Specific Stabilization of c-MYC and c-KIT G-Quadruplex DNA Structures by Indolylmethyleneindanone Scaffolds

Abstract

Stabilization of G-quadruplex DNA structures by small molecules has emerged as a promising strategy for the development of anticancer drugs. Since G-quadruplex structures can adopt various topologies, attaining specific stabilization of a G-quadruplex topology to halt a particular biological process is daunting. To achieve this, we have designed and synthesized simple structural scaffolds based on an indolylmethyleneindanone pharmacophore, which can specifically stabilize the parallel topology of promoter quadruplex DNAs (c-MYC, c-KIT1, and c-KIT2), when compared to various topologies of telomeric and duplex DNAs. The lead ligands (InEt2 and InPr2) are water-soluble and meet a number of desirable criteria for a small molecule drug. Highly specific induction and stabilization of the c-MYC and c-KIT quadruplex DNAs (ΔT1/2 up to 24 °C) over telomeric and duplex DNAs (ΔT1/2 ∼ 3.2 °C) by these ligands were further validated by isothermal titration calorimetry and electrospray ionization mass spectrometry experiments (Ka ∼ 10(5) to 10(6) M(-1)). Low IC50 (∼2 μM) values were emerged for these ligands from a Taq DNA polymerase stop assay with the c-MYC quadruplex forming template, whereas the telomeric DNA template showed IC50 values >120 μM. Molecular modeling and dynamics studies demonstrated the 5'- and 3'-end stacking modes for these ligands. Overall, these results demonstrate that among the >1000 quadruplex stabilizing ligands reported so far, the indolylmethyleneindanone scaffolds stand out in terms of target specificity and structural simplicity and therefore offer a new paradigm in topology specific G-quadruplex targeting for potential therapeutic and diagnostic applications.

Carbazole ligands as c-myc G-quadruplex binders

“…Also a large number of small molecules are potent G-quadruplex ligands that exhibit antiproliferative activity in cells [39,48]. Several small molecules, for example cyclic naphthalene diimide derivative [43], cationic porphyrins [2,[49][50][51][52] and pentaheteroaryls [53], quinacridines [52], PIPER [52], quarfloxin [54], methylene blue derivatives [55], fonsecin B [56], berberine derivatives A C C E P T E D M A N U S C R I P T [57], carbazoles [58,59], quindoline derivatives [6,60], platinum [61][62][63][64] and cobalt [65] complexes, bisquinoline-pyrrole oligoamide [66], indolylmethyleneindanones [67], amido phthalocyanines [68], bisbenzimidazole carboxamide derivatives of pyridine, 1,8-naphthyridine, and 1,10-phenanthroline [69], or perylene and coronene derivatives [70], have been identified to bind and stabilize Gquadruplex structures in the c-myc promoter region. Carbazole derivatives are very interesting compounds because of their biological and photophysical properties.…”

Identification of SLIRP as a G Quadruplex-Binding Protein

“…In this vein, the sequences derived from the promoters of the c KIT and c MYC genes yield maximum and minimum CD signals at around 260 and 240 nm, respectively (Figure S1), which are characteristic of parallel G4 folding topology. 20 The sequence arising from human telomere (hTel26) displayed maximum CD signals at 270 and 290 nm, which exhibit hydrid-type G4 folding with mixed parallel and antiparallel strands (Figure S1). 17 In contrast, the three mutated control sequences did not display CD signals that manifest G4 folding (Figure S1).…”

Modeling and Targeting MYC Genes in Childhood Brain Tumors

“…G-quadruplexes are four-stranded nucleic acid structures that may form in guanine-rich areas and can adopt various topologies. They can be stabilized in specific topologies that disrupt certain biological processes [143]. G-quadruplex sequences have been found in promoter regions of, for example, MYC .…”

“…G-quadruplex sequences have been found in promoter regions of, for example, MYC . Today, scaffolds based on an indolylmethyleneindanone pharmacophore, which specifically stabilizes the parallel topology of promoter quadruplex DNAs, have demonstrated a specific disruption of c-MYC and c-Kit promoter regions [143]. Further studies on these small molecules are however needed to properly evaluate their applicability in biological systems.…”