Experimental and Theoretical Examination of DNA-Binding Properties of Ruthenium(II)-Hydrazine Complexes

The DNA-binding properties of four Ru^II-hydrazine complexes [{RuCl(η⁶-p-cymene)}₂(μ-Cl)(μ-L¹-κ²N,N')]Cl (1, L¹: 3,4-dimethylphenylhydrazine) and [RuCl₂(η⁶-p-cymene)(L^1-3-κN)] complexes (2, L¹; 3, L3: 3-chlorophenylhydrazine; 4, L³: 3-nitrophenylhydrazine) were explored through a combination of fluorescence spectroscopy, molecular docking, and Our own N-layered Integrated molecular Orbital and Molecular Mechanic (ONIOM)-based quantum mechanics/molecular mechanics (QM/MM) simulations. Ethidium bromide (EtBr) displacement assays revealed that all compounds interact with DNA, with calculated quenching constants (K_SV) ranging from 2.44 to 4.79 × 10⁴M. The results led to the conclusion that all complexes interact with DNA with similar strength, although subtle differences were explained by the present structural groups and molecular electrostatic potential (MEP) maps. The presence of nitro and chloro substituents was important for the weak interactions with DNA, leading to partial removal of EtBr. Computational studies supported the experimental findings. Molecular docking confirmed minor groove binding for all four complexes, with favorable interaction geometries and binding energies. Complex 3 stood out, with the most negative docking score (ΔG_bind = -38.2 kJ mol^-1). The docking simulations with RNA, triplex DNA/RNA, and quadruplex DNA/RNA additionally proved that the size of the complex and the presence of substituents were determinants of selectivity. Further refinement using ONIOM-based QM/MM calculations yielded interaction energies with DNA that matched previous results, identifying compound 3 as the most stable DNA-binding species (ΔE = -532.7 kJ mol^-1). The correlation between spectroscopic and theoretical results highlights the role of Ru^II-hydrazine ligand structure in modulating DNA affinity. Complex 3, bearing electron-donating hydrazine functionality and favorable spatial orientation, emerged as a promising candidate for further development in DNA-targeted therapies.