Chembiodraw ultra 17

ChemBioDraw Ultra 17.0 was used to draw the two-dimensional structure of the main compounds of Mume Fructus, which was then transformed into a three-dimensional structure by using ChemBio3D Ultra 17.0, and was optimized with the MMFF94 force field.
The PPI network was incorporated with the top 10 genes in degree in KEGG, and the overlapping genes were used as the targets for molecular docking. The three-dimensional structure of the pre-targets was downloaded from the RCSB Protein Data Bank (www.rcsb.org).The corresponding ligands were found in RCSB as positive reference.
The three-dimensional structures of the pre targets and compounds were transformed into PDBQT format using AutoDockTools 1.5.6.^{[22 (link)]} AutoDock Vina 1.1.2^{[23 (link)]} was used for molecular docking. To increase the accuracy of the calculation, the “exhausitiveness” parameter was set to 20, with the other parameters adopting the default values. Finally, the highest-scoring conformation was selected and analyzed with Maestro 11.9 (Schrödinger).

ChemBioDraw Ultra 17.0 to was used to draw the structure of the compounds (emodin and salvianolic acid B), and ChemBio3D Ultra 17.0 was used to create three-dimensional structures and MMFF94 for force field optimization. The three-dimensional structure of Keap-1 (PDB ID was 4IQK) was downloaded from the RCSB Protein Data Bank (http://www.rcsb.org/). Keap-1 and the compounds (Emodin and salvianolic acid B) were converted to the PDBQT format using Autodock Tools 1.5.6. Autodock vina 1.1.2 was applied for molecular docking studies [12 (link), 13 (link)]. The accuracy of the calculation was increased by setting the parameter exhaustiveness to 20. Except specifically mentioned, other parameters are used as default values. The conformation with the highest score was selected, and the Free Maestro 11.9 was used to analyze the results.

The 3D structures of all candidate drug compounds were drawn by ChemBioDraw Ultra 17.0 and then subjected to energy optimization by the MMFF94 force field. The 3D structure of XDH (PDB ID: 2e1q), ATIC (PDB ID: 1pl0), CA9 (PDB ID: 5fl6), GAPDH (PDB ID: 3gpd) were downloaded from the PDB (http://www.rcsb.org/pdb/home/home.do), and 3D structure of SLC7A11 was obtained from homologous modeling. Before docking analysis, all protein and molecular files were converted into PDBQT format using AutodockTools 1.5.6. Molecular docking analysis were carried out by Autodock Vina 1.1.2. The docking parameter ‘exhaustiveness’ was set to ‘20’, and other parameters were set to default. The conformation with the highest score was selected to further analyze using Free Maestro 11.9. Pymol software 2.3 was applied for model visualization and MOE software 2019 was used for drawing the 2D depictions [34 (link)].