4.9.1. Binding affinity of L1 and L2 The highest anti-bacterial activity (zone of inhibition 12 mm) of compound L2 was detected with tyrosinase from Bacillus Megaterium (PDB ID: 4j6u) bacteria compared to L1. 6. In L1-4j6u, one conventional hydrogen bond (3.04 Å) of O-H----O-C observed between O-H of Tyr267A and O-C group of compounds L1. Pi-cation, pi-sulfur and amide-pi bonds were also noticed with LYS47A, PHE48A, ILE39A, ALA40A, GLY43B and ALA44B, respectively. Moreover, ALA44A, LYS47A, ALA44B, LYS47B, PRO52A, ALA40B and ILE139B were actively involved in the non-covalent interaction (hydrophobic pi-alkyl). L2-4j6u complex was stabilized by four NH….O hydrogen bonds and they were LYS47A (2.25 Å), GLY143B (3.04 Å), Tyr267A (3.07 Å) and PRO219B (2.91 Å) (Fig. 6). Like L1, L2 formed pi-cation and amide-pi bonds with LYS47A, ILE39A, GLY43B, where the distances were 3.73, 4.34, 3.54 Å. L2 also formed seven pi-alkyl bonds with ALA44A (5.19 Å), LYS47A (4.35 Å), ALA44B (3.95 Å), LYS47B (4.98 Å), PRO52A (5.04 Å), ALA40B (4.67 Å) and ILE139B (4.24 Å), respectively. We appreciate the recommendation and rewrote the Molecular Docking study as follows as suggested by the reviewer, 4.9. Molecular Docking Study Molecular docking is a powerful tool to investigate and provide a proper understanding of ligand-receptor interactions in order to facilitate the design of potential drugs [92-95]. To investigate and compare the antimicrobial activity of the synthesized compounds, docking analyses of L1 and L2 against tyrosinase from Bacillus Megaterium were performed. It is well-known that tyrosinase of Bacillus Megaterium bacteria is an attractive target for the development of antimicrobials or antibiotic adjuvants for the treatment of hyperpigmentation because of its similarity (33.5%) to the human enzyme [96-99]. The docking results were also compared with well-testified inhibitor arbutin [97]. Binding affinity of L1 and L2 The highest antibacterial activity (zone of inhibition 12 mm) of compound L2 was detected with tyrosinase from Bacillus Megaterium (PDB ID: 4j6u) bacteria compared to L1. The binding energies for L1 and L2 with Bacillus Megaterium were −7.7 and −8.8 kcal mol−1, respectively, whereas for arbutin-4j6u the value was -9.1 kcal mol-1 which were calculated by AutoDock Vina. The interactions of the 4j6u with compounds L1 and L2 are shown in Fig. It was observed that arbutin formed six conventional hydrogen bonds with 4j6u (Supplementary Fig. S11) by the following residues: ALA40A (one O-H----O-C hydrogen bond), Glu141A (four O-H----O-C hydrogen bond), and LYS47B (one O-H----O-C hydro-gen bond). Also several hydrophobic interactions were found with ILE139A, ILE39A, and ALA40A. Results of docking studies revealed that L1 and L2 formed bonds to the active site of tyrosinase and showed strong interactions with Tyr267A, Ala40A, Ala44A, ALA44B and Lys47B of tyrosinase enzyme (PDB ID: 4j6u), which are in close vicinity to the control arbutin and supports the literature [100-102].
The molecular study needs a control molecule to compare the results of L1 and L2. how would we know that −7.7 and −8.8 are good scores or not. Either perform a quick analysis for a molecule known for its tyrosinase inhibition or compare with other studies control that used the same methods in your paper.For exemple in this study "https://doi.org/10.1016/j.bmc.2011.10.078" they used Arbutin to compare the results of their studied molecule.