title: Structural investigation of idarubicin-DNA interaction: spectroscopic and molecular docking study.
abstract: Mechanistic understanding of interaction of drugs with their target molecule is important for development of new drug therapy regimes. Idarubicin (IDR) is a potent chemotherapeutic agent used to treat variety of cancers. Structural and conformational studies associated with binding of IDR on DNA double helix were investigated through spectroscopic techniques and molecular docking studies. Interaction studies were done by preparing different molar ratios of IDR with constant DNA concentration under physiological conditions. FTIR spectroscopy, UV-vis spectroscopy, CD spectroscopy were used to analyze interaction between IDR and DNA. FTIR results suggest IDR binds at major groove of DNA duplex via guanine and cytosine bases. UV-vis spectroscopy result indicates IDR gets intercalated between the DNA bases. The calculated binding constant shows that IDR is a moderate binder. Slight perturbation in the native B-conformation of DNA was observed in all IDR-DNA molar ratios examined. In silico investigation of IDR binding with DNA is in agreement with our experimental results, providing structural insight into DNA binding properties of IDR.
authors.affiliation: Quantum Optics and Photon Physics, CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi 110012, India.
authors.forename: Sonika
authors.initials: S
authors.lastname: Charak
authors.forename: Ranjana
authors.initials: R
authors.lastname: Mehrotra
mesh_terms: D000818:Animals; D002417:Cattle; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D015255:Idarubicin / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D017550:Spectroscopy, Fourier Transform Infrared
chemical_list: D004247:DNA; D015255:Idarubicin
keywords: Circular dichroism spectroscopy; FTIR spectroscopy; Idarubicin; Intercalation; Protein data bank; UV–vis spectroscopy