarity with any of them. The conducted studies showed the high similarity of K3G-A and remdesivir, the co-crystallized ligand of SARS-CoV-2 RNA-dependent RNA polymerase (PDB ID: 7BV2), RdRp. To validate these findings, a DFT study was conducted and confirmed the proposed similarity on the electronic and orbital levels. The binding of K3G-A against RdRp was confirmed through molecular docking studies exhibiting a binding energy of -27.43 kcal/mol, which was higher than that of remdesivir. Moreover, the RdRp-K3G-A complex was subjected to several MD studies at 100 ns that authenticated the accurate mode of binding and the correct dynamic behavior. Finally, in silico ADMET and toxicity evaluation of K3G-A was conducted and denoted the safety and the drug-likeness of K3G-A. In addition to K3G-A, two other metabolites were isolated and identified to be kaempferol (K) and β-sitosterol (β-S).

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9370365PMC
http://dx.doi.org/10.3390/plants11152072DOI Listing

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