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Nat Prod Res ; : 1-8, 2021 Dec 27.
Article in English | MEDLINE | ID: covidwho-1585376


In the present study, a new secoiridoid glycoside lisianthoside II 1, along with seven known compounds 2-8, were isolated from Centaurium spicatum L. In-silico molecular docking and molecular dynamic simulation against SARS-CoV-2 Main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) were conducted. The affinity docking scores revealed that 8 is the best bound ligand to Mpro active site with binding energy of -14.9877 kcal/mol (RSMD = 1.16 Å), while 6 was the highest against RdRp (-16.9572 kcal/mol, RMSD = 1.01 Å). Moreover, the molecular dynamic simulation revealed that 8 with a (ΔG) of -7.9 kcal/mol (RMSD value of 2.6 Å) and 6 (RMSD value of 1.6 Å) and binding free energy (ΔG) of -7.1 kcal/mol achieved the highest stability over 50 ns of MDS inside the Mpro and RdRp enzyme's active site, respectively. Hence, the isolated compounds could be a good lead for development of new leads targeting COVID-19.

RSC Adv ; 11(51): 32346-32357, 2021 Sep 27.
Article in English | MEDLINE | ID: covidwho-1517648


Wild plants growing in the Egyptian deserts are facing abiotic stress, which can lead to interesting & safe natural products possessing potential chemical profiles. Consequently, our study was designed to assess the phytochemical composition of the aerial parts of Limonium tubiflorum (family Plumbaginaceae) growing wild in Egypt for the first time. In addition, in silico screening and molecular dynamic simulation of all isolated phytoconstituents were run against the main protease (Mpro) and spike glycoprotein SARS-CoV-2 targets which displayed a crucial role in the replication of this virus. Our findings showed that the phytochemical investigation of 70% ethanol extract of L. tubiflorum aerial parts afforded six known flavonoids; myricetin 3-O-(2''-galloyl)-ß-d-galactopyranoside (1), myricetin 3-O-(2''-galloyl)-α-l-rhamnopyranoside (2), myricetin 3-O-(3''-galloyl)-α-l-rhamnopyranoside (3), myricetin 3-O-ß-d-galactopyranoside (5), apigenin (6), myricetin (7), along with two known phenolic acid derivatives; gallic acid (4) and ethyl gallate (8). Docking studies revealed that compounds (1) & (2) were the most effective compounds with binding energies of -17.9664 & -18.6652 kcal mol-1 against main protease and -18.9244 & -18.9272 kcal mol-1 towards spike glycoprotein receptors, respectively. The molecular dynamics simulation experiment agreed with the docking study and reported stability of compounds (1) and (2) against the selected targets which was proved by low RMSD for the tested components. Moreover, the structure-activity relationship revealed that the presence of the galloyl moiety is necessary for enhancement of the activity. Overall, the galloyl substructure of myricetin 3-O-glycoside derivatives (1 and 2) isolated from L. tubiflorum may be a possible lead for developing COVID-19 drugs. Further, in vitro and in vivo assays are recommended to support our in silico studies.

Molecules ; 26(6)2021 Mar 21.
Article in English | MEDLINE | ID: covidwho-1143541


Severe acute respiratory syndrome coronavirus (SARS-CoV-2) disease is a global rapidly spreading virus showing very high rates of complications and mortality. Till now, there is no effective specific treatment for the disease. Aloe is a rich source of isolated phytoconstituents that have an enormous range of biological activities. Since there are no available experimental techniques to examine these compounds for antiviral activity against SARS-CoV-2, we employed an in silico approach involving molecular docking, dynamics simulation, and binding free energy calculation using SARS-CoV-2 essential proteins as main protease and spike protein to identify lead compounds from Aloe that may help in novel drug discovery. Results retrieved from docking and molecular dynamics simulation suggested a number of promising inhibitors from Aloe. Root mean square deviation (RMSD) and root mean square fluctuation (RMSF) calculations indicated that compounds 132, 134, and 159 were the best scoring compounds against main protease, while compounds 115, 120, and 131 were the best scoring ones against spike glycoprotein. Compounds 120 and 131 were able to achieve significant stability and binding free energies during molecular dynamics simulation. In addition, the highest scoring compounds were investigated for their pharmacokinetic properties and drug-likeness. The Aloe compounds are promising active phytoconstituents for drug development for SARS-CoV-2.

Aloe/chemistry , Antiviral Agents/analysis , Antiviral Agents/chemistry , Coronavirus 3C Proteases/antagonists & inhibitors , Drug Development , Spike Glycoprotein, Coronavirus/antagonists & inhibitors , Antiviral Agents/metabolism , Antiviral Agents/pharmacokinetics , COVID-19/drug therapy , Computational Biology , Coronavirus 3C Proteases/metabolism , Drug Discovery/methods , Molecular Docking Simulation , Molecular Dynamics Simulation , Phytochemicals/analysis , Phytochemicals/chemistry , Phytochemicals/metabolism , Phytochemicals/pharmacokinetics , Protein Binding , SARS-CoV-2/drug effects , Spike Glycoprotein, Coronavirus/metabolism , Thermodynamics