Investigation of the binding affinity of a newly synthesized copper(II) complex to DNA and enzymes (catalase/trypsin/urease) using spectrofluorimetry and in silico approaches

Abstract

In recent years, there has been a growing interest in the synthesis of novel compounds with medicinal potential, particularly those exhibiting antioxidant properties, due to their ability to delay, prevent, or eliminate oxidative damage in target cells. Understanding the interactions between these compounds and major biological targets—including DNA, catalase, trypsin, and urease—is essential for improving their bioactivity and therapeutic potential. The synthesis and comprehensive characterization of a novel copper(II) complex, [Cu(3,5ClSal-Phe)(CH₃OH)]—featuring a Schiff base ligand derived from 3,5-chlorosalicylaldehyde and L-phenylalanine—were carried out using electronic absorption spectroscopy, FTIR, ESI-MS, ESR and X-ray diffraction. Electronic absorption and fluorescence spectroscopy were employed to investigate the interactions between the complex and key biomolecules such as CT-DNA, catalase, trypsin, and urease. The complex was found to bind CT-DNA through minor groove interaction, while its fluorescence quenching with catalase, trypsin, and urease proceeds via a static mechanism. To better understand the molecular basis of these biological effects, docking simulations were employed using DNA and three key enzymes, trypsin, urease, and catalase, as molecular targets. Among all targets, the strongest binding affinity was observed with catalase (−9.31 kcal/mol), where the complex formed hydrogen bonds with Arg111, His361, Phe333, and Arg71, as well as a halogen interaction with Tyr357. Interactions with trypsin and urease were also energetically favorable, predominantly involving polar and hydrophobic residues. Docking protocols were validated through redocking (RMSD <2.0 Å), ensuring reliability of the predicted binding modes. In vitro assessment of the complex's antioxidant activity, conducted using the DPPH radical scavenging assay, revealed a moderate scavenging efficiency.