Synthesis, characterization and molecular docking studies of new indol(1H-3-yl)pyrimidine derivatives: Insights into their role in DNA interaction.

This study reports the synthesis of new indol(1H-3-yl) pyrimidine derivatives 4(a-e) using various substituted indole-3-carbaldehydes, urea and malononitrile in the presence of ammonium chloride. The resulting compounds were characterized using analytical and spectroscopic methods. The molecular docking study exhibits that among the synthesized compounds, 4(c-e) have great binding ability toward B-DNA. The binding efficiencies of compounds 4(c-e) with CT-DNA were evaluated via UV-visible absorption spectral and viscosity studies. The findings establish that the compounds firmly bind through an intercalative mode to CT-DNA and provide a unique pattern of DNA binding. The photo-induced cleavage indicates that the compounds have UV-visible photo nuclease properties toward plasmid DNA as revealed by agarose gel electrophoresis approach.

4-Amino-6-(piperidin-1-yl)pyrimidine-5-carbo-nitrile.

In the title compound, C10H13N5, the piperidine ring adopts a chair conformation with the exocyclic N-C bond in an axial orientation, and the dihedral angle between the mean planes of piperidine and pyrimidine rings is 49.57 (11)°. A short intra-molecular C-H⋯N contact generates an S(7) ring. In the crystal, N-H⋯N hydrogen bonds link the mol-ecules into (100) sheets and a weak aromatic π-π stacking inter-action is observed [centroid-centroid separation = 3.5559 (11) Å] between inversion-related pyrimidine rings.