Protein-Ligand Docking Simulations

The docking study was performed using ezCADD [61 (link)] Smina [62 (link)] software (https://www.dxulab.org/software) (accessed on 1 August 2022). The ezCADD is a web-based CADD modeling environment where one of its applications is to simulate protein-ligand interactions. 2D/3D depictions were visualized using the BIOVIA discovery studio 2021 client software [63 ]. The simulation system was built on the crystal structures of PDB ID: 1AO6 [64 (link)], 1P0I [65 (link)], 1ACJ [66 (link)] and 1EVE [67 (link)], which were downloaded from the Protein Data Bank (https://www.rcsb.org (accessed on 1 August 2022)). These proteins were classified into antibodies against Human Serum Albumin (HAS) and Hydrolase (hydrolase carboxylic esterase and hydrolase inhibitor). The water molecules and ligands were removed from the PDB file using pymol [68 ] and polar hydrogen bonds were added [69 ]. Automatic cavity detection was performed using fpocket3 [70 (link)]. The minimum binding affinity values (kcal/mol) were calculated to evaluate the interactions between the docked ligands and the studied proteins.

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Al-Hazmy S.M., Zouaghi M.O., Amri N., Arfaoui Y., Alhagri I.A, & Hamdi N. (2023). DFT Study of Regio- and Stereoselective 13DC Reaction between Diazopropane and Substituted Chalcone Derivatives: Molecular Docking of Novel Pyrazole Derivatives as Anti-Alzheimer’s Agents. Molecules, 28(4), 1899.

Publication 2023

Antibodies Carboxylic esterase Cavity Human serum albumin Hydrogen bonds Hydrolase Ligands Proteins

Corresponding Organization :

Other organizations : Qassim University, Tunis El Manar University, Jazan University, Ibb University

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Variable analysis

independent variables

Docking software used: ezCADD and Smina

dependent variables

Minimum binding affinity values (kcal/mol) between docked ligands and studied proteins

control variables

Crystal structures of proteins PDB ID: 1AO6, 1P0I, 1ACJ, and 1EVE
Removal of water molecules and ligands from the PDB files
Addition of polar hydrogen bonds
Automatic cavity detection using fpocket3

controls

No positive or negative controls were explicitly mentioned.

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