Chimie et Biologie du Cancer

Publications de l’équipe

Année de publication : 2011

Deepak Koirala, Soma Dhakal, Beth Ashbridge, Yuta Sannohe, Raphaël Rodriguez, Hiroshi Sugiyama, Shankar Balasubramanian, Hanbin Mao (2011 Sep 24)

A single-molecule platform for investigation of interactions between G-quadruplexes and small-molecule ligands.

Nature chemistry : 782-7 : DOI : 10.1038/nchem.1126 En savoir plus
Résumé

Ligands that stabilize the formation of telomeric DNA G-quadruplexes have potential as cancer treatments, because the G-quadruplex structure cannot be extended by telomerase, an enzyme over-expressed in many cancer cells. Understanding the kinetic, thermodynamic and mechanical properties of small-molecule binding to these structures is therefore important, but classical ensemble assays are unable to measure these simultaneously. Here, we have used a laser tweezers method to investigate such interactions. With a force jump approach, we observe that pyridostatin promotes the folding of telomeric G-quadruplexes. The increased mechanical stability of pyridostatin-bound G-quadruplex permits the determination of a dissociation constant K(d) of 490 ± 80 nM. The free-energy change of binding obtained from a Hess-like process provides an identical K(d) for pyridostatin and a K(d) of 42 ± 3 µM for a weaker ligand RR110. We anticipate that this single-molecule platform can provide detailed insights into the mechanical, kinetic and thermodynamic properties of liganded bio-macromolecules, which have biological relevance.

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Nagaratna S Hegde, Deborah A Sanders, Raphaël Rodriguez, Shankar Balasubramanian (2011 Aug 24)

The transcription factor FOXM1 is a cellular target of the natural product thiostrepton.

Nature chemistry : 725-31 : DOI : 10.1038/nchem.1114 En savoir plus
Résumé

Transcription factors are proteins that bind specifically to defined DNA sequences to promote gene expression. Targeting transcription factors with small molecules to modulate the expression of certain genes has been notoriously difficult to achieve. The natural product thiostrepton is known to reduce the transcriptional activity of FOXM1, a transcription factor involved in tumorigenesis and cancer progression. Herein we demonstrate that thiostrepton interacts directly with FOXM1 protein in the human breast cancer cells MCF-7. Biophysical analyses of the thiostrepton-FOXM1 interaction provide additional insights on the molecular mode of action of thiostrepton. In cellular experiments, we show that thiostrepton can inhibit the binding of FOXM1 to genomic target sites. These findings illustrate the potential druggability of transcription factors and provide a molecular basis for targeting the FOXM1 family with small molecules.

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Keith I E McLuckie, Zoë A E Waller, Deborah A Sanders, David Alves, Raphaël Rodriguez, Jyotirmayee Dash, Grahame J McKenzie, Ashok R Venkitaraman, Shankar Balasubramanian (2011 Feb 8)

G-quadruplex-binding benzo[a]phenoxazines down-regulate c-KIT expression in human gastric carcinoma cells.

Journal of the American Chemical Society : 2658-63 : DOI : 10.1021/ja109474c En savoir plus
Résumé

There is considerable interest in the structure and function of G-quadruplex nucleic acid secondary structures, their cellular functions, and their potential as therapeutic targets. G-Quadruplex sequence motifs are prevalent in gene promoter regions and it has been hypothesized that G-quadruplex structure formation is associated with the transcriptional status of the downstream gene. Using a functional cell-based assay, we have identified two novel G-quadruplex ligands that reduce the transcription of a luciferase reporter driven from the G-quadruplex-containing c-KIT promoter. We have further shown that endogenous c-KIT expression in a human gastric carcinoma cell line is also reduced on treatment with these molecules. Biophysical analysis using surface plasmon resonance has shown that these molecules preferentially bind with high affinity to one of the two G-quadruplex sequences in the c-KIT promoter over double-stranded DNA. This work highlights the utility of cell-based reporter assays to identify new G-quadruplex binding molecules that modulate transcription and identifies benzo[a]phenoxazine derivatives as potential antitumor agents.

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Année de publication : 2010

Anthony Bugaut, Raphaël Rodriguez, Sunita Kumari, Shang-Te Danny Hsu, Shankar Balasubramanian (2010 May 4)

Small molecule-mediated inhibition of translation by targeting a native RNA G-quadruplex.

Organic & biomolecular chemistry : 2771-6 : DOI : 10.1039/c002418j En savoir plus
Résumé

Herein, we show that a naturally occurring RNA G-quadruplex element within the 5′ UTR of the human NRAS proto-oncogene is a target for a small molecule that inhibits translation in vitro. The present study provides a first demonstration that natural 5′ UTR mRNA G-quadruplexes have potential as molecular targets for small molecules that modulate translation.

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Sebastian Müller, Sunita Kumari, Raphaël Rodriguez, Shankar Balasubramanian (2010 Apr 29)

Small-molecule-mediated G-quadruplex isolation from human cells.

Nature chemistry : 1095-8 : DOI : 10.1038/nchem.842 En savoir plus
Résumé

Nucleic acids containing stretches of tandem guanines can fold into four-stranded structures called G-quadruplexes. The existence of such sequences in genomic DNA suggests the occurrence of these motifs in cells, with potential implications in a number of biological processes relevant to cancer. Small molecules have proven to be valuable tools to dissect cell circuitry. Here, we describe a synthetic small molecule derived from an N,N’-bis(2-quinolinyl)pyridine-2,6-dicarboxamide, which is designed to mediate the selective isolation of G-quadruplex nucleic acids. The methodology was successfully applied to a range of DNA and RNA G-quadruplexes in vitro. We demonstrate the general applicability of the method by isolating telomeric DNA-containing G-quadruplex motifs from cells. We show that telomeres are targets for the probe, providing further evidence of the formation of G-quadruplexes in human cells.

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Année de publication : 2008

Sebastian Müller, G Dan Pantoş, Raphaël Rodriguez, Shankar Balasubramanian (2008 Dec 17)

Controlled-folding of a small molecule modulates DNA G-quadruplex recognition.

Chemical communications (Cambridge, England) : 80-2 : DOI : 10.1039/b816861j En savoir plus
Résumé

Differential recognition of diverse G-quadruplex structures can be achieved by controlling the folding of a small molecule.

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Raphaël Rodriguez, Sebastian Müller, Justin A Yeoman, Chantal Trentesaux, Jean-François Riou, Shankar Balasubramanian (2008 Nov 4)

A novel small molecule that alters shelterin integrity and triggers a DNA-damage response at telomeres.

Journal of the American Chemical Society : 15758-9 : DOI : 10.1021/ja805615w En savoir plus
Résumé

We describe a novel synthetic small molecule which shows an unprecedented stabilization of the human telomeric G-quadruplex with high selectivity relative to double-stranded DNA. We report that this compound can be used in vitro to inhibit telomerase activity and to uncap human POT1 (protection of telomeres 1) from the telomeric G-overhang. We also show that the small molecule G-quadruplex binder induces a partial alteration of shelterin through POT1 uncapping from telomeres in human HT1080 cancer cells and the presence of gammaH2AX foci colocalized at telomeres.

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Himesh Fernando, Raphaël Rodriguez, Shankar Balasubramanian (2008 Aug 16)

Selective recognition of a DNA G-quadruplex by an engineered antibody.

Biochemistry : 9365-71 : DOI : 10.1021/bi800983u En savoir plus
Résumé

Particular guanine rich nucleic acid sequences can fold into stable secondary structures called G-quadruplexes. These structures have been identified in various regions of the genome that include the telomeres, gene promoters and UTR regions, raising the possibility that they may be associated with biological function(s). Computational analysis has predicted that intramolecular G-quadruplex forming sequences are prevalent in the human genome, thus raising the desire to differentially recognize genomic G-quadruplexes. We have employed antibody phage display and competitive selection techniques to generate a single-chain antibody that shows >1000-fold discrimination between G-quadruplex and duplex DNA, and furthermore >100-fold discrimination between two related intramolecular parallel DNA G-quadruplexes. The amino acid sequence composition at the antigen binding site shows conservation within the light and heavy chains of the selected scFvs, suggesting sequence requirements for G-quadruplex recognition. Circular dichroism (CD) spectroscopic data showed that the scFv binds to the prefolded G-quadruplex and does not induce G-quadruplex structure formation. This study demonstrates the strongest discrimination that we are aware of between two intramolecular genomic G-quadruplexes.

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Serena J Eade, Magnus W Walter, Colin Byrne, Barbara Odell, Raphaël Rodriguez, Jack E Baldwin, Robert M Adlington, John E Moses (2008 Jun 4)

Biomimetic synthesis of pyrone-derived natural products: exploring chemical pathways from a unique polyketide precursor.

The Journal of organic chemistry : 4830-9 : DOI : 10.1021/jo800220w En savoir plus
Résumé

Our biomimetic hypothesis proposes that families of diverse natural products with complex core structures such as 9,10-deoxytridachione, photodeoxytridachione and ocellapyrone A are derived in nature from a linear and conformationally strained all-( E) tetraene-pyrone precursor. We therefore synthesized such a precursor and investigated its biomimetic transformation under a variety of reaction conditions, both to the above natural products as well as to diverse isomers which we propose to be natural products « yet to be discovered ». We also report herein the first synthesis of the natural product iso-9,10-deoxytridachione.

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Zoë A E Waller, Pravin S Shirude, Raphaël Rodriguez, Shankar Balasubramanian (2008 Mar 14)

Triarylpyridines: a versatile small molecule scaffold for G-quadruplex recognition.

Chemical communications (Cambridge, England) : 1467-9 : DOI : 10.1039/b718854d En savoir plus
Résumé

The triarylpyridines are potent G-quadruplex ligands that are highly discriminating against duplex DNA and show promising selectivity between intramolecular quadruplexes.

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Anthony Bugaut, Katja Jantos, Jean-Luc Wietor, Raphaël Rodriguez, Jeremy K M Sanders, Shankar Balasubramanian (2008 Feb 27)

Exploring the differential recognition of DNA G-quadruplex targets by small molecules using dynamic combinatorial chemistry.

Angewandte Chemie (International ed. in English) : 2677-80 : DOI : 10.1002/anie.200705589 En savoir plus
Résumé

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Année de publication : 2007

Mallesham Bejugam, Sven Sewitz, Pravin S Shirude, Raphaël Rodriguez, Ramla Shahid, Shankar Balasubramanian (2007 Oct 9)

Trisubstituted isoalloxazines as a new class of G-quadruplex binding ligands: small molecule regulation of c-kit oncogene expression.

Journal of the American Chemical Society : 12926-7 En savoir plus
Résumé

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Raphaël Rodriguez, G Dan Pantoş, Diana P N Gonçalves, Jeremy K M Sanders, Shankar Balasubramanian (2007 Jun 15)

Ligand-driven G-quadruplex conformational switching by using an unusual mode of interaction.

Angewandte Chemie (International ed. in English) : 5405-7 En savoir plus
Résumé

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Année de publication : 2006

Diana P N Gonçalves, Raphaël Rodriguez, Shankar Balasubramanian, Jeremy K M Sanders (2006 Nov 17)

Tetramethylpyridiniumporphyrazines–a new class of G-quadruplex inducing and stabilising ligands.

Chemical communications (Cambridge, England) : 4685-7 En savoir plus
Résumé

3,4-Tetramethylpyridiniumporphyrazines bind strongly and selectively to human telomeric G-quadruplex DNA, inducing the formation of an antiparallel quadruplex in a process that mimics molecular chaperones.

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Katja Jantos, Raphaël Rodriguez, Sylvain Ladame, Pravin S Shirude, Shankar Balasubramanian (2006 Oct 19)

Oxazole-based peptide macrocycles: a new class of G-quadruplex binding ligands.

Journal of the American Chemical Society : 13662-3 En savoir plus
Résumé

Herein we report on the synthesis and DNA binding properties of a new class of water soluble oxazole-based peptide macrocycles that bind selectively to quadruplex DNA, with no detectable binding to duplex DNA. We have recently identified one quadruplex in the proto-oncogene c-kit that is suspected to act as a regulatory element for the expression of the c-kit gene. Here we provide the first example of a ligand binding to and stabilizing the c-kit quadruplex. Moreover, we show that these macrocycles show a preference for the c-kit quadruplex as compared to the human telomeric quadruplex.

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