Interaction of two key biological targets -trypsin and dna- with phenolic phytochemicals: Insights from molecular docking and radical scavenging potential

Abstract

Phenolic acids represent a diverse class of phytochemicals that are abundantly present in fruits, vegetables, and other plant-based sources. The wide-ranging biological properties of these compounds have stimulated considerable interest within the scientific community. Syringic and isovanillic acid, the aromatic natural phytochemicals, are found in fruits and vegetables and exhibit a range of biological activities, including antioxidant and enzyme-modulating effects. In this study, we investigated their binding interactions with biologically significant macromolecules: calf thymus DNA (CT-DNA) and trypsin. The effects of both the phenolic acids on the structure and activity of these macromolecules were analyzed using fluorescence spectroscopy, including quenching type, binding constants, binding sites, thermodynamic parameters, synchronous fluorescence, fluorescence resonance energy transfer (FRET) analysis, two-dimensional (2D), and three-dimensional (3D) fluorescence analysis, effect of metal ions), Fourier transform infrared spectroscopy (FTIR) and molecular docking techniques. The results show that both phenolic acids could bind to CT-DNA via a minor groove mode. The fluorescence experiments indicated that both the phenolic acids bind and cause quenching of trypsin fluorescence. Molecular docking simulations were carried out to examine the interaction profiles of both the phenolic acids with CT-DNA and trypsin. Results revealed that both phenolic acids bind to the DNA minor groove via hydrogen bonding and pi-pi interactions, with syringic acid showing slightly higher affinity. In the case of trypsin, the isovanillic acid exhibited a stronger binding energy and formed a more compact interaction pattern within the enzyme's active site. These findings support the potential of both the phenolic acids to form stable, noncovalent complexes with biologically relevant macromolecules and contribute to their observed antioxidant and enzymatic effects. The radical scavenging activity of both phenolic acids was measured via the 2,2-Diphenyl1-picrylhydrazyl (DPPH) method and reported in terms of their IC50 value. Based on the results, it can be inferred that the radical scavenging potential of both phenolic acids is significantly affected by the number and position of their substituents.