Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex-Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent.

Authors

Holli-Joi Sullivan
Carolyn Readmond
Christina Radicella
Victoria Persad
Thomas J Fasano
Chun Wu, Rowan UniversityFollow

Document Type

Article

Version Deposited

Published Version

Publication Date

11-30-2018

Publication Title

ACS Omega

DOI

10.1021/acsomega.8b01574

Abstract

A promising anticancer therapeutic strategy is the stabilization of telomeric G-quadruplexes using G-quadruplex-binding small molecules. Although many G-quadruplex-specific ligands have been developed, their low potency and selectivity to G-quadruplexes over duplex remains unsolved. Recently, a crystal structure of a telomeric 3' quadruplex-duplex hybrid was reported and the quadruplex-duplex interface was suggested to a good target to address the issues. However, there are no high-resolution complex structures reported for G-quadruplex ligands except for a docked BSU6037. In this study, molecular dynamic (MD) binding simulations with a free ligand were used to study binding poses and dynamics of four representative ligands: telomestatin, TMPyP4, BSU6037, and BRACO19. The MD data showed that BSU6037 was able to fully intercalate into the interface whereas TMPyP4 and BRACO19 could only maintain partial intercalation into the interface and telomestatin only binds at the quadruplex and duplex ends. Both linear ligands, BSU6037 and BRACO19, were able to interact with the interface, yet they were not selective over duplex DNA. The DNA geometry, binding modes, and binding pathways were systematically characterized, and the binding energy was calculated and compared for each system. The interaction of the ligands to the interface was by the means of an induced-fit binding mechanism rather than a lock-key mechanism, consisting of the DNA unfolding at the interface to allow entrance of the drug and then the refolding and repacking of the DNA and the ligand to further stabilize the G-quadruplex. On the basis of the findings in this study, modifications were suggested to optimize the interface binding for TMPyp4 and telomestatin.

Comments

This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.

Open access to this article was paid for by the Rowan University Libraries Open Access Publication Fund.

Recommended Citation

Sullivan, H-J., Readmond, C., Radicella, C., Persad, V., Fasano, T., & Wu, C. (2018) Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G‑Quadruplex−Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. ACS Omega 2018, 3, 14788-14806.