Selectivity of small molecule ligands for parallel and anti-parallel DNA G-quadruplex structures

Abstract

We report CD, ESI-MS and molecular modelling studies of ligand binding interactions with DNA quadruplex structures derived from the human telomeric repeat sequence (h-Tel) and the proto-oncogenic c-kit promoter sequence. These sequences form anti-parallel (both 2 + 2 and 3 + 1) and parallel conformations, respectively, and demonstrate distinctively different degrees of structural plasticity in binding ligands. With h-Tel, we show that an extended heteroaromatic 1,4-triazole (TRZ), designed to exploit pi-stacking interactions and groove-specific contacts, shows some selectivity for parallel folds, however, the polycyclic fluorinated acridinium cation (RHPS4), which is a similarly potent telomerase inhibitor, shows selectivity for anti-parallel conformations implicating favourable interactions with lateral and diagonal loops. In contrast, the unique c-kit parallel-stranded quadruplex shows none of the structural plasticity of h-Tel with either ligand. We show by quantitative ESI-MS analysis that both sequences are able to bind a ligand on either end of the quadruplex. In the case of h-Tel the two sites have similar affinities, however, in the case of the c-kit quadruplex the affinities of the two sites are different and ligand-dependent. We demonstrate that two different small molecule architectures result in significant differences in selectivity for parallel and anti-parallel quadruplex structures that may guide quadruplex targeted drug-design.

Dominant Driving Forces in Human Telomere Quadruplex Binding-Induced Structural Alterations

“…3 and S9) suggest for both ligands (Phen-DC3, 360A-Br) that their binding is accompanied by quadruplex conformational changes and that the resulting complexes (Q 0 L, Q 00 L 2 ) have similar structures in solutions with K þ and Na þ ions. CD spectra of Q 0 L and Q 00 L 2 complexes show characteristics of the A Na þ spectrum (15). Interestingly, difference CD spectra (Fig.…”

“…By contrast, in Na þ solutions Tel22 adopts a conformation with antiparallel strand orientation (denoted as A Na þ) (11). As shown recently, binding of ligands capable of inducing binding-coupled conformational transitions of G-quadruplexes may be an additional cause of the observed ht-quadruplex polymorphism (12)(13)(14)(15)(16).…”

Ligand selectivity in stabilising tandem parallel folded G-quadruplex motifs in human telomeric DNA sequences

“…[6][7][8] Telomeric sequences are known to be highly polymorphic and quadruplex binding ligands have been shown to induce different conformations within these individual structural motifs. 16 Here, we report biophysical studies of two quadruplex-selective ligands binding to telomeric sequences which form multiple (two or three) quadruplex motifs in series. We have demonstrated that a hybrid oxazole-triazole ligand 16,18 induces parallel-folded structure which leads to preferential stabilisation of longer telomeric sequences where quadruplex motifs are formed in tandem.…”

“…16 Here, we report biophysical studies of two quadruplex-selective ligands binding to telomeric sequences which form multiple (two or three) quadruplex motifs in series. We have demonstrated that a hybrid oxazole-triazole ligand 16,18 induces parallel-folded structure which leads to preferential stabilisation of longer telomeric sequences where quadruplex motifs are formed in tandem. In contrast, the quinoacridinium cation (RHPS4) enforces a largely anti-parallel fold which, although significantly stabilising at the level of the individual quadruplex motif (DT m B 15-20 1C), shows no evidence for preferential stabilisation of the longer sequences.…”

Chemical Biology: What is Its Role in Drug Discovery?

“…The chemical biology of DNA quadruplexes continues to develop. The binding of ligands to the human telomeric repeat sequence (h-Tel) and the c-kit promoter has also been explored by Moses and Searle using a range of techniques ( Figure 4C) (Garner et al, 2009). Two different classes of h-Tel ligands were developed and showed selectivity for parallel or antiparallel conformations respectively.…”