In-silico studies on effective phytochemicals of Crocus sativus, Ocimum tenuiflorum and its modifications targeting NIPAH virus
摘要
In this investigation, we examined forty-nine novel phytochemical compounds from two common herbs, Crocus sativus and Ocimum tenuiflorum, and determined which phytochemicals were most effective in targeting the glycoprotein of the nipah virus. The three proteins taken for docking studies have the PDB ID: 2VWD, 3D11, and 2VSM. Following the classification of all phytochemicals according to their docking scores, DFT was used to modify and optimize the top two phytochemicals, cadinene and colchicine, and docking analysis was performed. The phytochemicals and derivatives that scored highest were then subjected to a thorough molecular dynamics (MD) analysis. We determined from these screenings that the compounds with the highest binding affinity values were colchicine, cadinene and its derivatives - C4, C6, and C8 which were found to be better than the popular reference drug ribavirin. The top eight protein-ligand complexes underwent a thorough examination for structural stability (RMSD), intermolecular hydrogen bond interactions, the impact of solvent accessibility (SASA), and compactness (Rg) factors. MM/GBSA calculations reveal that compound 4 the highest binding energy with 2VSM, while compound 6 has highest binding affinity with 2VWD. FEL and PCA were constructed using Geo-Measure plugin in the Pymol tool. The results showed that these complexes are highly stable and display folding behaviour. In addition to the docking and MD testing, additional drug-likeness and toxicity tests have identified compounds like cadinene, colchicine, and its derivatives (C4 of colchicine derivative, and C6 and C8 of cadinene derivatives) as effective against the Nipah virus.
Graphical abstract