Prime tool

To predict the binding sites of human tyrosinase to EG, molecular docking was performed using the Glide module of the Schrodinger Package [22 (link),23 (link)]. The X-ray crystal structure of tyrosinase (PDB ID: 2Y9X) was retrieved from the Protein Data Bank (http://www.rcsb.org, accessed on 10 October 2022). The retrieved protein structures were processed using Protein Preparation Wizard in the Schrodinger package to remove the crystallographic water molecules, add hydrogen atoms, and assign protonated states and partial charges. The missing side chains and loops were built and refined using the Prime tool of the Schrodinger suite [24 (link)]. All protein residues were parameterized using the OPLS3e force field [25 (link),26 (link)]. Finally, restrained minimization was performed until the converged average root mean square deviation of heavy atoms was 0.3 Å.

Molecular docking was performed to predict the binding site of mushroom tyrosinase and TRP-1 to nomilin using the Glide module in the Schrodinger package [22 (link),23 (link)]. The X-ray crystal structures of tyrosinase (PDB ID: 2Y9X) and TRP-1 (PDB ID: 5M8O) were retrieved from the Protein Data Bank (http://www.rcsb.org (accessed on 10 October 2020)). The retrieved protein structures were processed using Protein Preparation Wizard in the Schrodinger package to remove crystallographic water molecules, add hydrogen atoms, and assign protonated states and partial charges. The missing side chains and loops were built and refined using the Prime tool of the Schrodinger suite [24 (link)]. All protein residues were parameterized using the OPLS3e force field [25 (link),26 (link)]. Finally, restrained minimization was performed until the converged average root mean square deviation of heavy atoms was 0.3 Å. Binding mode predictions of nomilin with mushroom tyrosinase and TRP1 were performed using the Glide docking tool in the Schrodinger package. Docking grid boxes were generated considering the catalytic sites of mushroom tyrosinase and TRP-1. Nomilin was docked into the catalytic site of each protein using standard precision scoring modes. The 3D structure of nomilin was minimized using the Macromodel module of the Schrodinger suite.

Molecular docking was performed to confirm the binding site of mushroom tyrosinase and TRP-1 to quercetin and OQ using the Glide module in Schrodinger [40 (link),41 (link)]. The X-ray crystal structures of tyrosinase (PDB ID: 2Y9X) and TRP-1 (PDB ID: 5M8O) were retrieved from the Protein Data Bank (http://www.rcsb.org (accessed on 10 October 2020)). The retrieved protein structures were processed using Protein Preparation Wizard in the Schrodinger package to remove the crystallographic water molecules, add hydrogen atoms, and assign protonated states and partial charges. The missing side chains and loops were built and refined using the Prime tool of the Schrodinger suite [42 (link)]. All protein residues were parameterized using the OPLS3e force field [43 (link),44 (link)]. Finally, restrained minimization was performed until the converged average root mean square deviation of heavy atoms was 0.3 Å. Docking studies of quercetin and OQ with mushroom tyrosinase and TRP1 were performed using the Glide docking tool in the Schrodinger package. Docking grid boxes were generated considering the catalytic sites of mushroom tyrosinase and TRP-1. Quercetin and OQ were docked into the catalytic site of each protein using standard precision scoring modes. The 3D molecular structures of quercetin and OQ were minimized using the macromodel module of Schrodinger.