Evaluation of docking methodologies for DNA-ligand systems

DNA is a target in the treatment of several genetic diseases, especially cancer, due to its importance in the cell cycle. However, the best docking methodology for nucleic acids is not clear. Thus, Molecular Architect (MolAr -BR512018052442-7)⁠, a structure-based drug design workflow, was used to evaluate the performance of Autodock Vina, Dock 6 and the consensus among the docking methodologies that use a receiver operating characteristic curve (ROC curve). The active compounds were obtained from the previous report. The best five of them were used to generate the decoys by DUD-E platform. Initially, the ligands were refined by Parametric Method 7 (PM7). Then, all the compounds were docked against 1VZK⁠ molecular target through MolAr. As a result, the area under the ROC curve (AUC) was 0.98, 0.88 and 0.99 for Autodock Vina, Dock 6 and consensus respectively. We conclude that the consensus routine of MolAr can improve the docking results.