New fluorescent heterocyclic systems from imidazo[1,2- a ]pyridine: Design, synthesis, spectral studies and quantum-chemical investigations

Stabilization and fluorescence light-up of G-quadruplex nucleic acids using indolyl-quinolinium based probes

G-Quadruplexes (G4s) are four-stranded motifs formed by G-rich nucleic acid sequences. These structures harbor significant biological importance as they are involved in telomere maintenance, transcription, and translation. Owing to their dynamic and polymorphic nature, G4 structures relevant for therapeutic applications need to be stabilized by small-molecule ligands. Some of these ligands turn on fluorescence upon binding to G4 structures, which provides a powerful detection platform for G4 structures. Herein, we report the synthesis of fluorescent ligands based on the indolyl-quinolinium moiety to specifically stabilize G4 structures and sense DNA. CD titration and melting experiments have shown that the lead ligand induces the formation of parallel G4 with preferential stabilization of the c-MYC and c-KIT1 promoter G4s over the telomeric, h-RAS1 G4, and duplex DNA. Fluorimetric titration data revealed fluorescence enhancement when these ligands interact with G4 DNA structures. The fluorescence lifetime experiment of the ligand with different DNAs revealed three excited state lifetimes (ns), which indicates more than one binding site. MD studies showed that the ligand exhibits 3 : 1 stoichiometry of binding with c-MYC G4 DNA and revealed the unique structural features, which impart selectivity toward parallel topology. The ligand was found to have low cytotoxicity and exhibited preferential staining of DNA over RNA. Collectively, the results presented here offer avenues to harness indolyl-quinolinium scaffolds for sensing and selective stabilization of G4 structures.

Conjugating a groove binder analogue to a styryl-quinolinium scaffold for the light-up detection of duplex and G-Quadruplex DNA with different binding modes

The rational design of novel small molecules, which can target specific DNA sequences or secondary structural DNAs, is one of the most important goals in medicinal chemistry. Also the studies of DNA binding potency which can give fundamental insight into binding mechanisms and specificity are essential. In this paper, a N-methylated quinolinium probe NSQ functionalized with a G-Quadruplex DNA groove binder analogue was designed and synthesized. NSQ was found to express selective and sensitive for "light-up" detection of both G-Quadruplex and duplex DNAs over RNA and other biomolecules. The characteristics of NSQ and its interactions with DNAs were comprehensively evaluated by means of fluorescence, UV-Vis, circular dichroism, FID assay, DFT calculation and molecular docking. NSQ exhibited higher binding affinity to G-Quadruplex than to duplex DNA. Binding mechanism analysis indicated NSQ interacted with G-Quadruplex DNA mainly through end-stacking mode, while bound with duplex DNA into the minor groove of AT-rich regions. Further, NSQ exhibited potent in vitro anti-tumor activity, and to elucidate the cellular applications, confocal cell imaging was carried out and validated its mainly nuclear localization.

Facile synthesis of 2-arylimidazo[1,2-a]pyridines catalysed by DBU in aqueous ethanol

A facile protocol for the synthesis of 2-arylimidazo[1,2-a]pyridines was developed using two-component cyclization of substituted 2-aminopyridines and substituted phenacyl bromides in 65–94% yield. The reaction was DBU catalysed using green solvent, aqueous ethanol (1 : 1 v/v) at room temperature. The atom economy of the products was calculated to be 66.25–73.41%. The developed protocol successfully exhibits a broad substrate scope, less reaction time, high to moderate yield and multigram scale synthesis.

Tuning the selectivity of N-alkylated styrylquinolinium dyes for sensing of G-quadruplex DNA

Selective and sensitive detection of G-quadruplex DNA structures is an important issue and attracts extensive interest. To this end, numerous small molecular fluorescent probes have been designed. Here, we present a series of N-alkylated styrylquinolinium dyes named Ls-1, Ls-2 and Ls-3 with varying side groups at the chain end. We found that these dyes exhibited different binding behaviors to DNAs, and Ls-2 with a sulfonato group at the chain end displayed sensitivity and selectivity to G-quadruplex DNA structures in vitro. The characteristics of this dye and its interaction with G-quadruplex DNA were comprehensively investigated by means of UV-vis spectrophotometry, fluorescence, circular dichroism and molecular docking. Furthermore, confocal fluorescence images and MTT assays indicated dye Ls-2 could pass through membrane and enter the living HepG2 cells with low cytotoxicity.

Synthesis, characterisation, optical properties and theoretical calculations of a new fluorescent heterocyclic system: 3H-benzo[a]pyrazolo[3,4-j]acridine

Four new fluorescent dyes derived from the 3 H-benzo[ a]pyrazolo[3,4- j]acridine system were synthesised and fully characterised by 1H NMR, 13C NMR, mass and analytical data. These new fluorophores were prepared from the reaction of 1-alkyl-5-nitro-1 H-indazoles with 1-naphthylacetonitrile via nucleophilic substitution of hydrogen, in high yields. The optical properties of the dyes were also investigated and the results revealed that, in some cases, they have higher quantum yields compared with well-known fluorescent dyes such as fluorescein. Solvent effects on the fluorescence characteristics of the four compounds indicated that the emission wavelength is red-shifted with increasing solvent polarity. Furthermore, density functional theory calculations using the B3LYP hybrid functional and the 6-311++G(d,p) basis set provided the optimised geometries and relevant frontier orbitals of the compounds. Calculated electronic absorption spectra were also obtained using the time-dependent density functional theory method.