Molecular docking study of binding of TMPyP4 to a bimolecular human telomeric G-quadruplex.
We carried out molecular docking simulation of binding of cationic porphyrin TMPyP4 to a bimolecular human telomeric G-quadruplex using DOCK6.1 to examine whether or not to reproduce the loop binding mode of TMPyP4 in the crystal structure. The simulation gave the two highest-ranked docking poses of TMPyP4, and the binding modes were external stacking on the terminal guanine-tetrad and groove binding.
Ishikawa
Yoshinobu
Y
School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka-shi, Shizuoka 422-8526, Japan. ishi206@u-shizuoka-ken.ac.jp
Fujii
Satoshi
S
D003198:Computer Simulation; D054856:G-Quadruplexes; D006801:Humans; D008958:Models, Molecular; D011166:Porphyrins / Q000737:chemistry*; D016615:Telomere / Q000737:chemistry*
D011166:Porphyrins; C021096:tetra(4-N-methylpyridyl)porphine