Molecular mechanism of anionic stabilizer for telomere G-quadruplex

Abstract

Telomere DNA assumes a high-order G-quadruplex (G4) structure, stabilization of which prevents telomere lengthening by telomerase in cancer. Through applying combined molecular simulation methods, an investigation on the selective binding mechanism of anionic phthalocyanine 3,4ʹ,4ʹʹ,4ʹʹʹ-tetrasulfonic acid (APC) and human hybrid (3 + 1) G4s was firstly performed at the atomic level. Compared to the groove binding mode of APC and the hybrid type I (hybrid-I) telomere G4, APC preferred to bind to the hybrid type II (hybrid-II) telomere G4 via end-stacking interactions, which showed much more favorable binding free energies. Analyses of the non-covalent interaction and binding free energy decomposition revealed a decisive role of van der Waals interaction in the binding of APC and telomere hybrid G4s. And the binding of APC and hybrid-II G4 that showed the highest binding affinity adopted the end-stacking binding mode to form the most extensive van der Waals interactions. These findings add new knowledge to the design of selective stabilizers targeting telomere G4 in cancer.

Graphical abstract

Keywords

Telomere G-quadruplex / Anionic stabilizer / Selective mechanism / Molecular dynamics / MM/GBSA

Acknowledgements

This work was funded by Zhejiang Provincial Natural Science Foundation of China (LY18H250002) and National Natural Science Foundation of China (81501204, 81530039, 81871112 and 91849124).