In silico Investigation of inhibitory characteristics of phytoconstituents from Moringa oleifera against SARS-CoV-2 viral proteins

Abstract

The global pandemic situation caused by rare viral pneumonia occurs in late December 2019 in Wuhan, China, which we now recognize as COVID-19. The molecular docking was used to identify potential phytoconstituents of Moringa oleifera and reference drug hydroxychloroquine on SARS-CoV-2 main protein by using AutoDock 4.2.6 and Auto dock Vina. All the physicochemical and bioactive parameters (ADME, toxicity study, receptor interaction, PASS analysis, drug-likeness) were determined using different online validated software. The binding energy of all SAR-CoV-2 proteins with selected phytoconstituents of Moringa oleifera were found to be beta carotene, vitamin E; myricetin, quercetin showed the highest binding affinity with all interacting proteins comparable with other drugs and reference drug hydroxychloroquine as an order: beta carotene > myricetin > quercetin > vitamin E> hydroxychloroquine>quinic acid. The MD simulation analysis of viral protein (6MOJ) with beta carotene, vitamin E and myricetin demonstrated strong stability at 300 K. All three complexes exhibit persistent RMSDs value (0.25 – 1.5 Å) of protein side-chain Cα atoms during the 3 ns MD simulation time scale. The minor changes of all three ligands with 2 different viral proteins increasing the compactness of ligands with protein in radius of gyration suggested the strong structural activity of ligands and the least fluctuation during the MD simulation (31.2, 30.0 and 31.2), respectively. In the present study revealed that all the active constituents of Moringa oleifera show good binding affinity, but beta carotene and myricetin have an excellent affinity with SARS-CoV-2 proteins respectively.