Molecular Docking of Anthracene with Cytochrome C

For the simulations, the file with an sdf extension containing the molecular structure of anthracene was downloaded from Zinc12 (ZINC01586329) [47 (link)] and transformed into files with extension mol2 using Openbabel 2.3.1 [48 (link)]. This tool was also used to minimize the structure of the ligand by applying the steepest descent algorithm, MMFF94 force field, and 50,000 steps for fitting after adding hydrogens to the molecule. We used Autodock Tools 4 (ver. 1.5.6) [49 (link)] to prepare the molecule as ligands for docking analysis. We visualized and set the torsion parameters, and then saved the file with the extension pdbqt for its submission for docking analysis. The molecular structure of Cc was downloaded from the Protein Data bank (PDB file: 1HRC), which corresponds to the high-resolution three-dimensional structure of horse heart Cc. For docking preparation, water molecules were removed from the structure, hydrogens were added (polar only), and Kollmand charges were added using Autodock Tools 4. The prepared file for docking was saved as a pdbqt file. The grid for the docking analysis was structured as follows: center x = 46.839, center y = 23.029, center z = 5.505 with a box size of: 52 for x, 52 for y and 52 for z.
The docking analysis was performed with AutodockVina 1.1.2 and the previously indicated files for the receptor (PDB:1HRC.pdbqt) and the ligand (anthracene.pdbqt) [50 (link)] by using the previously indicated grid for Cc and an exhaustiveness value of 9. The top 10 ranked poses associated with models of the ligand–Cc complex were visually analyzed using UCSF Chimera 1.15 [51 (link)] and clustered by homology. The binding site for anthracene was defined and selected based on the residues making contact and clashing with the ligand within a distance of 0.1 Å. We gathered similar poses together in subclusters for each experiment. Each experiment was performed in triplicate. A cluster was defined as the set of residues present in subclusters in all the performed individual experiments. The lowest energy value of the top-ranked pose present in a subcluster forming a cluster was selected as the energy value for the selected cluster.