Computational protocol: In silico analysis and molecular docking studies of potential angiotensin-converting enzyme inhibitor using quercetin glycosides

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Protocol publication

[…] For docking analysis, PDB coordinates of the target protein and quercetin molecule were optimized by Drug Discovery Studio version 3.0 software and UCSF Chimera tool, respectively (adding missing residues). These coordinates had minimum energy and stable conformation. [...] A computational ligand-target docking approach was used to analyze structural complexes of the ACE (target) with quercetin glycoside (ligand) in order to understand the structural basis of this protein target specificity. Initially, protein–ligand attraction was investigated for hydrophobic/hydrophilic properties of these complexes by Platinum software web server.[] Finally, docking was carried out by PyRx, AutoDock Vina option based on scoring functions. The energy of interaction of quercetin glycoside with the ACE is assigned “grid point.” At each step of the simulation, the energy of interaction of ligand and protein was evaluated using atomic affinity potentials computed on a grid. The remaining parameters were set as default. […]

Pipeline specifications

Software tools UCSF Chimera, PyRx, AutoDock Vina
Applications Drug design, Protein interaction analysis
Organisms Allium cepa
Diseases Heart Failure, Hypertension, Myocardial Infarction
Chemicals Enalapril, Quercetin