Computer-Aided Drug Discovery: Molecular Docking of Diminazene Ligands to DNA Minor Groove

Abstract

The reported project-based laboratory unit introduces upper-division undergraduate students to the basics of computer-aided drug discovery as a part of a computational chemistry laboratory course. The students learn to perform model binding of organic molecules (ligands) to the DNA minor groove with computer-aided drug discovery (CADD) tools. The purpose of this laboratory unit is to dock diminazene and its derivatives to DNA, to estimate their binding energies, and to elucidate details of DNA–ligand intermolecular interactions. The computational procedure also helps to screen binding capabilities of DNA ligands.