Synthesis and DNA binding studies of novel triazine-isatin hybrids: experimental and computational insights

Abstract

DNA binding is a crucial determinant in developing novel anticancer agents, as it plays a key role in the mechanism of action for many chemotherapeutic drugs. In this study, a series of novel s-triazine-isatin hybrids (7a–f) was synthesized, and their binding interactions with salmon sperm DNA (SS-DNA) were investigated under physiological conditions (pH 7.4) using UV-vis absorption spectroscopy. The experimental findings demonstrated strong DNA-binding affinity through absorption and intensity shifts via groove-binding modes with SS-DNA. The binding constants (K_b) of synthesized hybrids with SS-DNA calculated from the Benesi–Hildebrand plot, ranged from 10⁴ to 10⁵ M⁻¹, with compound 7f exhibiting the highest binding constant (9.51 × 10⁵ M⁻¹) at 298 K, surpassing the reference cabozantinib. The Gibbs free energy change in the binding interaction of 7f, was found to be ΔG = −34.1 kJ mol⁻¹ indicating a spontaneous binding process. The molecular docking results supported experimental findings with a docking score of −10.3 kcal mol⁻¹ for 7f, highlighting hydrophobic and hydrogen bonding interactions within the AT-rich region of DNA grooves. In addition, DFT and in silico studies provided insights into the charge density of structures and drug-likeness, hence the s-triazine-isatin hybrid core holds promise as a potential therapeutic agent.