Exploration of bioactive molecules from Tinospora cordifolia and Actinidia deliciosa as an immunity modulator via molecular docking and molecular dynamics simulation study

Abstract

Tinospora cordifolia and Actinidia deliciosa are the widely used plant in Ayurvedic systems of medicine. Both plants are well known for their immunomodulatory activity. In the current study, in silico exploration was performed using advanced computational techniques such as molecular docking and molecular dynamics simulation approach. Bioactive molecules from the Tinospora cordifolia and Actinidia deliciosa were docked against the Human IL-2. Out of all the docked bioactive molecules, Pygenic acid-B (PubChem CID:146157192) showed the highest negative binding affinity.

Synthesis, Characterization, In Silico DFT, Molecular Docking, and Dynamics Simulation Studies of Phenylhydrazono Phenoxyquinolones for Their Hypoglycemic Efficacy

“…BIOVIA Discovery Studio was used to protonate the sketched chemical structures of synthesized phenylhydrazono phenoxyquinoline derivatives ( 5a – 5x ) . The prepared chemical structures were then energy minimized and optimized employing the steepest descent algorithm and the MMFF94 force field. , Ligand structure optimization was performed using the OpenBabel module from PyRx 0.8. , …”

“…Docking studies were conducted using the AutoDock Vina module in PyRx 0.8 with a maximized grid spacing. ,,, Initially, protein structures obtained from the RCSB Protein Data Bank were thoroughly cleaned, with prior ligands and water molecules. Polar hydrogen atoms were added, and the structures were optimized using BIOVIA Discovery Studio, ensuring accurate tautomeric states .…”

“…30 The prepared chemical structures were then energy minimized and optimized employing the steepest descent algorithm and the MMFF94 force field. 25,31 Ligand structure optimization was performed using the OpenBabel module from PyRx 0.8. 32,33 Drug-Likeness and In Silico ADMET Prediction.…”