Design and synthesis of benzofused biaryl polyamides as G-quadruplex targeting agents

• Main Author: Nahar, Kamrun
• Other Authors: Thurston, David Edwin ; Rahman, Khondaker Mirazur
• Published: King's College London (University of London) 2017
• Online Access: http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.727019

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 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 [1]. Using a distamycin scaffold as a starting point, we introduced biaryl building blocks in place of pyrroles to switch preference from duplex to quadruplex DNA. This alteration in shape ensures that the molecules have low affinity for duplex DNA while increasing their interaction with a G-quadruplex structure, since the ligands have similar dimensions. The structures of the biaryl polyamides previously reported by the Thurston group were tailored to enhance affinity for specific G-quadruplexes (e.g., c-kit1 vs c-kit2 vs HT4) while retaining the quadruplex vs duplex selectivity. A 66 member focused second generation biaryl polyamide library was synthesized based on structural information obtained from the previously reported polyamide types. Assessment of the G-quadruplex interaction of the library members was initially carried out using a FRET-based melting assay. Compound KN-242 with hybrid benzofused and biaryl building blocks showed significant selective stabilization of human Telomeric G-quadruplex. At 1 μm concentration it stabilized human Telomeric G-quadruplex by 32 ºC, while showing insignificant affinity for duplex DNA. FRET competition assays with C-kit quadruplexes and CT DNA further confirmed selective stabilization of telomeric quadruplexes. A short-term growth inhibitory experiment against six different cancer cell lines, MiaPaCa2, A549 MCF7, HeLa, U87MG, A431 and WI38 gave low micromolar IC50 values and between 5-8 fold selectivity for cancer cell lines compared with the non-cancerous WI 38 cell line. Therefore, given their low molecular weight, good water solubility and excellent cellular penetration properties, molecules of this type have the potential to be developed into either potential therapeutic agents or reagents that can probe DNA structure, and/or down-regulate individual signalling pathways in cells.