Benzothiazole hydrazones of furylbenzamides preferentially stabilize c-MYC and c-KIT1 promoter G-quadruplex DNAs

Abstract

The stabilization of G-quadruplex DNA structures by using small molecule ligands having simple structural scaffolds has the potential to be harnessed for developing next generation anticancer agents. Because of the structural diversity of G-quadruplexes, it is challenging to design stabilizing ligands, which can specifically bind to a particular quadruplex topology. To address this, herein, we report the design and synthesis of three benzothiazole hydrazones of furylbenzamides having different side chains (ligands 1, 2 and 3), which show preferential stabilization of promoter quadruplex DNAs (c-MYC and c-KIT1) having parallel topologies over telomeric and duplex DNAs. The CD melting study revealed that all the ligands, in particular ligand 2, exhibit higher stabilization toward parallel promoter quadruplexes (ΔTm = 10-15 °C) as compared to antiparallel promoter quadruplex (h-RAS1), telomeric quadruplex and duplex DNAs (ΔTm = 0-3 °C). FID assay and fluorimetric titration results also reveal the preferential binding of ligands toward c-MYC and c-KIT1 promoter quadruplex DNAs over telomeric and duplex DNAs. Validating these results further, Taq DNA polymerase stop assay showed IC50∼ 6.4 μM for ligand 2 with the c-MYC DNA template, whereas the same for the telomeric DNA template was found to be >200 μM. Molecular modeling and dynamics studies demonstrated a 1 : 1 binding stoichiometry in which stacking and electrostatic interactions play important roles in stabilizing the c-MYC G-quadruplex structure. Taken together, the results presented here provide new insights into the design of structurally simple scaffolds for the preferential stabilization of a particular G-quadruplex topology.

Arene Ru(II) Complexes with Difluorinated Ligands Act as Potential Inducers of S-Phase Arrest via the Stabilization of c-myc G-Quadruplex DNA

“…The arene Ru(II) complexes (0–60 μM) were added to the c-myc G-quadruplex DNA–TO complex, and the emission spectra were recorded for each addition after 2 min of equilibration. The fluorescence area under each curve was calculated and converted to the percentage of the TO displacement value using the equation: Percentage of TO displacement = 100 − [( F / F 0 ) × 100], where F 0 = fluorescence area without a ligand, and F = fluorescence area in the presence of a ligand [ 28 ]. The percentage of TO displacement was plotted against the concentration of ligands, and the DC 50 values were determined.…”

Recent Update on Targeting c-MYC G-Quadruplexes by Small Molecules for Anticancer Therapeutics

“…Pradeepkumar et al have subsequently reported benzothiazole hydrazones of furylbenzamide 47 with different side chains as potent G4 stabilizing ligands. 146 CD melting, FID assay, and Taq DNA polymerase stop assay indicated that these ligands are capable of preferentially stabilizing the parallel topology of c-MYC and c-KIT1 promoter G4s over the antiparallel topology of the h-RAS1 promoter and telomeric quadruplex and ds DNA. Molecular dynamics studies suggested that π−π stacking of the aromatic units of the molecule with the G-quartet and electrostatic interactions of the positively charged side chains play major roles in stabilizing the parallel quadruplex DNA topology.…”

Quadruplex DNA-guided ligand selection from dynamic combinatorial libraries of acylhydrazones

“…Despite more than 20 years of active research, only moderate progress has been achieved in terms of intra-G4 selectivity of ligands. 5,7,8 Clearly, the conventional strategies that rely on the synthesis of small libraries of putative ligands and subsequent assessment of their binding to a panel of G4 structures are insufficient to generate ligands with better affinity and selectivity, and novel approaches allowing tailor-made ligand design are urgently needed. Several strategies have been explored towards this end, including fragment-based screening, 9,10 small-molecule microarrays, 11 kinetic target-guided synthesis, 12 and peptide libraries, 13,14 resulting in identifications of novel G4 ligands with intriguing properties.…”