The binding site residues predicted by CASTp for tyrosinase were used for grid generation. Protein-ligand Docking 3.2.1. Ligand and Protein preparation: The structures of L1 and L2 have been fully optimized by using Gaussian 09 software at B3LYP/6-311G+ (d, p) level. The 3D crystal structure of tyrosinase from Bacillus Megaterium (PDB ID: 4j6u; resolution: 2.5Å, Chain A, B) was obtained in pdb format from online RCSB protein data bank (PDB) database. The structure was verified, and an energy minimization was performed with the Swiss-Pdb Viewer software packages (version 4.1.0) [44], since the crystal structure contains a variety of issues related to improper bond order, side chains geometry, and missing hydrogen atoms. Prior to docking, all the heteroatoms and water molecules were removed from the crystal structure using PyMol (version 1.3) software packages [45]. The active binding pocket of tyrosinase was predicted by CASTp—having the highest pocket area and volume are 95.432 Å2 and 137.877 Å3, respectively [46]. Both the structures of the proteins and ligands were saved in .pdbqt format by AutoDock Vina (version 1.1.2, May 11, 2011) for docking analysis [47]. 3.2.2. Molecular docking Analysis: The docking calculations were performed using default parameters and 8 docked conformations were generated for both compounds. The energy calculations were done by genetic algorithms. Nonpolar hydrogen atoms, Gasteiger partial charges, rotatable bonds, and grid box with dimensions 66.57 × 58.25 × 84.98 Å3 created on the tyrosinase with the aid of Auto Dock Tools 1.1.2 and spacing of 0.3750 Å. The docked conformation of the respective protein conformer with lowest binding free energy and root mean-square deviation value (RMSD) 0.0 Å was analyzed using PyMOL Molecular Graphics System (version 1.7.4) and Accelrys Discovery Studio 4.1 [49]. We appreciate the recommendation, and splitted the data into 2 more subheads as, 3.2.1. Ligand and Protein preparation and 3.2.2. Molecular docking analysis. Also, more information was added about the software used as shown below: 3.2.
The conclusion must remind the reader why the article was written in the first place and why it is important in the field.