Molecular Docking Analysis of pGlu Binding

The RCSB Protein Data Bank (www.rcsb.org) was employed to retrieve the 3D-crystal structure of phosphodiesterase 5A1 (PDE5A1) catalytic domain in complex with sildenafil (PDB ID: 2H42), 3D-crystal structure of human angiotensin-converting enzyme (ACE) docked with captopril (PDB ID: 1UZF), 3D-crystal structure of jack bean urease (JBU; PDB ID: 3LA4), and 3D-structure of pGlu (SDF file ID: PCA). PyRx docking software fitted with Autodock VINA (version 0.8, The Scripps Research Institute, La Jolla, CA, USA) was exploited to accomplish the molecular docking studies and to assess the binding modes of pGlu in the active sites of the above-mentioned enzymes.
To ascertain the optimal parameters for reliable docking analyses, sildenafil was extracted from the 3D-crystal structure of (PDB ID: 2H42) and further re-docked back into the crystal structure of the enzyme, while captopril was erased from the 3D-crystal structure of (PDB ID: 1UZF) and re-docked back into the enzyme. All optimal parameters, settings, calculations, protonation conditions, and the overall charges were tracked, as previously designated [28 (link),29 (link)]. Additionally, Zn⁺² and Mg⁺² ions were assigned during the processing of docking analysis for PDE5A1. All graphical presentations of the docked complexes were illustrated using Discovery studio visualizer version v19.1.0.18287 (BIOVIA, San Diego, CA, USA) [30 ].