DNA binding study of antifungal drug Ketoconazole by molecular docking and spectroscopic analysis

The process of developing new drug molecules is long-term, costly, and especially the process of moving to clinical trials takes a long time. Consequently, conducting experimental and theoretical binding studies of drugs or drug candidates with biological materials, such as DNA and RNA, are crucial to reduce costs and minimize time requirements. As the DNA a fundamental biological molecule constitutes a major target for numerous pharmaceuticals, binding studies of various molecules with DNA is a broad field of research. DNA binding properties of antifungal drugs are of great importance in understanding their biological activities and elucidating their mechanisms of action. DNA binding studies also provide critical information to optimize the effects of antifungal drugs on target cells and to increase the selective toxicity of drugs. Ketoconazole (KTZ) is an azole-containing antifungal drug, and azole-containing drugs have many pharmacological properties. In this study, the interaction between the KTZ molecule and calf-thymus DNA (ct-DNA) was examined using various spectroscopic methods. The binding constant between ct-DNA and KTZ molecule was calculated using results obtained from different spectroscopic methods. UV-vis and fluorescence studies indicated a binding constant was calculated as 5.8 × 10⁴ M^-1 and 6.21 × 10⁴ M^-1 for the interaction between KTZ and ct-DNA, respectively. ct-DNA quenched the fluorescence of KTZ with a quenching constant approximately equal to 13 × 10¹² M^-1.s^-1. Fluorescence displacement experiments using ethidium bromide (EB) and Hoechst 33,258 revealed interaction between KTZ and ct-DNA occurred through minor groove binding mode. This conclusion was further supported by viscosity measurements, DNA melting studies, and KI quenching experiments. In light of experimental results, KTZ molecule quenches the fluorescence of DNA with a static mechanism due to the negative values of thermodynamic parameters such as ΔH^o and ΔS^o. In addition, the interaction of the KTZ molecule with ct-DNA was investigated theoretically by Molecular Docking. It interacts with the minor groove of DNA through a combination of van der Waals forces and hydrogen bonding interactions.