Chimie et Biologie du Cancer

Publications de l’équipe

Année de publication : 2015

Tatiana Cañeque, Filipe Gomes, Trang Thi Mai, Giovanni Maestri, Max Malacria, Raphaël Rodriguez (2015 Aug 21)

Synthesis of marmycin A and investigation into its cellular activity.

Nature Chemistry : 744-51 : DOI : 10.1038/nchem.2302 En savoir plus
Résumé

Anthracyclines such as doxorubicin are used extensively in the treatment of cancers. Anthraquinone-related angucyclines also exhibit antiproliferative properties and have been proposed to operate via similar mechanisms, including direct genome targeting. Here, we report the chemical synthesis of marmycin A and the study of its cellular activity. The aromatic core was constructed by means of a one-pot multistep reaction comprising a regioselective Diels-Alder cycloaddition, and the complex sugar backbone was introduced through a copper-catalysed Ullmann cross-coupling, followed by a challenging Friedel-Crafts cyclization. Remarkably, fluorescence microscopy revealed that marmycin A does not target the nucleus but instead accumulates in lysosomes, thereby promoting cell death independently of genome targeting. Furthermore, a synthetic dimer of marmycin A and the lysosome-targeting agent artesunate exhibited a synergistic activity against the invasive MDA-MB-231 cancer cell line. These findings shed light on the elusive pathways through which anthraquinone derivatives act in cells, pointing towards unanticipated biological and therapeutic applications.

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Angelica Mariani, Alexandra Bartoli, Mandeep Atwal, Ka C Lee, Caroline A Austin, Raphaël Rodriguez (2015 May 7)

Differential Targeting of Human Topoisomerase II Isoforms with Small Molecules.

Journal of medicinal chemistry : 4851-6 : DOI : 10.1021/acs.jmedchem.5b00473 En savoir plus
Résumé

The TOP2 poison etoposide has been implicated in the generation of secondary malignancies during cancer treatment. Structural similarities between TOP2 isoforms challenge the rational design of isoform-specific poisons to further delineate these processes. Herein, we describe the synthesis and biological evaluation of a focused library of etoposide analogues, with the identification of two novel small molecules exhibiting TOP2B-dependent toxicity. Our findings pave the way toward studying isoform-specific cellular processes by means of small molecule intervention.

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Année de publication : 2014

Sebastian Müller, Katta Laxmi-Reddy, Prakrit V. Jena, Benoit Baptiste, Zeyuan Dong, Frédéric Godde, Taekjip Ha, Raphaël Rodriguez, Shankar Balasubramanian, Ivan Huc (2014 Nov 24)

Targeting DNA G-quadruplexes with helical small molecules

Chembiochem : 15 : DOI : 10.1002/cbic.201402439 En savoir plus
Résumé

We previously identified quinoline-based oligoamide helical foldamers and a trimeric macrocycle as selective ligands of DNA quadruplexes. Their helical structures might permit targeting of the backbone loops and grooves of G-quadruplexes instead of the G-tetrads. Given the vast array of morphologies G-quadruplex structures can adopt, this might be a way to achieve sequence selective binding. Here, we describe the design and synthesis of molecules based on macrocyclic and helically folded oligoamides. We tested their ability to interact with the human telomeric G-quadruplex and an array of promoter G-quadruplexes by using FRET melting assay and single-molecule FRET. Our results show that they constitute very potent ligands—comparable to the best so far reported. Their modes of interaction differ from those of traditional tetrad binders, thus opening avenues for the development of molecules specific for certain G-quadruplex conformations.

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Delphine Larrieu, Raphaël Rodriguez, Sébastien Britton (2014 Nov 2)

Chemical inhibition of NAT10 corrects defects of laminopathic cells

Science : 344 : 527 : DOI : 10.1126/science.1252651 En savoir plus
Résumé

Down-regulation and mutations of the nuclear-architecture proteins lamin A and C cause misshapen nuclei and altered chromatin organization associated with cancer and laminopathies, including the premature-aging disease Hutchinson-Gilford progeria syndrome (HGPS). Here, we identified the small molecule « Remodelin » that improved nuclear architecture, chromatin organization, and fitness of both human lamin A/C-depleted cells and HGPS-derived patient cells and decreased markers of DNA damage in these cells. Using a combination of chemical, cellular, and genetic approaches, we identified the acetyl-transferase protein NAT10 as the target of Remodelin that mediated nuclear shape rescue in laminopathic cells via microtubule reorganization. These findings provide insights into how NAT10 affects nuclear architecture and suggest alternative strategies for treating laminopathies and aging.

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Raphaël Rodriguez, Kyle M Miller (2014 Oct 14)

Unravelling the genomic targets of small molecules using high-throughput sequencing.

Nature reviews. Genetics : 783-96 : DOI : 10.1038/nrg3796 En savoir plus
Résumé

Small molecules–including various approved and novel cancer therapeutics–can operate at the genomic level by targeting the DNA and protein components of chromatin. Emerging evidence suggests that functional interactions between small molecules and the genome are non-stochastic and are influenced by a dynamic interplay between DNA sequences and chromatin states. The establishment of genome-wide maps of small-molecule targets using unbiased methodologies can help to characterize and exploit drug responses. In this Review, we discuss how high-throughput sequencing strategies, such as ChIP-seq (chromatin immunoprecipitation followed by sequencing) and Chem-seq (chemical affinity capture and massively parallel DNA sequencing), are enabling the comprehensive identification of small-molecule target sites throughout the genome, thereby providing insights into unanticipated drug effects.

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Ján Cvengroš, Raphaël Rodriguez (2014 Oct 1)

A Ray of Light Piercing through the Clouds The 49th EUCHEMS Conference on Stereochemistry Bürgenstock Conference 2014

Chimia (Aarau) : 68 -10 : 742-745 En savoir plus
Résumé

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Iren Wang, Madzia P Kowalski, Alexander R Langley, Raphaël Rodriguez, Shankar Balasubramanian, Shang-Te Danny Hsu, Torsten Krude (2014 Aug 26)

Nucleotide contributions to the structural integrity and DNA replication initiation activity of noncoding y RNA.

Biochemistry : 5848-63 : DOI : 10.1021/bi500470b En savoir plus
Résumé

Noncoding Y RNAs are small stem-loop RNAs that are involved in different cellular processes, including the regulation of DNA replication. An evolutionarily conserved small domain in the upper stem of vertebrate Y RNAs has an essential function for the initiation of chromosomal DNA replication. Here we provide a structure-function analysis of this essential RNA domain under physiological conditions. Solution state nuclear magnetic resonance and far-ultraviolet circular dichroism spectroscopy show that the upper stem domain of human Y1 RNA adopts a locally destabilized A-form helical structure involving eight Watson-Crick base pairs. Within this helix, two G:C base pairs are highly stable even at elevated temperatures and therefore may serve as clamps to maintain the local structure of the helix. These two stable G:C base pairs frame three unstable base pairs, which are located centrally between them. Systematic substitution mutagenesis results in a disruption of the ordered A-form helical structure and in the loss of DNA replication initiation activity, establishing a positive correlation between folding stability and function. Our data thus provide a structural basis for the evolutionary conservation of key nucleotides in this RNA domain that are essential for the functionality of noncoding Y RNAs during the initiation of DNA replication.

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Sebastian Müller, Raphaël Rodriguez (2014 Aug 5)

G-quadruplex interacting small molecules and drugs: from bench toward bedside.

Expert review of clinical pharmacology : 663-79 : DOI : 10.1586/17512433.2014.945909 En savoir plus
Résumé

G-quadruplexes are non-Watson-Crick four-stranded nucleic acid structures. Recent evidence points toward their existence in vivo and their implication in various biological processes. Over the past two decades, small molecules have been developed to specifically and selectively target these structures in order to dissect mechanisms they have been linked to. This has led to the development of potential therapeutic agents, particularly for anti-carcinogenic activity. Here, we first present how major biological roles of G-quadruplexes have been uncovered by the use of specifically designed small molecule probes. We use this to highlight how fundamental research has contributed to identifying biological functions of G-quadruplexes and their potential as therapeutic targets. We then discuss the development of G-quadruplex interacting small molecules as potential drug candidates.

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Valentina Abet, Angelica Mariani, Fiona R Truscott, Sébastien Britton, Raphaël Rodriguez (2014 May 10)

Biased and unbiased strategies to identify biologically active small molecules.

Bioorganic & medicinal chemistry : 4474-89 : DOI : 10.1016/j.bmc.2014.04.019 En savoir plus
Résumé

Small molecules are central players in chemical biology studies. They promote the perturbation of cellular processes underlying diseases and enable the identification of biological targets that can be validated for therapeutic intervention. Small molecules have been shown to accurately tune a single function of pluripotent proteins in a reversible manner with exceptional temporal resolution. The identification of molecular probes and drugs remains a worthy challenge that can be addressed by the use of biased and unbiased strategies. Hypothesis-driven methodologies employs a known biological target to synthesize complementary hits while discovery-driven strategies offer the additional means of identifying previously unanticipated biological targets. This review article provides a general overview of recent synthetic frameworks that gave rise to an impressive arsenal of biologically active small molecules with unprecedented cellular mechanisms.

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Delphine Larrieu, Sébastien Britton, Mukerrem Demir, Raphaël Rodriguez, Stephen P Jackson (2014 May 3)

Chemical inhibition of NAT10 corrects defects of laminopathic cells.

Science (New York, N.Y.) : 527-32 : DOI : 10.1126/science.1252651 En savoir plus
Résumé

Down-regulation and mutations of the nuclear-architecture proteins lamin A and C cause misshapen nuclei and altered chromatin organization associated with cancer and laminopathies, including the premature-aging disease Hutchinson-Gilford progeria syndrome (HGPS). Here, we identified the small molecule « Remodelin » that improved nuclear architecture, chromatin organization, and fitness of both human lamin A/C-depleted cells and HGPS-derived patient cells and decreased markers of DNA damage in these cells. Using a combination of chemical, cellular, and genetic approaches, we identified the acetyl-transferase protein NAT10 as the target of Remodelin that mediated nuclear shape rescue in laminopathic cells via microtubule reorganization. These findings provide insights into how NAT10 affects nuclear architecture and suggest alternative strategies for treating laminopathies and aging.

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Valentina Abet, Robert Evans, Florian Guibbal, Stefano Caldarelli, Raphaël Rodriguez (2014 Feb 13)

Modular construction of dynamic nucleodendrimers.

Angewandte Chemie (International ed. in English) : 4862-6 : DOI : 10.1002/anie.201402400 En savoir plus
Résumé

Isoguanosine-containing dendritic small molecules self-assemble into decameric nucleodendrimers as observed by 1D NMR spectroscopy, 2D DOSY, and mass spectrometry. In particular, apolar building blocks readily form pentameric structures in acetonitrile while the presence of alkali metals promotes the formation of stable decameric assemblies with a preference for cesium ions. Remarkably, co-incubation of guanosine and isoguanosine-containing nucleodendrons results in the formation of decameric structures in absence of added salts. Further analysis of the mixture indicated that guanosine derivatives facilitate the formation, but are not involved in decameric structures; a process reminiscent of molecular crowding. This molecular system provides a powerful canvas for the rapid and modular assembly of polyfunctional dendritic macromolecules.

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Année de publication : 2012

Marco Di Antonio, Giulia Biffi, Angelica Mariani, Eun-Ang Raiber, Raphaël Rodriguez, Shankar Balasubramanian (2012 Oct 6)

Selective RNA versus DNA G-quadruplex targeting by in situ click chemistry.

Angewandte Chemie (International ed. in English) : 11073-8 : DOI : 10.1002/anie.201206281 En savoir plus
Résumé

It all clicks into place: A potent telomere-targeting small molecule has been identified by using the copper-free 1,3-dipolar cycloaddition of a series of alkyne and azide building blocks catalyzed by a non-Watson-Crick DNA secondary structure (see picture). This method rapidly identifies, otherwise unanticipated, potent small-molecule probes to selectively target a given RNA or DNA.

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Sebastian Müller, Deborah A Sanders, Marco Di Antonio, Stephanos Matsis, Jean-François Riou, Raphaël Rodriguez, Shankar Balasubramanian (2012 Jul 14)

Pyridostatin analogues promote telomere dysfunction and long-term growth inhibition in human cancer cells.

Organic & biomolecular chemistry : 6537-46 : DOI : 10.1039/c2ob25830g En savoir plus
Résumé

The synthesis, biophysical and biological evaluation of a series of G-quadruplex interacting small molecules based on a N,N’-bis(quinolinyl)pyridine-2,6-dicarboxamide scaffold is described. The synthetic analogues were evaluated for their ability to stabilize telomeric G-quadruplex DNA, some of which showed very high stabilization potential associated with high selectivity over double-stranded DNA. The compounds exhibited growth arrest of cancer cells with detectable selectivity over normal cells. Long-time growth arrest was accompanied by senescence, where telomeric dysfunction is a predominant mechanism together with the accumulation of restricted DNA damage sites in the genome. Our data emphasize the potential of a senescence-mediated anticancer therapy through the use of G-quadruplex targeting small molecules based on the molecular framework of pyridostatin.

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Marco Di Antonio, Raphaël Rodriguez, Shankar Balasubramanian (2012 Feb 21)

Experimental approaches to identify cellular G-quadruplex structures and functions.

Methods (San Diego, Calif.) : 84-92 : DOI : 10.1016/j.ymeth.2012.01.008 En savoir plus
Résumé

Guanine-rich nucleic acids can fold into non-canonical DNA secondary structures called G-quadruplexes. The formation of these structures can interfere with the biology that is crucial to sustain cellular homeostases and metabolism via mechanisms that include transcription, translation, splicing, telomere maintenance and DNA recombination. Thus, due to their implication in several biological processes and possible role promoting genomic instability, G-quadruplex forming sequences have emerged as potential therapeutic targets. There has been a growing interest in the development of synthetic molecules and biomolecules for sensing G-quadruplex structures in cellular DNA. In this review, we summarise and discuss recent methods developed for cellular imaging of G-quadruplexes, and the application of experimental genomic approaches to detect G-quadruplexes throughout genomic DNA. In particular, we will discuss the use of engineered small molecules and natural proteins to enable pull-down, ChIP-Seq, ChIP-chip and fluorescence imaging of G-quadruplex structures in cellular DNA.

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Année de publication : 2011

Raphaël Rodriguez, Kyle M Miller, Josep V Forment, Charles R Bradshaw, Mehran Nikan, Sébastien Britton, Tobias Oelschlaegel, Blerta Xhemalce, Shankar Balasubramanian, Stephen P Jackson (2011 Sep 26)

Small-molecule-induced DNA damage identifies alternative DNA structures in human genes.

Nature chemical biology : 301-10 : DOI : 10.1038/nchembio.780 En savoir plus
Résumé

Guanine-rich DNA sequences that can adopt non-Watson-Crick structures in vitro are prevalent in the human genome. Whether such structures normally exist in mammalian cells has, however, been the subject of active research for decades. Here we show that the G-quadruplex-interacting drug pyridostatin promotes growth arrest in human cancer cells by inducing replication- and transcription-dependent DNA damage. A chromatin immunoprecipitation sequencing analysis of the DNA damage marker γH2AX provided the genome-wide distribution of pyridostatin-induced sites of damage and revealed that pyridostatin targets gene bodies containing clusters of sequences with a propensity for G-quadruplex formation. As a result, pyridostatin modulated the expression of these genes, including the proto-oncogene SRC. We observed that pyridostatin reduced SRC protein abundance and SRC-dependent cellular motility in human breast cancer cells, validating SRC as a target of this drug. Our unbiased approach to define genomic sites of action for a drug establishes a framework for discovering functional DNA-drug interactions.

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