Raphaël Rodriguez

A Novel Small Molecule That Alters Shelterin Integrity and Triggers a DNA-Damage Response at Telomeres

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.

Chemical Inhibition of NAT10 Corrects Defects of Laminopathic Cells

Remodelin Nuclear Defects Deregulation of A-type lamin proteins leads to disorganization of chromatin structure and misshapen nuclei, which are believed to underlie the pathologies of various human diseases, including the premature aging disorder Hutchinson Gilford progeria syndrome (HGPS) and various cancers. Larrieu et al. (p. 527) developed a small molecule, Remodelin, that not only improved nuclear shape defects of human lamin A/C–depleted cells, HGPS cells, and aged normal cells, but also decreased the levels of a DNA damage marker and improved global cellular fitness. The small molecule Remodelin can correct nuclear architecture defects and improve cellular fitness of progeric human cells. 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.

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

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.

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

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.

Salinomycin kills cancer stem cells by sequestering iron in lysosomes

Cancer stem cells (CSCs) represent a subset of cells within tumours that exhibit self-renewal properties and the capacity to seed tumours. CSCs are typically refractory to conventional treatments and have been associated to metastasis and relapse. Salinomycin operates as a selective agent against CSCs through mechanisms that remain elusive. Here, we provide evidence that a synthetic derivative of salinomycin, which we named ironomycin (AM5), exhibits a more potent and selective activity against breast CSCs in vitro and in vivo, by accumulating and sequestering iron in lysosomes. In response to the ensuing cytoplasmic depletion of iron, cells triggered the degradation of ferritin in lysosomes, leading to further iron loading in this organelle. Iron-mediated production of reactive oxygen species promoted lysosomal membrane permeabilization, activating a cell death pathway consistent with ferroptosis. These findings reveal the prevalence of iron homeostasis in breast CSCs, pointing towards iron and iron-mediated processes as potential targets against these cells. Cancer stem cells are typically refractory to conventional treatments. Now, an unprecedented mechanism has been discovered by which salinomycin and derivatives can sequester iron in lysosomes leading to cytoplasmic iron depletion and the subsequent production of reactive oxygen species that are lethal to the cell. This discovery of the importance of iron in cancer stem cell maintenance provides an opportunity for developing new therapeutics.

Synthesis of marmycin A and investigation into its cellular activity

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.

Differential Targeting of Human Topoisomerase II Isoforms with Small Molecules

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.

Guanosine and isoguanosine derivatives for supramolecular devices

Guanosine and isoguanosine derivatives can self-assemble by means of hydrogen-bonding, π–π and cation–dipole interactions, yielding supramolecules that have found broad applications in diverse areas, such as material science, medicinal chemistry or nanotechnology. This article reviews the different self-organized architectures generated by guanosine and isoguanosine scaffolds and reports on recent examples of their use in the preparation of functional devices.

Biased and unbiased strategies to identify biologically active small molecules

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.

Click Quantitative Mass Spectrometry Identifies PIWIL3 as a Mechanistic Target of RNA Interference Activator Enoxacin in Cancer Cells

Enoxacin is a small molecule that stimulates RNA interference (RNAi) and acts as a growth inhibitor selectively in cancer but not in untransformed cells. Here, we used alkenox, a clickable enoxacin surrogate, coupled with quantitative mass spectrometry, to identify PIWIL3 as a mechanistic target of enoxacin. PIWIL3 is an Argonaute protein of the PIWI subfamily that is mainly expressed in the germline and that mediates RNAi through piRNAs. Our results suggest that cancer cells re-express PIWIL3 to repress RNAi through miRNAs and thus open a new opportunity for cancer-specific targeting.