Tools 1.5.4 44

The binding mechanisms of surfactants inside the peptidoglycan glycosyltransferase protein were explored using Autodock Vina molecular docking simulation [32 (link)]. The target enzyme was the 3D Crystal structure of a peptidoglycan glycosyltransferase (PDB ID: 2OQO) (Figure 2) [33 (link)]. PYMOL [34 (link)] was used to remove water molecules, ligands, and other species not included in the protein structure from the target crystal structure (2OQO). Polar hydrogen atoms were introduced to the constructed protein structure to correct ionization and tautomeric states of amino acid residues [35 (link)]. AutoGrid was used to prepare the geometry of the binding site by employing a grid box with 14 (20, 62, 24) points that enclose the original ligand (CPS), and the box spacing was 0.37 Å. All parameters were set to their default values in Autodock Tools 1.5.4 44 [32 (link)]. Chemdraw12.0 software was used to create all of the surfactant ligands [36 (link)]. The geometry of these ligands and Cn benzalkonium derivatives references (From C8 to C14 carbons atoms) was then adjusted using Molecular Force Field to determine the most stable conformation (MMFF94). To enable docking in AutoDock Vina, the ligand and target protein files were converted to PDBQT format. Discovery Studio Client v16 [37 ] software was used to examine the interactions of complicated protein–ligand conformations.

In order to elucidate the binding modes of the surfactants within enzymes evaluated, a molecular docking simulation was carried out using AutodockVina [55 (link)]. The crystal structure of the collagenase unit of a Vibrio collagenase from Vibrio harveyi VHJR7 (PDB ID: 7ESI), 3D structures of porcine pancreatic elastase (PDB ID: 1ELE) and crystal structure of bee venom hyaluronidase (PDB ID: 1FCV) were selected. Polar hydrogen atoms have been added to the protein’s structures for correcting ionization and tautomeric states of amino acid residues [56 (link)]. The binding sites on the structure of collagenase, elastase and hyaluronidase were made using the Auto Grid step using the original ligands as a reference. The grid box with number points in the box (x, y, z) (16, 38, 16) has been chosen. All parameters were default settings using Autodock Tools 1.5.4 44. The surfactants and EGCG ligands were drawn using Chemdraw20.1.1 software v.1. To select the most stable conformation, the geometry of ligands was subsequently optimized using Molecular Force Field (MMFF94). The ligand and target protein files were converted to the PDBQT format to make it suitable for docking in AutoDock Vina. The interactions of complex protein–ligand conformations were analyzed by Discovery Studio Client software 22.1.