title: NMR structure of dual site binding of mitoxantrone dimer to opposite grooves of parallel stranded G-quadruplex [d-(TTGGGGT)]4.
abstract: The formation of complex between anti-cancer drug mitoxantrone (MTX) and tetra-molecular parallel G-quadruplex DNA [d-(TTGGGGT)]4 has been studied by solution state one and two dimensional NMR spectroscopy. Mitoxantrone forms a head-to-tail dimer and binds at two opposite grooves of the G-quadruplex. The Job's method of continuous variation and thermal melting studies independently ascertain binding stoichiometry of 4:1 in mitoxantrone:DNA complex. The existence of only four guanine NH peaks corresponding to the four G-quartets during the course of titration shows that C4 symmetry of G-quadruplex is intact upon binding of mitoxantrone. The specific inter molecular short distance contacts between protons of two mitoxantrone molecules of dimer, that is, ring A protons with ring C and side chain methylene protons, confirms the formation of mitoxantrone head-to-tail dimer. The observed 38 Nuclear Overhauser Enhancement (NOE) cross peaks between MTX and G-quadruplex DNA indicate formation of a well-defined complex. The three dimensional structure of 4:1 mitoxantrone:[d-(TTGGGGT)]4 complex computed by using experimental distance restraints followed by restrained Molecular Dynamics (rMD) simulations envisages the critical knowledge of specific molecular interactions within ligand-G-quadruplex complex. The findings are of direct interest in development of anti-cancer therapeutic drug based on G-quadruplex stabilization, resulting in telomerase inhibition.
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India.
authors.forename: Tarikere Palakshan
authors.initials: TP
authors.lastname: Pradeep
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India. Electronic address: ritubfbs@iitr.ac.in.
authors.forename: Ritu
authors.initials: R
authors.lastname: Barthwal
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D019281:Dimerization; D054856:G-Quadruplexes; D006801:Humans; D008942:Mitoxantrone / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D009691:Nucleic Acid Denaturation; D066244:Proton Magnetic Resonance Spectroscopy / Q000379:methods*
chemical_list: D004247:DNA; D008942:Mitoxantrone
keywords: G-quadruplex; Groove binding; Mitoxantrone dimer; Nuclear magnetic resonance spectroscopy; Thermal stabilization