Isolation and In Silico Inhibitory Potential against SARS-CoV-2 RNA Polymerase of the Rare Kaempferol 3-O-(6″-O-acetyl)-Glucoside from Calligonum tetrapterum
Suleimen Y.M. Jose R.A. Mamytbekova G.K. Suleimen R.N. Ishmuratova M.Y. Dehaen W. Alsfouk B.A. Elkaeed E.B. Eissa I.H. Metwaly A.M.
August 2022MDPI
Plants
2022#11Issue 15
The phytochemical constituents of Calligonum tetrapterum Jaub. & Spach (Family Polygonaceae) were studied for the first time. The study resulted in the isolation of the rare flavonol glycoside, kaempferol 3-O-(6″-O-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).
ADMET , Calligonum tetrapterum , DFT , MD simulations , molecular docking , SARS-CoV-2 RNA-dependent RNA polymerase , structural similarity
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Technopark Department, Kazakh University of Technology and Business, Nur-Sultan, 010000, Kazakhstan
The Laboratory of Engineering Profile of NMR Spectroscopy, Ualikhanov Kokshetau University, Sh, Kokshetau, 020000, Kazakhstan
Molecular Design & Synthesis KU Leuven, Department of Chemistry, Celestijnenlaan 200F, Leuven, B-3001, Belgium
Department of Chemistry, St. Dominic’s College, Mahatma Gandhi University, Kanjirappally, 686512, India
Department of Technical Physics, Faculty of Physics and Technology, L.N. Gumilyov, Eurasian National University, Nur-Sultan, 010010, Kazakhstan
Department of Botany, E.A. Buketov Karaganda University, Karaganda, 100024, Kazakhstan
Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, 13713, Saudi Arabia
Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
Biopharmaceutical Product Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria, 21934, Egypt
Technopark Department
The Laboratory of Engineering Profile of NMR Spectroscopy
Molecular Design & Synthesis KU Leuven
Department of Chemistry
Department of Technical Physics
Department of Botany
Department of Pharmaceutical Sciences
Department of Pharmaceutical Sciences
Pharmaceutical Medicinal Chemistry & Drug Design Department
Pharmacognosy and Medicinal Plants Department
Biopharmaceutical Product Research Department
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