Exploring the Differential Recognition of DNA G‐Quadruplex Targets by Small Molecules Using Dynamic Combinatorial Chemistry

Abstract

The search for small-molecule ligands of biological targets remains a challenge with major implications for both fundamental studies and drug discovery. [1] We are interested in the discovery of small molecules that specifically interact with regulatory nucleic acid elements. Such molecules have the potential to alter the expression of particular genes and thus influence cellular functions.Certain guanine-rich (G-rich) regions in genomic DNA can form four-stranded structures, called G quadruplexes, which have emerged as biologically important elements.[2] Gquadruplex formation has been linked to cancer-related biology, most notably by remodeling of the telomere structure or by the regulation of oncogenic expression.[3] The two key challenges in the design of small-molecule[4] ligands for quadruplex DNA are: 1) to attain specificity for G-quadruplex-forming sequences over duplex DNA and 2) to achieve specificity for a given G-quadruplex structure and/or G-quadruplex-forming sequence. The latter criterion has become more important in the light of the recently revealed prevalence of G-quadruplex-forming sequences in the human genome,[5a,b] and particularly in promoter regions. [5c] Although G quadruplexes all contain G quartets, there is considerable scope for structural variations within the loop and groove regions, [6] suggesting that specificity in the molecular recognition of a quadruplex is attainable. However, the rational design of quadruplexbinding molecules requires a good understanding of the interactions between the ligand and its host. Owing to the paucity of structural data and the dynamic nature of G quadruplexes, combinatorial searches are appealing.Herein, we report on a study that employs a dynamic combinatorial approach to explore the differential recognition of G-quadruplex targets by closely related small molecules. Dynamic combinatorial chemistry (DCC) is a powerful approach for the rapid identification of binders for small molecules and biological targets. [7] Owing to its adaptive nature, small changes in the composition of a dynamic combinatorial library (DCL) upon introduction of a ** This study was supported by the Cancer Research UK, the EU, and EPSRC. We thank the EPSRC Mass Spectrometry Service for mass analysis.

Design, synthesis and evaluation of 4,7-diamino-1,10-phenanthroline G-quadruplex ligands

“…The clear trend towards higher melting temperatures for the guanidinium ligands thus indicates that the off-rates of the ligands have higher influence on thermal stability than the on-rates. A preferred role of the guanidinium group in quadruplex ligands is supported by two independent dynamic combinatorial libraries targeting quadruplex DNA, which both identified the guanidinium-containing compounds as the favored library members, 43,44 and by the higher efficiency of the guanidinium-containing steroid FG exhibited compared to the analogous trimethylammonium steroid maouetine. 45 …”

Adaptive Correction from Virtually Complex Dynamic Libraries: The Role of Noncovalent Interactions in Structural Selection and Folding

“…In aqueous media, disulfide exchange provides an excellent tool for the generation of dynamic libraries 11. This methodology has rendered some impressive results, with the formation of some remarkable receptors for biologically relevant structures such as carbohydrates,12 anions,13 and DNA G‐quadruplexes 14. In addition, disulfide chemistry has shown its potential in the formation of complex linked structures such as catenanes15 and knots 16…”

Targeting Nucleic Acids using Dynamic Combinatorial Chemistry

“…[38] Based on previous results that indicated that both the number and length of simple alkylamine side chains appended to the macrocycle are strong determinants of quadruplex affinity, [39] the library building blocks included derivatives of p-benzylic thiols and neutral carbohydrate derivatives with different potential for H-bonding and electrostatic interactions (Fig. 6).…”

“…Structures of (a) oxazole-based peptide macrocycle 7, (b) cationic benzylic thiols, and (c) neutral carboydrate benzylic thiols used to generate a dynamic combinatorial library for recognition of quadruplex DNA targets. [38] by screening against a DCL with a theoretical size of 11325 members. [35] The library was constructed from 150-resin attached Cys-containing building blocks and an identical set of solution-phase building blocks (Fig.…”