Correction: Structure and Stability of Human Telomeric G-Quadruplex with Preclinical 9-Amino Acridines

Ferreira, Rubén; Artali, Roberto; Benoit, Adam R.; Gargallo, Raimundo; Eritja, Ramón; Ferguson, David M.; Sham, Yuk Y.; Mazzini, Stefania

doi:10.1371/annotation/e49600ba-2cfa-45c6-9984-2b337ad73add

Cited by 11 publications

(3 citation statements)

References 42 publications

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“…But when working with buffers in the presence of potassium ions, the addition of SDS leads to the formation of a white precipitate. Ferreira et al have solved this problem by digesting the complex (DNA) with snake venom phosphodiesterase at the end of the dialysis experiment [46,47,48]. Alternative way includes the application of other surfactants e.g., nonionic, to dissociate the ligand-DNA complex [36,37].…”

Section: Resultsmentioning

confidence: 99%

Practical Microwave Synthesis of Carbazole Aldehydes for the Development of DNA-Binding Ligands

Głuszyńska

Juskowiak

2019

Molecules

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Microwave formylation of carbazole derivatives was investigated and 3-monoaldehydes were obtained in high yield. A potential DNA-binding ligand, 3-[(3-ethyl)-2-vinylbenzothiazolium]-9-N-ethyl carbazole iodide, was synthesized and characterized including spectral properties (UV-Vis absorption and fluorescence spectra). The binding selectivity and affinity of three carbazole ligands for double-stranded and G-quadruplex DNA structures were studied using a competitive dialysis method in sodium- and potassium-containing buffer solutions.

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Section: Resultsmentioning

confidence: 99%

Practical Microwave Synthesis of Carbazole Aldehydes for the Development of DNA-Binding Ligands

Głuszyńska

Juskowiak

2019

Molecules

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“…The ligand molecules were refined using a systematic conformer search followed by geometry optimization of the lowest energy structure with MOPAC7 (PM3 Method, RMS gradient 0.0100) [49]. The starting 3D structure of the d(TTAGGGT) 4 parallel-stranded DNA Gquadruplex was taken from the NMR ensemble deposited in the Protein Data Bank (PDB accession code: 2JWQ) [50] and prepared following the directions previously described [51].…”

Section: Molecular Modeling Studiesmentioning

confidence: 99%

Synthesis and Investigation of the G-Quadruplex Binding Properties of Kynurenic Acid Derivatives with a Dihydroimidazoquinoline-3,5-dione Core

et al. 2022

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G-quadruplexes are secondary structures originating from nucleic acid regions rich in guanines, which are well known for their involvement in gene transcription and regulation and DNA damage repair. In recent studies from our group, kynurenic acid (KYNA) derivative 1 was synthesized and found to share the structural features typical of G-quadruplex binders. Herein, structural modifications were conducted on this scaffold in order to assist the binding with a G-quadruplex, by introducing charged hydrophilic groups. The antiproliferative activity of the new analogues was evaluated on an IGROV-1 human ovarian cancer cell line, and the most active compound, compound 9, was analyzed with NMR spectrometry in order to investigate its binding mode with DNA. The results indicated that a weak, non-specific interaction was set with duplex nucleotides; on the other hand, titration in the presence of a G-quadruplex from human telomere d(TTAGGGT)4 showed a stable, although not strong, interaction at the 3′-end of the nucleotidic sequence, efficiently assisted by salt bridges between the quaternary nitrogen and the external phosphate groups. Overall, this work can be considered a platform for the development of a new class of potential G-quadruplex stabilizing molecules, confirming the crucial role of a planar system and the ability of charged nitrogen-containing groups to facilitate the binding to G-quadruplex grooves and loops.

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“…In particular, DNA G-quadruplexes may be the main target of anticancer UAs owing to negatively charged groups present in nucleic acids. Considering the above, it is crucial to fully understand variations in charge between pH-dependent structures of UAs, especially considering their potential to interact with DNA [25][26][27].…”

Section: Introductionmentioning

confidence: 99%

Acid–Base Equilibrium and Self-Association in Relation to High Antitumor Activity of Selected Unsymmetrical Bisacridines Established by Extensive Chemometric Analysis

et al. 2022

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Unsymmetrical bisacridines (UAs) represent a novel class of anticancer agents previously synthesized by our group. Our recent studies have demonstrated their high antitumor potential against multiple cancer cell lines and human tumor xenografts in nude mice. At the cellular level, these compounds affected 3D cancer spheroid growth and their cellular uptake was selectively modulated by quantum dots. UAs were shown to undergo metabolic transformations in vitro and in tumor cells. However, the physicochemical properties of UAs, which could possibly affect their interactions with molecular targets, remain unknown. Therefore, we selected four highly active UAs for the assessment of physicochemical parameters under various pH conditions. We determined the compounds’ pKa dissociation constants as well as their potential to self-associate. Both parameters were determined by detailed and complex chemometric analysis of UV-Vis spectra supported by nuclear magnetic resonance (NMR) spectroscopy. The obtained results indicate that general molecular properties of UAs in aqueous media, including their protonation state, self-association ratio, and solubility, are strongly pH-dependent, particularly in the physiological pH range of 6 to 8. In conclusion, we describe the detailed physicochemical characteristics of UAs, which might contribute to their selectivity towards tumour cells as opposed to their effect on normal cells.

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Correction: Structure and Stability of Human Telomeric G-Quadruplex with Preclinical 9-Amino Acridines

Cited by 11 publications

References 42 publications

Practical Microwave Synthesis of Carbazole Aldehydes for the Development of DNA-Binding Ligands

Practical Microwave Synthesis of Carbazole Aldehydes for the Development of DNA-Binding Ligands

Synthesis and Investigation of the G-Quadruplex Binding Properties of Kynurenic Acid Derivatives with a Dihydroimidazoquinoline-3,5-dione Core

Acid–Base Equilibrium and Self-Association in Relation to High Antitumor Activity of Selected Unsymmetrical Bisacridines Established by Extensive Chemometric Analysis

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