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Naphthalene Diimides Carrying Two β-Cyclodextrins Prefer Telomere RNA G-Quadruplex Recognition.

ABSTRACT: Newly synthesized naphthalene diimide carrying two β-cyclodextrins (NDI-β-CyDs) showed improved specificity for the parallel G-quadruplex structure alongside the hybrid G-quadruplex structure. Specifically, the highest binding affinity of NDI-β-CyDs for the telomere RNA G-quadruplex was observed. The binding simulation indicated that β-cyclodextrins might be available for loop nucleobase inclusion under its complex.

SUBMITTER: Zou T

PROVIDER: S-EPMC9268153 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Disentangling the Structure-Activity Relationships of Naphthalene Diimides as Anticancer G-Quadruplex-Targeting Drugs.

Project description:In the context of developing efficient anticancer therapies aimed at eradicating any sort of tumors, G-quadruplexes represent excellent targets. Small molecules able to interact with G-quadruplexes can interfere with cell pathways specific of tumors and common to all cancers. Naphthalene diimides (NDIs) are among the most promising, putative anticancer G-quadruplex-targeting drugs, due to their ability to simultaneously target multiple G-quadruplexes and their strong, selective in vitro and in vivo anticancer activity. Here, all the available biophysical, biological, and structural data concerning NDIs targeting G-quadruplexes were systematically analyzed. Structure-activity correlations were obtained by analyzing biophysical data of their interactions with G-quadruplex targets and control duplex structures, in parallel to biological data concerning the antiproliferative activity of NDIs on cancer and normal cells. In addition, NDI binding modes to G-quadruplexes were discussed in consideration of the structures and properties of NDIs by in-depth analysis of the available structural models of G-quadruplex/NDI complexes.

| S-EPMC8041303 | biostudies-literature

Trifunctionalized Naphthalene Diimides and Dimeric Analogues as G-Quadruplex-Targeting Anticancer Agents Selected by Affinity Chromatography.

Project description:A focused library of newly designed monomeric and dimeric naphthalene diimides (NDIs) was analyzed in its ability to recognize specific G-quadruplex (G4) structures discriminating duplex DNA. The best G4 ligands-according to an affinity chromatography-based screening method named G4-CPG-were tested on human cancer and healthy cells, inducing DNA damage at telomeres, and in parallel, showing selective antiproliferative activity on HeLa cancer cells with IC50 values in the low nanomolar range. CD and fluorescence spectroscopy studies allowed detailed investigation of the interaction in solution with different G4 and duplex DNA models of the most promising NDI of the series, as determined by combining the biophysical and biological assays' data.

| S-EPMC7139804 | biostudies-literature

Naphthalene diimides with improved solubility for visible light photoredox catalysis.

Project description:Five core-substituted naphthalene diimides bearing two dialkylamino groups were synthesized as potential visible light photoredox catalysts and characterized by methods of optical spectroscopy and electrochemistry in comparison with one unsubstituted naphthalene diimide as reference. The core-substituted naphthalene diimides differ by the alkyl groups at the imide nitrogens and at the nitrogens of the two substituents at the core in order to enhance their solubility in DMF and thereby enhance their photoredox catalytic potential. The 1-ethylpropyl group as rather short and branched alkyl substituent at the imide nitrogen and the n-propyl group as short and unbranched one at the core amines yielded the best solubilities. The electron-donating diaminoalkyl substituents together with the electron-deficient aromatic core of the naphthalene diimides increase the charge-transfer character of their photoexcited states and thus shift their absorption into the visible light (500-650 nm). The excited state reduction potential was estimated to be approximately +1.0 V (vs SCE) which is sufficient to photocatalyze typical organic reactions. The photoredox catalytic activity in the visible light range was tested by the ?-alkylation of 1-octanal as benchmark reaction. Irradiations were performed with LEDs in the visible light range between 520 nm and 640 nm. The irradiation by visible light together with the use of an organic dye instead of a transition metal complex as photoredox catalyst improve the sustainability and make photoredox catalysis "greener".

| S-EPMC6720061 | biostudies-literature

Performance of TDDFT Vertical Excitation Energies of Core-Substituted Naphthalene Diimides.

Project description:We have evaluated the performance of various density functionals, covering generalized gradient approximation (GGA), global hybrid (GH) and range-separated hybrid (RSH), using time dependent density functional theory (TDDFT) for computing vertical excitation energies against experimental absorption maximum (?max ) for a set of 10 different core-substituted naphthalene diimides (cNDI) recorded in dichloromethane. The computed excitation in case of GH PBE0 is most accurate while the trend is most systematic with RSH LCY-BLYP compared to ?max . We highlight the importance of including solvent effects for optimal agreement with the ?max . Increasing the basis set size from TZ2P to QZ4P has a negligible influence on the computed excitation energies. Notably, RSH CAMY-B3LYP gave the least error for charge-transfer excitation. The poorest agreement with ?max is obtained with semi-local GGA functionals. Use of the optimally-tuned RSH LCY-BLYP* is not recommended because of the high computational cost and marginal improvement in results.

| S-EPMC7317478 | biostudies-literature

π-Extended Diaza[7]helicenes by Hybridization of Naphthalene Diimides and Hexa-peri-hexabenzocoronenes.

Project description:The synthesis of an unprecedented, π-extended hexabenzocorene (HBC)-based diaza[7]helicene is presented. The target compound was synthesized by an ortho-fusion of two naphthalene diimide (NDI) units to a HBC-skeleton. A combination of Diels-Alder and Scholl-type oxidation reactions involving a symmetric di-NDI-tolane precursor were crucial for the very selective formation of the helical superstructure via a hexaphenyl-benzene (HPB) derivative. The formation of the diaza[7]helicene moiety in the final Scholl oxidation is favoured, affording the symmetric π-extended helicene as the major product as a pair of enantiomers. The separation of the enantiomers was successfully accomplished by HPLC involving a chiral stationary phase. The absolute configuration of the enantiomers was assigned by comparison of circular dichroism spectra with quantum mechanical calculations.

| S-EPMC7898888 | biostudies-literature

Donor-Acceptor Dyads and Triads Employing Core-Substituted Naphthalene Diimides: A Synthetic and Spectro (Electrochemical) Study.

Project description:Donor-acceptor dyads and triads comprising core-substituted naphthalene diimide (NDI) chromophores and either phenothiazine or phenoxazine donors are described. Synthesis combined with electrochemical and spectroelectrochemical investigations facilitates characterisation of the various redox states of these molecules, confirming the ability to combine arrays of electron donating and accepting moieties into single species that retain the redox properties of these individual moieties.

| S-EPMC9783862 | biostudies-literature

Hybrid-type and two-tetrad antiparallel telomere DNA G-quadruplex structures in living human cells.

Project description:Although the telomeric sequence has been reported to form various G-quadruplex topologies in vitro and in Xenopus laevis oocytes, in living human cells, the topology of telomeric DNA G-quadruplex remains a challenge. To investigate the human telomeric DNA G-quadruplex in a more realistic human cell environment, in the present study, we demonstrated that the telomeric DNA sequence can form two hybrid-type and two-tetrad antiparallel G-quadruplex structures by in-cell 19F NMR in living human cells (HELA CELLS). This result provides valuable information for understanding the structures of human telomeric DNA in living human cells and for the design of new drugs that target telomeric DNA.

| S-EPMC6547409 | biostudies-literature

Thermodynamic characterization of human telomere quadruplex unfolding.

Project description:The 3'-terminal extensions of eukaryotic chromosomes are unique examples of functional single-stranded DNA. Human telomeres are constructed of the repeated DNA sequence 5'-d(TTAGGG). Four-repeats of human telomeric DNA have been characterized by high-resolution techniques to be capable of forming at least five distinct monomeric conformations. The predominant solution topology is influenced by solution conditions and the presence of 3'- or 5'-flanking residues. This study describes the unfolding mechanisms for human telomeric quadruplexes formed by eight sequence variants that form three unique antiparallel topologies in K(+) solution. Thermal unfolding monitored by circular dichroism is analyzed by singular value decomposition to enumerate the number of significant spectral species required to model the unfolding process. Thermal denaturation of all quadruplexes studied is found to be best modeled by a four-state sequential mechanism with two populated intermediates. The thermal unfolding was also investigated in 50% (v/v) acetonitrile in which a parallel topology is favored. Under these dehydrating conditions, quadruplex thermal denaturation is best modeled by a three-state sequential unfolding mechanism with one populated intermediate. Dehydrated parallel quadruplexes demonstrate increased thermal stability. The spectral properties of the unfolding intermediate suggest that it is most likely a triple-helical structure.

| S-EPMC4274053 | biostudies-literature

Selective parallel G-quadruplex recognition by a NIR-to-NIR two-photon squaraine.

Project description:Fluorescence imaging probes for specific G-quadruplex (G4) conformations are of considerable interest in biomedical research. Herein, we present the synthesis and the binding properties of a new water-soluble near-infrared (NIR) amphiphilic squaraine dye (CAS-C1) which is capable of selective detection of parallel over non-parallel and non G4 topologies. The striking changes in its linear optical response upon binding to parallel G4s give rise to high fluorescence quantum yields (? f ? 0.7) and one-photon molecular brightness in the far-red-NIR region. The outstanding recognition process of CAS-C1 for parallel G4s via end-stacking provides binding constants in the nanomolar regime (K b = 107 to 108 M-1) awarding it as one of the most potent parallel G4 binders currently available. Moreover, the CAS-C1-parallel G4 system exhibits large two-photon absorption (TPA) cross-sections and molecular brightness in the second NIR biological transparency window (? ? 1275 nm), making it an ideal candidate for NIR-to-NIR ultrasensitive two-photon procedures.

| S-EPMC6240894 | biostudies-literature

Asymmetrically-substituted quadruplex-binding napththalene diimides showing potent activity in models for pancreatic cancer

Project description:Targeting quadruplexes in cancer genes and pathways by a novel class of asymmetrically-substituted napththalene diimides (SOP1812) with potent cellular and antitumour activity in models for pancreatic cancer.

2020-06-04 | GSE151741 | GEO

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