Preferential Binding of π-Ligand Porphyrin Targeting 5′-5′ Stacking Interface of Human Telomeric RNA G-Quadruplex Dimer

Non-macrocyclic heteroaryls represent a valuable class of ligands for nucleic acid recognition. In this regard, non-macrocyclic pyridyl polyoxazoles and polyoxadiazoles were recently identified as selective G-quadruplex stabilizing compounds with high cytotoxicity and promising anticancer activity. Herein, we describe the synthesis of a new family of heteroaryls containing oxadiazole and pyridine moieties targeting DNA G-quadruplexes. To perform a structure–activity analysis identifying determinants of activity and selectivity, we followed a convergent synthetic pathway to modulate the nature and number of the heterocycles (1,3-oxazole vs. 1,2,4-oxadiazole and pyridine vs. benzene). Each ligand was evaluated towards secondary nucleic acid structures, which have been chosen as a prototype to mimic cancer-associated G-quadruplex structures (e.g., the human telomeric sequence, c-myc and c-kit promoters). Interestingly, heptapyridyl-oxadiazole compounds showed preferential binding towards the telomeric sequence (22AG) in competitive conditions vs. duplex DNA. In addition, G4-FID assays suggest a different binding mode from the classical stacking on the external G-quartet. Additionally, CD titrations in the presence of the two most promising compounds for affinity, TOxAzaPy and TOxAzaPhen, display a structural transition of 22AG in K-rich buffer. This investigation suggests that the pyridyl-oxadiazole motif is a promising recognition element for G-quadruplexes, combining seven heteroaryls in a single binding unit.

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A Fragment-Based Approach for the Development of G-Quadruplex Ligands: Role of the Amidoxime Moiety

Molecules ◽

10.3390/molecules23081874 ◽

2018 ◽

Vol 23 (8) ◽

pp. 1874 ◽

Cited By ~ 2

Author(s):

Martina Tassinari ◽

Alberto Lena ◽

Elena Butovskaya ◽

Valentina Pirota ◽

Matteo Nadai ◽

...

Keyword(s):

High Throughput Screening ◽

Viral Gene Expression ◽

Viral Gene ◽

Screening Methods ◽

Lead Compounds ◽

Immunodeficiency Virus ◽

G Quadruplex ◽

Preferential Binding ◽

Nucleic Acid Structures ◽

Hiv 1

G-quadruplex (G4) nucleic acid structures have been reported to be involved in several human pathologies, including cancer, neurodegenerative disorders and infectious diseases; however, G4 targeting compounds still need implementation in terms of drug-like properties and selectivity in order to reach the clinical use. So far, G4 ligands have been mainly identified through high-throughput screening methods or design of molecules with pre-set features. Here, we describe the development of new heterocyclic ligands through a fragment-based drug discovery (FBDD) approach. The ligands were designed against the major G4 present in the long terminal repeat (LTR) promoter region of the human immunodeficiency virus-1 (HIV-1), the stabilization of which has been shown to suppress viral gene expression and replication. Our method is based on the generation of molecular fragment small libraries, screened against the target to further elaborate them into lead compounds. We screened 150 small molecules, composed by structurally and chemically different fragments, selected from commercially available and in-house compounds; synthetic elaboration yielded several G4 ligands and two final G4 binders, both embedding an amidoxime moiety; one of these two compounds showed preferential binding for the HIV-1 LTR G4. This work presents the discovery of a novel potential pharmacophore and highlights the possibility to apply a fragment-based approach to develop G4 ligands with unexpected chemical features.

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Differences in affinity of arylstilbazolium derivatives to tetraplex structures

Chemical Papers ◽

10.2478/s11696-010-0078-7 ◽

2011 ◽

Vol 65 (2) ◽

Cited By ~ 1

Author(s):

Izabella Czerwinska ◽

Bernard Juskowiak

Keyword(s):

Small Molecules ◽

Therapeutic Agent ◽

Equilibrium Dialysis ◽

Structural Features ◽

Acid Number ◽

Strong Interactions ◽

Dna Structures ◽

G Quadruplex ◽

Preferential Binding ◽

Important Field

AbstractResearch into the interactions of small molecules (ligands) with DNA is a very important field of biochemistry. A ligand interacts with a DNA structure in many ways, depending on the structural features of the ligand (the presence of rings, substituent groups, length of bonds, etc.) or nucleic acid (number and association of strands, base sequence etc.). This study reports on an investigation of the preferential binding of arylstilbazolium ligands to a four-stranded DNA. For this purpose, an equilibrium dialysis was used. Equilibrium dialysis is a versatile method which enables many DNA structures to be investigated at the same time. A dozen different DNA structures of (single-stranded, double-stranded (duplex), triple-stranded (triplex), and four-stranded (tetraplex)) were involved in experiments with each ligand. Following the dissociation of DNA-ligand complexes by SDS, the concentration of the ligand bound was calculated from fluorescence and absorbance calibration curves. As a result, the amount of the ligand bound was directly related to the ligand-binding affinity. Equilibrium dialysis was used as a powerful tool to indicate which of the arylstilbazolium ligands investigated was the best therapeutic agent targeting G-quadruplex. Arylstilbazolium derivatives demonstrated strong interactions with the DNA samples used in the assay. The most interesting finding was a selective, preferential binding of anthryl derivative to c-MYC DNA (c-MYC is a DNA sequence that appears in an oncogene). Furthermore, as this derivative binds preferentially to one of the triplexes investigated, it can find an application in the TFO-triplex forming oligonucleotides which are used in gene therapy.

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Preferential binding of a G-quadruplex ligand to human chromosome ends

Nucleic Acids Research ◽

10.1093/nar/gki722 ◽

2005 ◽

Vol 33 (13) ◽

pp. 4182-4190 ◽

Cited By ~ 168

Author(s):

C. Granotier

Keyword(s):

Human Chromosome ◽

G Quadruplex ◽

Preferential Binding

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A U-Tetrad Stabilizes Human Telomeric RNA G-Quadruplex Structure

Journal of the American Chemical Society ◽

10.1021/ja909708a ◽

2010 ◽

Vol 132 (21) ◽

pp. 7231-7233 ◽

Cited By ~ 43

Author(s):

Yan Xu ◽

Takumi Ishizuka ◽

Takashi Kimura ◽

Makoto Komiyama

Keyword(s):

Quadruplex Structure ◽

G Quadruplex ◽

Telomeric Rna

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Importance of the hydroxyl substituents in the B–ring of plant flavonols on their preferential binding interactions with VEGF G–quadruplex DNA: Multi-spectroscopic and molecular modeling studies

International Journal of Biological Macromolecules ◽

10.1016/j.ijbiomac.2018.06.115 ◽

2018 ◽

Vol 118 ◽

pp. 629-639 ◽

Cited By ~ 7

Author(s):

Snehasish Bhattacharjee ◽

Sandipan Chakraborty ◽

Erik Chorell ◽

Pradeep K. Sengupta ◽

Sudipta Bhowmik

Keyword(s):

Molecular Modeling ◽

Binding Interactions ◽

Quadruplex Dna ◽

Modeling Studies ◽

G Quadruplex ◽

Preferential Binding ◽

Molecular Modeling Studies

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Single-Stranded Condensation Stochastically Blocks G-Quadruplex Assembly in Human Telomeric RNA

The Journal of Physical Chemistry Letters ◽

10.1021/acs.jpclett.8b00722 ◽

2018 ◽

Vol 9 (10) ◽

pp. 2498-2503

Author(s):

Irene Gutiérrez ◽

Miguel Garavís ◽

Sara de Lorenzo ◽

Alfredo Villasante ◽

Carlos González ◽

...

Keyword(s):

G Quadruplex ◽

Telomeric Rna

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Integrative analysis reveals RNA G-Quadruplexes in UTRs are selectively constrained and enriched for functional associations

10.1101/666842 ◽

2019 ◽

Cited By ~ 2

Author(s):

David S.M. Lee ◽

Louis R. Ghanem ◽

Yoseph Barash

Keyword(s):

Regulatory Networks ◽

Rna Binding ◽

Purifying Selection ◽

Regulatory Elements ◽

Messenger Rnas ◽

Multiple Sources ◽

Protein Coding ◽

G Quadruplex ◽

Preferential Binding ◽

Missense Variation

ABSTRACTIdentifying regulatory elements in the noncoding genome is a fundamental challenge in biology. G-quadruplex (G4) sequences are abundant in untranslated regions (UTRs) of human messenger RNAs, but their functional importance remains unclear. By integrating multiple sources of genetic and genomic data, we show that putative G-quadruplex forming sequences (pG4) in 5’ and 3’ UTRs are selectively constrained, and enriched for cis-eQTLs and RNA-binding protein (RBP) interactions. Using over 15,000 whole-genome sequences, we uncover a degree of negative (purifying) selection in UTR pG4s comparable to that of missense variation in protein-coding sequences. In parallel, we identify new proteins with evidence for preferential binding at pG4s from ENCODE annotations, and delineate putative regulatory networks composed of shared binding targets. Finally, by mapping variants in the NIH GWAS Catalogue and ClinVar, we find enrichment for disease-associated variation in 3’UTR pG4s. At a GWAS pG4-variant associated with hypertension in HSPB7, we uncover robust allelic imbalance in GTEx RNA-seq across multiple tissues, suggesting that changes in gene expression associated with pG4 disruption underlie the observed phenotypic association. Taken together, our results establish UTR G-quadruplexes as important cis-regulatory features, and point to a putative link between disruption within UTR pG4 and susceptibility to human disease.

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