Free energy calculations reveal the interaction and stability of ligands in the vicinity of B-DNA dodecamer

The double stranded Deoxyribonucleic acid (DNA) is stated as one of the idyllic targets for cancer and other various diseases. The in-depth investigation of DNA-drug interaction plays a crucial role for the recognition of drug mechanism action as well as in advance scheming of more proficient drugs with minor aftermath. Imidazoles and molecules possessing them are well known for their antimicrobial action and also possess different therapeutic properties. With the intention to improve a computational protocol towards the development of novel improvised antimicrobial agent, di-cationic molecules. Primarily, four diarylfuran derivatives having varied substituted groups have been proposed, analysed and compared for antimicrobial potential by studying their binding strength and steady complex formation with DNA. Molecular docking analysis was used to forecast the binding mode involved for DNA-drug complex and molecular dynamics was employed for studying the kinetics of interaction. The docking investigation revealed AT rich region binding for all the proposed ligands which is the preferred location for DNA minor groove binders establishing Mol-1 and Mol-3 as lead molecules. The stability of drug-DNA complexes was inferred from an analysis of the data from Molecular dynamics (MD) analysis, which showed that ligands remained coupled to the preferred binding locations of DNA without experiencing any significant changes in the minor groove.