Selectivity of small molecule ligands for parallel and anti-parallel DNA G-quadruplex structures.
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.
Garner
Thomas P
TP
Centre for Biomolecular Sciences, School of Chemistry, University Park, Nottingham, NG7 2RD, UK.
Williams
Huw E L
HE
Gluszyk
Katarzyna I
KI
Roe
Stephen
S
Oldham
Neil J
NJ
Stevens
Malcolm F G
MF
Moses
John E
JE
Searle
Mark S
MS
D000166:Acridines / Q000737:chemistry* / Q000494:pharmacology*; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology; D054856:G-Quadruplexes / Q000187:drug effects*; D006801:Humans; D008024:Ligands; D013058:Mass Spectrometry; D056004:Molecular Dynamics Simulation; D019009:Proto-Oncogene Proteins c-kit / Q000235:genetics; D013379:Substrate Specificity; D019098:Telomerase / Q000037:antagonists & inhibitors; D016615:Telomere / Q000235:genetics; D014230:Triazoles / Q000737:chemistry* / Q000494:pharmacology*
C438609:3,11-difluoro-6,8,13-trimethyl-8H-quino(4,3,2-kl)acridinium; D000166:Acridines; D004791:Enzyme Inhibitors; D008024:Ligands; D014230:Triazoles; D004247:DNA; D019009:Proto-Oncogene Proteins c-kit; D019098:Telomerase