Molecular Docking Study of the Interaction of N-Ferrocenylmethyl-N-Phenylacetamide with DNA

In the present study, the interaction of the optimised structure of ligand N-ferrocenylmethyl-N-phenylacetamide (FPA) with double-stranded DNA (PDB ID: 1BNA) extracted from protein data bank (http://www.rcsb.org./pdb) was investigated by performing docking studies using AutoDock 4.2 docking software. The binding energy of the docked structure of the FMNA ligand with DNA was found to be -20.69 KJ.mol-1 at the 5th run. The magnitude of the calculated binding energy indicates a high binding affinity between DNA and the studied ligand. The results indicate that the ligand FPA interacts with DNA by the oxygen atom of the amide function to the the hydrogen atoms H7 and H62 of the base pair deoxyadenosine-5.