In silico screening of hundred phytocompounds of ten medicinal plants as potential inhibitors of nucleocapsid phosphoprotein of COVID-19: an approach to prevent virus assembly

Abstract

Currently, there is no specific treatment to cure COVID-19. Many medicinal plants have antiviral, antioxidant, antibacterial, antifungal, anticancer, wound healing etc. Therefore, the aim of the current study was to screen for potent inhibitors of N-terminal domain (NTD) of nucleocapsid phosphoprotein of SARS-CoV-2. The structure of NTD of RNA binding domain of nucleocapsid phosphoprotein of SARS coronavirus 2 was retrieved from the Protein Data Bank (PDB 6VYO) and the structures of 100 different phytocompounds were retrieved from Pubchem. The receptor protein and ligands were prepared using Schrodinger's Protein Preparation Wizard. Molecular docking was done by using the Schrodinger's maestro 12.0 software. Drug likeness and toxicity of active phytocompounds was predicted by using Swiss adme, admetSAR and protox II online servers. Molecular dynamic simulation of the best three protein-ligand complexes (alizarin, aloe-emodin and anthrarufin) was performed to study the interaction stability. We have identified three potential active sites (named as A, B, C) on receptor protein for efficient binding of the phytocompounds. We found that, among 100 phytocompounds, emodin, aloe-emodin, anthrarufin, alizarine, and dantron of Rheum emodi showed good binding affinity at all the three active sites of RNA binding domain of nucleocapsid phosphoprotein of COVID-19.The binding energies of emodin, aloe-emodin, anthrarufin, alizarine, and dantron were

Tartary Buckwheat in Human Nutrition

“…It appears to be a precursor in the synthesis of hypericin, and of Tartary buckwheat fagopyrin [92]. Of importance here, emodin isolated from Tartary buckwheat grain has been shown to dock into all three active sites of the RNA-binding domain of the nucleocapsid phosphoprotein of SARS-CoV-2 [91][92][93][94]. Quercetin has potential therapeutic effects against acute kidney injury, and for treatment of impaired renal function.…”

Indian Ethnomedicinal Phytochemicals as Promising Inhibitors of RNA-Binding Domain of SARS-CoV-2 Nucleocapsid Phosphoprotein: An In Silico Study

“…The chemical structure of phytocompounds was obtained from the Pubchem database (https://pubchem.ncbi.nlm.nih.gov/) in .sdf (structure date file) format. Then the file format was converted to PDB (Protein Data Bank) coordinate file format using the Open Babel (http://openbabel.org) (Rolta et al, 2020).…”

Phytocompounds from Himalayan Medicinal Plants as Potential Drugs to Treat Multidrug-Resistant Salmonella typhimurium: An In Silico Approach

“…Absorption, distribution, metabolism, excretion, and toxicity (ADMET) screening was performed to evaluate the absorption, toxicity, and drug-likeness properties of the selected phytocompounds. The 3-D structures of 11 phytocompounds (asiaticoside, betasitosterol, bryophyllin A, madecassoside, Mahanimbine, Pennogenin, Rutin, Solasonine, Solamargine, Withaferin A, and Withanone) were saved in smiles format and uploaded on the SWISSADME (http://www.swissadme.ch/) (Molecular Modeling Group of the SIB (Swiss Institute of Bioinformatics) and PROTOX-II (https://tox-new.charite.de/protox_II/) web servers (Charite University of Medicine, Institute for Physiology, Structural Bioinformatics Group, Berlin, Germany) [69][70][71][72] for ADMET screening. SWISSADME is an online tool used to predict ADME and pharmacokinetic and physicochemical features of a molecule, which are the main determinants for clinical trials.…”