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Computational docking is a globally used tool now-a-days in bioinformatics. All the drugs/ligands generate their effect only when they interact/bind with the target molecule, here DNA. The potential drugs/ligands can only be identified by the study of their relative binding energies and preferential binding modes. Due to availability of huge numbers of such drugs/ligands; the evaluation of their relative potency is a challenging task. In the present work, carbazoles and its derivatives were studied for their DNA binding abilities using computational molecular docking. All the docked ligands had planar structures which allowed them to adopt crescent shape and thus minor groove binding to DNA was preferred by most of them. Computational docking revealed that DNA binding energies of carbazoles and its analogs followed the same trend as their thermal melting values. Also the drugs/ligands preferred themselves to bind at AT-rich regions of the minor groove of the selected DNA sequences.

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The combination of experimental and computational strategies has been of great value in the identification and development of metabolism of drugs. Nowadays modern drug design, molecular docking methods are helpful in exploring the ligand conformations adopted within the binding sites of macro-molecular targets such as DNA, proteins, and enzymes, there by reducing cost, time and wayward efforts of chemist. Since the development of the algorithms in the 1980s, molecular docking became an important tool in drug discovery like investigation of crucial molecular events, including ligand binding modes and the corresponding intermolecular interactions that stabilize the ligand-receptor complex, can be conveniently performed. In present study we have tried to investigate the drug binding pocket of various cytochrome (CYP) enzymes found in humans. All structures of drugs are optimized at B3LYP/6-31** level of theory using Gaussian program suite. Docking of substrate-enzyme duo was done using AUTODOCK 4.0. Computational docking revealed that almost all drugs have same binding pocket with varied binding affinities due to change in interactions and interacting distance from heme prosthetic moiety with transition metal iron as chelating ion.