Synthesis of Azole-Linked s-Triazine-Isatin Molecular Architectures as Nanoscale DNA-Targeting Agents: A Combined Spectroscopic and Computational Study

Abstract

DNA, a ~2 nm diameter biopolymer, represents a fundamental nanoscale target for anticancer therapeutics due to its central role in replication and transcription. In parallel, DNA topoisomerase II (topo II), a key regulator of DNA topology, remains a validated enzymatic target for chemotherapeutic intervention. Herein, we report the synthesis of a series of azole-linked s-triazine–isatin hybrids 9a-f designed as multifunctional nanoscale DNA-targeting architectures. The nano-bio interactions of these hybrids with salmon sperm DNA (SS-DNA) were systematically investigated under physiological conditions (pH 7.4) using UV-Vis absorption spectroscopy. Binding constants (Kb), determined from Benesi–Hildebrand analyses, ranged from 103 to 105 M-1, with 9f showing the highest affinity (1.20 × 105 M-1 at 298 K), comparable to the standard. The Gibbs free energy change (∆G = –28.9 kJ·mol-1) indicated that the binding of 9f is spontaneous. Molecular docking studies supported these experimental findings, revealing that 9f forms stabilizing hydrophobic and hydrogen-bonding interactions within AT-rich DNA grooves (docking score: –10.3 kcal·mol-1, PDB: 3EY0) and binds topoisomerase II with a docking score of –10.7 kcal·mol-1 (PDB: 3QX3). Molecular dynamics simulations further confirmed the structural stability and dynamic behavior of the DNA–ligand and protein–ligand complexes. In addition, DFT calculations and in silico drug-likeness evaluations provided insights into electronic properties and pharmacokinetic potential. Collectively, these results highlight azole-linked s-triazine-isatin hybrids as promising nanoscale DNA-targeting scaffolds for anticancer development.