title: Binding interaction between sorafenib and calf thymus DNA: spectroscopic methodology, viscosity measurement and molecular docking.
abstract: The binding interaction of sorafenib with calf thymus DNA (ct-DNA) was studied using UV-vis absorption spectroscopy, fluorescence emission spectroscopy, circular dichroism (CD), viscosity measurement and molecular docking methods. The experimental results revealed that there was obvious binding interaction between sorafenib and ct-DNA. The binding constant (Kb) of sorafenib with ct-DNA was 5.6×10(3) M(-1) at 298 K. The enthalpy and entropy changes (ΔH(0) and ΔS(0)) in the binding process of sorafenib with ct-DNA were -27.66 KJ mol(-1) and -21.02 J mol(-1) K(-1), respectively, indicating that the main binding interaction forces were van der Waals force and hydrogen bonding. The docking results suggested that sorafenib preferred to bind on the minor groove of A-T rich DNA and the binding site of sorafenib was 4 base pairs long. The conformation change of sorafenib in the sorafenib-DNA complex was obviously observed and the change was close relation with the structure of DNA, implying that the flexibility of sorafenib molecule played an important role in the formation of the stable sorafenib-ct-DNA complex.
authors.affiliation: College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China; State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, Zhejiang University of Technology, Hangzhou 310032, China. Electronic address: shijh@zjut.edu.cn.
authors.forename: Jie-Hua
authors.initials: JH
authors.lastname: Shi
authors.affiliation: College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Chen
authors.affiliation: College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.affiliation: College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China.
authors.forename: Ying-Yao
authors.initials: YY
authors.lastname: Zhu
mesh_terms: D000818:Animals; D002417:Cattle; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D006860:Hydrogen Bonding; D007700:Kinetics; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D009536:Niacinamide / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D009994:Osmolar Concentration; D010671:Phenylurea Compounds / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D000077157:Sorafenib; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics; D014783:Viscosity
chemical_list: D010671:Phenylurea Compounds; D009536:Niacinamide; D004247:DNA; C427203:calf thymus DNA; D000077157:Sorafenib
keywords: Calf thymus-DNA; Circular dichroism; Fluorescence spectroscopy; Molecular docking; Sorafenib; UV–vis spectroscopy