Combined theoretical and experimental studies reveal the newly synthesized pyrimidinones as potential apoptotic agents

Reaction of acetophenone thiosemicarbazones (5–8) and (2-methyl) diethyl malonate in absolute ethanol under reflux conditions furnished the corresponding pyrimidinone analogs (9–12) in good to excellent yields. The resulting pyrimidines were characterised using spectral and analytical data analysis. The resulting products were studied for DNA interaction studies of by various techniques like UV–VIS, fluorescence spectroscopy, viscosity measurements, molecular docking and gel electrophoresis. To look into the various structural and molecular properties of the target compounds, theoretical DFT involving B3LYP/6-31G∗∗ level of theory was employed. Frontier molecular orbital analysis (FMO) was carried out which in turn helped us to determine and evaluate the descriptors like chemical hardness, potential, nucleophilicity and electrophilicity index, etc. Molecular docking and viscosity studies indicated that the synthesized pyrimidinones are minor groove binders of DNA with corresponding intrinsic binding constants of 3.41 × 103 M−1, 2.91 × 103 M−1, 3.24 × 103 M−1 and 3.04 × 103 M−1 for compounds (9–12) respectively indicating higher binding affinity of 9 towards DNA. Gel electrophoresis depicted that all new compounds display a dose dependent cleavage activity with pBR322 DNA and efficient nuclease activity was found at 2 μM. An in vitro MTT cytotoxicity assay revealed that the compounds (9–12) possess potential toxicity against the different human cancer cells. The AO/EB staining showed that compound 9 caused apoptosis as revealed by the notable apoptotic features like nuclear shrinkage, blebbing and chromatin condensation in HepG2 cells. Compound 9 also caused decrease in the level of apoptotic marker Bcl-XL in Western blotting indicating its prompt ability to cause apoptosis.