Computational protocol: Antioxidant and Cholinesterase Inhibitory Activities of Ethyl Acetate Extract of Terminalia chebula: Cell-free In vitro and In silico Studies

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Protocol publication

[…] The compounds appearing in GC-MS analysis were further subjected to molecular docking analysis. The three-dimensional structures for all the compounds were downloaded from PubChem database. AChE and BuChE protein structures were retrieved from protein data bank (AChE - PDB ID: 1EVE; BuChE - PDB ID: 1P0P). Before performing the molecular docking, the protein and ligand structures were prepared using “protein preparation” and “ligand preparation” modules available in Grid-based Ligand Docking with Energetics (GLIDE) software from Schrodinger.[] AChE and BuChE were subjected to energy minimization to remove the geometric constraints using the optimized potentials for liquid simulations (OPLS) force field. The ligands were processed with the LigPrep program to assign the suitable protonation states at physiological pH (7.0 ± 1.0). Conformer generation was carried out with the ConfGen torsional sampling using OPLS_2005 force field. The van der Waals radii were scaled using a default scaling factor of 0.80 and default partial cutoff charge of 0.15 to decrease the penalties. All the compounds were docked into the binding site of AChE and BuChE proteins using Grid GLIDE software. The docking was performed with OPLS_2005 force field using extra precision (XP) module of the Schrodinger Suite. The XP GLIDE score function was used to order the best-ranked compounds and the specific interactions, such as hydrogen bond interaction. […]

Pipeline specifications

Software tools Glide, LigPrep, ConfGen
Applications Drug design, Protein interaction analysis
Diseases Alzheimer Disease, Metabolism, Inborn Errors, Neurodegenerative Diseases
Chemicals Butylated Hydroxytoluene, Edetic Acid, Gallic Acid, Hydrochloric Acid, Nitrogen, Oxygen, Trichloroacetic Acid