Abstract
Introduction: DNA serves as a key target for drug development due to its structural accessibility, making it ideal for interaction with small molecules. The traditional drug discovery process is often slow and costly, prompting the need for more efficient approaches. In this study, we employed a combination of computational drug repositioning and molecular docking techniques to identify pyridine-4-carbohydrazide Schiff base derivatives with potential DNA-binding activity, expediting the identification of promising candidates for synthesis and experimental validation. Methods: Nineteen pyridine-4-carbohydrazide Schiff base derivatives (INH01-INH19) were screened using molecular docking to predict their binding affinity to various DNA fragments. Compounds with the highest predicted affinities were synthesized using a microwave-assisted method and characterized via FTIR, 1H, and 13C-NMR. The DNA-binding interactions of the synthesized compounds were further evaluated through UV-visible absorption titration and competitive binding assays with Rhodamine B to validate the computational predictions. Results: Molecular docking identified key interactions between the derivatives and DNA, with aromatic planar structures and specific substitution patterns contributing to binding activity. Four lead compounds (INH03, INH09, INH14, and INH19) were synthesized and characterized. UV-visible absorption titration and competitive assays confirmed minor groove binding to genomic DNA. The binding constants (Kb) ranged from 6.3×10⁴ to 7.4×10⁴ M⁻¹, with negative Gibbs free energy values indicating spontaneous interactions. Conclusion: This study identified four pyridine-4-carbohydrazide Schiff base derivatives with strong DNA-binding properties, underscoring their potential as DNA-targeting agents. The correlation between in silico predictions and experimental data demonstrates the utility of computational methods in guiding the design and development of DNA-interacting drugs.