Investigation of cytotoxic indoleninyl-thiobarbiturate zwitterions as DNA targeting agents

• A series of indoleninyl-thiobarbiturate zwitterions were synthesized. • All zwitterions are likely to exhibit high bioavailability. • Zwitterion 2f is a DNA minor groove binder. A series of indoleninyl-thiobarbiturate zwitterions were synthesized in up to 83% yields from the Knoevenagel condensation between N -substituted diformyl indolenine and thiobarbiturate. The structures were characterized by spectroscopic methods such as NMR ( 1 H, 13 C), FT-IR, high-resolution mass spectrometry (HR-MS) and elemental analysis. However, their physicochemical properties and biological activities remain elusive. Herein, results from in silico ADMET calculations and cytotoxicity predictions suggest that all zwitterions are likely to exhibit a higher bioavailability and more specific cytotoxicity than doxorubicin. The notably high predicted cytotoxicity of 2d and drug-likeness score of 2f may be linked to the position of the fused benzene ring and methoxy groups, respectively. The initial biological assessment of these compounds began with in vitro DNA-binding studies because the treatment of numerous diseases such as cancer and bacterial infections is linked to DNA interactions. Zwitterion 2f demonstrated the most significant spectral change in DNA binding studies, suggesting a possible role of the methoxy group in inducing DNA binding activity. The hypothesis that 2f interacts with DNA through groove binding was confirmed by observations made during salt-back titration and DNA denaturation experiments. It was anticipated that the non-zwitterionic 2f would interact more stably with DNA (PDB code: 453D) at the minor groove than its zwitterionic form based on molecular docking calculations and molecular dynamic (MD) simulations. Additionally, the MTT assay demonstrates that 2f is moderately cytotoxic to the human breast cancer cell line MDA-MD-231, most probably as a result of the previously stated DNA binding mechanisms. Overall, the computational and in vitro data suggest the potential application of 2f as a cytotoxic DNA-targeting agent.