In Silico ADMET Profiling and DNA Interaction Study of Xanthoxylin: Assessment of Pbr322 DNA Protection Against Oxidative Damage

DNA is one of the primary intracellular targets for various anticancer drugs. Insight into the ligand-DNA interactions is critical for developing novel, promising bioactive molecules for therapeutic use. This is greatly aided by interpreting the interaction mechanism between small molecules and natural polymeric DNAs. The binding of small molecules to the DNA alters the mechanics of the strands, resulting in the inhibition of replication and transcription, providing information on the influence of gene expression. Xanthoxylin (XAN) is a phenolic compound recognised for various therapeutic activities, including anticancer; however, its mode of interaction with DNA has not been elucidated yet. This study investigated the interaction between XAN and calf thymus DNA (Ct-DNA) using docking simulation and spectroscopic techniques. Before DNA-binding studies, XAN was subjected to in silico ADMET analysis using SwissADME and pkCSM web servers. ADMET predictions are crucial to assess the drug-likeness and the safety profile of the bioactive molecules early in the development phase. XAN demonstrated acceptable physicochemical properties, conformance to drug-likeness, and a low risk of toxicity. Docking analysis revealed two distinct binding modes: intercalation and possible minor groove binding. Hyperchromic shifts observed in absorption spectroscopy confirmed the complex formation between XAN and Ct-DNA, with an estimated association constant (Ka) in the order of 104 M−1. The thermodynamic parameters indicated a spontaneous and exothermic binding process, involving van der Waals forces and hydrogen bonding. Dye dislocation studies revealed that XAN binds via the minor groove. Circular dichroism and thermal denaturation profiles further manifested the groove binding mode of XAN. However, molecular docking studies were inconsistent in predicting the precise binding mode, only partially corroborating the in vitro findings. Plasmid nicking assays indicated that XAN does not induce DNA damage and is not a prooxidant. Conversely, it significantly reduced DNA lesions induced by the Fenton reaction, suggesting its role as a reactive oxygen species (ROS)-scavenging agent. These computational and in vitro results evinced that XAN has drug-relevant attributes and can act as a DNA-binding agent and an antioxidant.