Molecular docking of porphyrins with cationic limbs on intramolecular G-quadruplex.
We performed molecular docking simulations of porphyrins with cationic limbs on an intramolecular anti-parallel G-quadruplex and molecular dynamics simulations for the model complexes to explore plausible binding regions and modes. With grid-based scoring, GB/SA scoring and MM-PBSA method, two low-energy binding regions, a groove and a loop, for the porphyrins were identified.
Ishikawa
Yoshinobu
Y
Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto 8620973, Japan. ishikawa@gpo.kumamoto-u.ac.jp
Higashi
Eiki
E
Morioka
Hiroshi
H
D003198:Computer Simulation; D054856:G-Quadruplexes; D008958:Models, Molecular; D011166:Porphyrins / Q000737:chemistry*; D016615:Telomere / Q000737:chemistry
D011166:Porphyrins