DNA-Binding Studies of Ofloxacin Using a Series of Spectroscopic, Electrochemical Techniques and in Silico Approaches

Ofloxacin (OFL), a quinolone antibiotic, shows a bactericidal effect by inhibiting the DNA gyrase enzyme in bacteria. In addition to its use in various infections has a wide range of benefits from urinary system disorders to pneumonia and bronchitis. DNA is the main molecular target for many small molecules of therapeutic importance. In this article, the interaction between OFL and fsDNA (fish sperm DNA) is reported using a combination of biophysical (spectroscopic and electrochemical) and in silico techniques (molecular docking and molecular dynamics). The interaction and complex formation were studied using UV-visible and steady-state fluorescence spectroscopy. Ethidium bromide (EtBr), Rhodamine B (RB) competitive displacement, potassium iodide quenching, and ionic strength assays confirmed the binding mode between OFL and DNA via minor groove binding. Thermodynamic parameters at various temperatures supported the enthalpically driven, exothermic, and spontaneous reaction between OFL and fsDNA. It was found that hydrogen bond interaction and van der Waals forces play a dominant role in forming the complex form. DNA melting experiments corroborated these findings. In-silico molecular docking and molecular dynamics simulation studies revealed the interaction mode, major stabilizing forces, and the nucleotide sequences OFL binds and dock into the GC-rich region of the DNA minor groove, confirming the in vitro experiment results.