Abstract 1357: In silico design and biological evaluation of benzofused polyamides targeting G-quadruplex DNA structures
Authors: Rahman Khondaker M. , Rahman AKM Azadur , Jackson Paul J. M. , Thurston David E. 
Published: July 2016

Abstract
Guanine-rich nucleic acids can fold into distinctive four-stranded G-quadruplex structures which are found in telomeric DNA repeats as well as in sequences in the promoter and other regulatory regions of genes, especially those involved in cellular proliferation. Small molecules that can selectively bind and stabilize the G-quadruplex structure have become of significant interest to researchers, and are gaining momentum as a possible new class of anticancer agents.
We recently reported a series of novel biaryl polyamides with significant selectively toward G-quadruplex compared to duplex DNA. Using a distamycin scaffold as a starting point, we introduced biaryl building blocks in place of pyrroles to switch preference from duplex to G-quadruplex DNA. This alteration in shape ensured that the molecules had low affinity for duplex DNA while increasing their interaction with a G-quadruplex structure. We have now used a molecular modeling approach to modify the structure of the previously reported biaryl polyamides by incorporating benzofused building blocks to improve affinity for G-quadruplexes while further reducing affinity for duplex DNA to enhance selectivity for G-quadruplex versus duplex DNA.
A small, focused benzofused-polyamide library (17 molecules) was initially synthesized and evaluated for the ability of members to stabilize G-quadruplex structures using a FRET-based DNA thermal denaturation assay and molecular dynamics (MD) simulations. However, these compounds failed to stabilize the human telomeric G-quadruplex and c-Kit quadruplexes, and MD simulations suggested that the shape of the molecules required further modification to facilitate G-quadruplex interaction. A second library of molecules (50 in total) was then designed and synthesized using a molecular modeling based approach. In this series, the shape of the polyamide fragment was changed, while retaining the original scaffold, by introducing benzofused moieties with 3,5-substitutions. Evaluation of these molecules in the same FRET assay showed a notable increase in stabilization of the F21T quadruplex for many library members. For example, compounds AR-130 and AR-168 stabilized the G-quadruplex by 15°C and 17°C, respectively (at 1 μM concentration), while showing insignificant affinity for duplex DNA. Cytotoxicity in the micromolar region is anticipated based on recent studies on related compounds, and a full growth inhibition evaluation is presently underway in MiaPaCa2, MDA-MB 231, HeLa and NCIH1975 cell lines.
Given their low molecular weight (e.g., between 422-646 Daltons), reasonable water solubility and good cellular penetration properties compared to other known G-quadruplex inhibitors which are mostly non-drug-like, molecules of this type have the potential to be developed into reagents that can probe DNA structure, and novel therapeutic agents based on G-quadruplex targeting.
Citation Format: Khondaker M. Rahman, AKM Azadur Rahman, Paul J. M. Jackson, David E. Thurston. In silico design and biological evaluation of benzofused polyamides targeting G-quadruplex DNA structures. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1357.