UMR9187 / U1196 – Chimie et Modélisation pour la Biologie du Cancer (CMBC)

Publications de l’unité

Année de publication : 2019

Xiao Xie, Michela Zuffo, Marie-Paule Teulade-Fichou, Anton Granzhan (2019 Aug 6)

Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries

Beilstein Journal of Organic Chemistry : 15 : 1872–1889 : DOI : 10.3762/bjoc.15.183 En savoir plus

A library of 52 distyryl and 9 mono-styryl cationic dyes was synthesized and investigated with respect to their optical properties, propensity to aggregation in aqueous medium, and capacity to serve as fluorescence “light-up” probes for G-quadruplex (G4) DNA and RNA structures. Among the 61 compounds, 57 dyes showed preferential enhancement of fluorescence intensity in the presence of one or another G4-DNA or RNA structure, while no dye displayed preferential response to double-stranded DNA or single-stranded RNA analytes employed at equivalent nucleotide concentration. Thus, preferential fluorimetric response towards G4 structures appears to be a common feature of mono- and distyryl dyes, including long-known mono-styryl dyes used as mitochondrial probes or protein stains. However, the magnitude of the G4-induced “light-up” effect varies drastically, as a function of both the molecular structure of the dyes and the nature or topology of G4 analytes. Although our results do not allow to formulate comprehensive structure–properties relationships, we identified several structural motifs, such as indole- or pyrrole-substituted distyryl dyes, as well as simple mono-stryryl dyes such as DASPMI [2-(4-(dimethylamino)styryl)-1-methylpyridinium iodide] or its 4-isomer, as optimal fluorescent light-up probes characterized by high fluorimetric response (I/I0 of up to 550-fold), excellent selectivity with respect to double-stranded DNA or single-stranded RNA controls, high quantum yield in the presence of G4 analytes (up to 0.32), large Stokes shift (up to 150 nm) and, in certain cases, structural selectivity with respect to one or another G4 folding topology. These dyes can be considered as promising G4-responsive sensors for in vitro or imaging applications. As a possible application, we implemented a simple two-dye fluorimetric assay allowing rapid topological classification of G4-DNA structures.

Identification of optimal fluorescent probes for G-quadruplex nucleic acids

Birzu C., Hillairet A., Giry M., Grandin N., Verrelle P., Mokhtari K., Marie Y., Hoang-Xuan K., Delattre J., Idbaih A., Charbonneau M., Sanson M., Alentorn A. (2019 Aug 1)

OS9.7 Telomere length, TERTp mutation and ALT status in adult diffuse gliomas

Neuro-Oncology : 21 : iii19-iii20 : DOI : 10.1093/neuonc/noz126.065 En savoir plus


The current classification of adult diffuse gliomas integrates two alternative telomere maintenance mechanisms: reactivation of telomerase activity by TERT promoter (TERTp) mutations or ATRX mutations associated with alternative length telomere (ALT). We investigated here the relation between these two mechanisms, telomere length, and outcome in a large series of diffuse gliomas.


We performed C-circle assay (CCA) to determine ALT status, determined telomere length in tumor (RTLt) and leukocyte (RTLl) in a cohort of 354 adult diffuse gliomas, and sequenced ATRX gene. We calculated an age-adjusted telomere score considering tumor and leukocyte (blood) telomere length and corrected by age. This score was used in univariate and multivariate survival analyses to evaluate the potential impact of telomere length on the prognosis of gliomas. We used the TCGA LGG-GBM dataset to validate our findings in an independent cohort.


RTLl and RTLt were associated with ATRX mutation and ALT phenotype, and negatively associated with age and TERTp mutations. ATRX mutations (found in 52% (64/123) of samples) were mostly transitions (C>T or T>C), and were associated with ALT phenotype. None of 1p/19q co-deleted oligodendrogliomas harbored an ALT phenotype. No patients with TERTp mutations had ALT phenotype except for a very small subgroup of patients (3/87, 3.4%) suggesting that multiple ways of telomere maintenance, may co-exist in a single tumor, probably expressed in different clones. Telomere age-adjusted score was independently associated with better outcome (HR= 0.73 [95% CI 0.56–0.97], p-value 0.03 adjusted for age, TERTp mutation, IDH mutation, 1p/19q co-deletion and WHO grade). These results were validated using the LGG-GBM TCGA dataset.


We unravel the relation between RTLl and RTLt, TERTp mutation and ALT phenotype and describe a novel telomere age-adjusted score independently associated with better prognosis in adult diffuse gliomas.

Paulina Prorok, Marie Artufel, Antoine Aze, Philippe Coulombe, Isabelle Peiffer, Laurent Lacroix, Aurore Guédin, Jean-Louis Mergny, Julia Damaschke, Aloys Schepers, Benoit Ballester, Marcel Méchali (2019 Jul 24)

Involvement of G-quadruplex regions in mammalian replication origin activity.

Nature communications : 10 : 3274 : DOI : 10.1038/s41467-019-11104-0 En savoir plus

Genome-wide studies of DNA replication origins revealed that origins preferentially associate with an Origin G-rich Repeated Element (OGRE), potentially forming G-quadruplexes (G4). Here, we functionally address their requirements for DNA replication initiation in a series of independent approaches. Deletion of the OGRE/G4 sequence strongly decreased the corresponding origin activity. Conversely, the insertion of an OGRE/G4 element created a new replication origin. This element also promoted replication of episomal EBV vectors lacking the viral origin, but not if the OGRE/G4 sequence was deleted. A potent G4 ligand, PhenDC3, stabilized G4s but did not alter the global origin activity. However, a set of new, G4-associated origins was created, whereas suppressed origins were largely G4-free. In vitro Xenopus laevis replication systems showed that OGRE/G4 sequences are involved in the activation of DNA replication, but not in the pre-replication complex formation. Altogether, these results converge to the functional importance of OGRE/G4 elements in DNA replication initiation.

Emilia Puig Lombardi, Allyson Holmes, Daniela Verga, Marie-Paule Teulade-Fichou, Alain Nicolas, Arturo Londoño-Vallejo (2019 Jul 9)

Thermodynamically stable and genetically unstable G-quadruplexes are depleted in genomes across species.

Nucleic acids research : 47 : 6098-6113 : DOI : 10.1093/nar/gkz463 En savoir plus

G-quadruplexes play various roles in multiple biological processes, which can be positive when a G4 is involved in the regulation of gene expression or detrimental when the folding of a stable G4 impairs DNA replication promoting genome instability. This duality interrogates the significance of their presence within genomes. To address the potential biased evolution of G4 motifs, we analyzed their occurrence, features and polymorphisms in a large spectrum of species. We found extreme bias of the short-looped G4 motifs, which are the most thermodynamically stable in vitro and thus carry the highest folding potential in vivo. In the human genome, there is an over-representation of single-nucleotide-loop G4 motifs (G4-L1), which are highly conserved among humans and show a striking excess of the thermodynamically least stable G4-L1A (G3AG3AG3AG3) sequences. Functional assays in yeast showed that G4-L1A caused the lowest levels of both spontaneous and G4-ligand-induced instability. Analyses across 600 species revealed the depletion of the most stable G4-L1C/T quadruplexes in most genomes in favor of G4-L1A in vertebrates or G4-L1G in other eukaryotes. We discuss how these trends might be the result of species-specific mutagenic processes associated to a negative selection against the most stable motifs, thus neutralizing their detrimental effects on genome stability while preserving positive G4-associated biological roles.

Oksana Reznichenko, Alicia Quillévéré, Rodrigo Prado Martins, Nadège Loaëc, Hang Kang, María José Lista, Claire Beauvineau, Jorge González-García, Régis Guillot, Cécile Voisset, Chrysoula Daskalogianni, Robin Fåhraeus, Marie-Paule Teulade-Fichou, Marc Blondel, Anton Granzhan (2019 May 23)

Novel cationic bis(acylhydrazones) as modulators of Epstein–Barr virus immune evasion acting through disruption of interaction between nucleolin and G-quadruplexes of EBNA1 mRNA

European Journal of Medicinal Chemistry : 178 : 13-29 : DOI : 10.1016/j.ejmech.2019.05.042 En savoir plus


The oncogenic Epstein-Barr virus (EBV) evades the immune system through limiting the expression of its highly antigenic and essential genome maintenance protein, EBNA1, to the minimal level to ensure viral genome replication, thereby also minimizing the production of EBNA1-derived antigenic peptides. This regulation is based on inhibition of translation of the virally-encoded EBNA1 mRNA, and involves the interaction of host protein nucleolin (NCL) with G-quadruplex (G4) structures that form in the glycine–alanine repeat (GAr)-encoding sequence of the EBNA1 mRNA. Ligands that bind to these G4-RNA can prevent their interaction with NCL, leading to disinhibition of EBNA1 expression and antigen presentation, thereby interfering with the immune evasion of EBNA1 and therefore of EBV (M.J. Lista et al., Nature Commun., 2017, 8, 16043). In this work, we synthesized and studied a series of 20 cationic bis(acylhydrazone) derivatives designed as G4 ligands. The in vitro evaluation showed that most derivatives based on central pyridine (Py), naphthyridine (Naph) or phenanthroline (Phen) units were efficient G4 binders, in contrast to their pyrimidine (Pym) counterparts, which were poor G4 binders due to a significantly different molecular geometry. The influence of lateral heterocyclic units (N-substituted pyridinium or quinolinium residues) on G4-binding properties was also investigated. Two novel compounds, namely PyDH2 and PhenDH2, used at a 5 μM concentration, were able to significantly enhance EBNA1 expression in H1299 cells in a GAr-dependent manner, while being significantly less toxic than the prototype drug PhenDC3 (GI50 > 50 μM). Antigen presentation, RNA pull-down and proximity ligation assays confirmed that the effect of both drugs was related to the disruption of NCL–EBNA1 mRNA interaction and the subsequent promotion of GAr-restricted antigen presentation. Our work provides a novel modular scaffold for the development of G-quadruplex-targeting drugs acting through interference with G4–protein interaction.

El Hassen Mokrani, Abderrahmane Bensegueni, Ludovic Chaput, Claire Beauvineau, Hanane Djeghim, Liliane Mouawad (2019 May 1)

Identification of New Potent Acetylcholinesterase Inhibitors Using Virtual Screening and In Vitro Approaches.

Molecular informatics : 38 : 1800118 : DOI : 10.1002/minf.201800118 En savoir plus

Acetylcholinesterase (AChE) is currently the most favorable target for the symptomatic treatment and reduction of Alzheimer’s disease (AD). In order to identify new potent inhibitors of this enzyme, we describe herein a new structure‐based virtual screening (SBVS) using the Institut Curie‐CNRS chemical library (ICCL), which contained at the screening date 14307 compounds. The strategy undertaken in this work consisted of the use of several docking programs in SBVS calculations followed by the application of a consensus method (vSDC) and a scrupulous visual analysis. It allowed us to obtain a high degree of success, with a yield of almost 86 %, since 12 hits were identified among only 14 molecules tested in vitro. Still more remarkably, 6 of these hits were more active than galantamine, the reference inhibitor. These hits were predicted to have good ADMET properties. The two most promising compounds can serve as leads for AD treatment.

Katerina Duskova, Jérémy Lamarche, Souheila Amor, Coralie Caron, Nicolas Queyriaux, Marie Gaschard, Marie-Jose Penouilh, Guillaume De Robillard, Dominique Delmas, Charles H Devillers, Anton Granzhan, Marie-Paule Teulade-Fichou, Murielle Chavarot-Kerlidou, Bruno Therrien, Sébastien Britton, David Monchaud (2019 Apr 3)

Identification of three-way DNA junction ligands through screening of chemical libraries and validation by complementary in vitro assays.

Journal of Medicinal Chemistry : 62 : 4456-4466 : DOI : 10.1021/acs.jmedchem.8b01978 En savoir plus

The human genome is replete with repetitive DNA sequences that can fold into thermodynamically stable secondary structures such as hairpins and quadruplexes. Cellular enzymes exist to cope with these structures whose stable accumulation would result in DNA damage through interference with DNA transactions such as transcription and replication. Therefore, chemical stabilization of secondary DNA structures offers an attractive way to foster DNA transaction-associated damages to trigger cell death in proliferating cancer cells. While much emphasis has been recently given to DNA quadruplexes, we focused here on three-way DNA junctions (TWJ) and report on a strategy to identify TWJ-targeting agents through a combination of in vitro techniques (TWJ-Screen, PAGE, FRET-melting, ESI-MS, dialysis equilibrium and SRB assays). We designed a complete workflow and screened 1200 compounds to identify promising three-way DNA junction ligands selected on stringent criteria in terms of TWJ folding ability, affinity and selectivity.


Paul D., Marchand A., Verga D., Bombard S., Teulade-Fichou M.P., Rosu F., Gabelica V. (2019 Feb 28)

Probing Ligand and Cation Binding Sites in G-Quadruplex Nucleic Acids by Mass Spectrometry and Electron Photodetachment Dissociation Sequencing

Analyst : 144 : 3518-3524 : DOI : 10.1039/C9AN00398C En savoir plus

Mass spectrometry provides exquisite detail on ligand and cation binding stoichiometries with a DNA target. The next important step is to develop reliable methods to determine the cation and ligand binding sites in each complex separated by the mass spectrometer. To circumvent the caveat of ligand derivatization for cross-linking, which may alter the ligand binding mode, we explored a tandem mass spectrometry (MS/MS) method that does not require ligand derivatization, and is therefore also applicable to localize metal cations. By obtaining more negative charge states for the complexes using supercharging agents, and by creating radical ions by electron photodetachment, oligonucleotide bonds become weaker than the DNA-cation or DNA-ligand noncovalent bonds upon collision-induced dissociation of the radicals. This electron photodetachment (EPD) method allows to locate the binding regions of cations and ligands by top-down sequencing of the oligonucleotide target. The very potent G-quadruplex ligands 360A and PhenDC3 were found to replace a potassium cation and bind close to the central loop of 4-repeat human telomeric sequences.

Daghildjian K., Kasselouri A., N’Diaye M., Michel J.P., Vergnaud J., Poyer F., Maillard P., Rosilio V. (2019 Feb 23)

Mannose distribution in glycoconjugated tetraphenylporphyrins governs their uptake mechanism and phototoxicity

Journal of Porphyrins and Phthalocyanines : 23 : 175-184 : DOI : 10.1142/S1088424619500184 En savoir plus

Tetraphenylporphyrins (TPPs) have been proposed for the treatment of retinoblastoma by photodynamic therapy. Glycoconjugated compounds were synthesized for improving TPP solubility and amphipathy, and to specifically target mannose receptors overexpressed at the surface of cells. The efficiency of four TPP derivatives with different chemical structures was compared by phototoxicity tests and flow cytometry experiments. Interestingly, the absence/presence and distribution of saccharide moieties in the various compounds affected differently their mechanism of interaction with cancer cells and their phototoxic efficiency. For glycodendrimeric TPP-1 and TPP-2 incubated with retinoblastoma cells, a fast two-step uptake-equilibrium process was observed, whereas for a dendrimeric TPP without saccharide moieties (TPP-1c) and a glycoconjugated compound with no dendrimeric structure (TPP(DegMan)3) uptake was very slow. The difference in uptake profiles and kinetics between TPP-1c on the one hand and TPP-1 and TPP-2 on the other hand would account for the interaction of the two glycodendrimeric compounds with a mannose receptor. These TPPs encapsulated in endosomes would induce less damage to cells upon illumination. TPP(DegMan)3 showed the highest phototoxicity, but its efficiency was unaffected by pretreatment of cells by mannan. The penetration of this glycoconjugated compound in cells and its phototoxic effect appeared independent of its interaction with a mannose receptor. Thus, if glycoconjugation influenced TPPs behavior in solution and interaction with serum proteins, phototoxicity was not necessarily related to upfront molecular recognition.

Morgan Pellerano, Delphine Naud-Martin, Florence Mahuteau-Betzer, Marie Morille, May Catherine Morris (2019 Feb 15)

Fluorescent biosensor for detection of the R248Q aggregation-prone mutant of p53.

Chembiochem : a European journal of chemical biology : 20 : 605-613 : DOI : 10.1002/cbic.201800531 En savoir plus

The p53 tumour suppressor and guardian of the genome undergoes missense mutations which lead to functional inactivation in 50% human cancers. These mutations occur mostly in the DNA-binding domain of the protein and several of these induce conformational changes which lead to amyloid-like protein aggregation. Here we describe a fluorescent biosensor that reports on the R248Q mutant of p53 in vitro and in living cells, engineered through conjugation of an environmentally-sensitive probe onto a peptide derived from the primary aggregation segment of p53.This biosensor was characterized both in vitro and by fluorescence microscopy following facilitated delivery into cultured cells. We show that this biosensor preferentially reports on the p53 R248Q mutant in PC9 lung cancer cell line compared to other lung cancer cell lines harbouring either wildtype or no p53.

Coralie Caron, Xuan N T Duong, Régis Guillot, Sophie Bombard, Anton Granzhan (2019 Feb 6)

Interaction of Functionalized Naphthalenophanes with Abasic Sites in DNA: DNA Cleavage, DNA Cleavage Inhibition, and Formation of Ligand-DNA Adducts.

Chemistry - A European Journal : 25 : 1949–1962 : DOI : 10.1002/chem.201805555 En savoir plus

GA-ChemEurJ-2018-2Ligands interacting with abasic (AP) sites in DNA may generate roadblocks in base-excision DNA repair (BER) due to indirect inhibition of DNA repair enzymes (e.g., APE1) and/or formation of toxic byproducts, resulting from ligand-induced strand cleavage or covalent cross-links. Herein, we prepared and systematically studied a series of 12 putative AP-site ligands, sharing the common naphthalenophane scaffold but endowed with a variety of substituents. Our results demonstrate that most naphthalenophanes bind to AP-sites in DNA and inhibit the APE1-induced hydrolysis of the latter in vitro. Remarkably, their APE1 inhibitory activity, as characterized by IC50 and Ki values, can be directly related to their affinity and selectivity to AP-sites, assessed from the fluorescence-melting experiments. On the other hand, the molecular design of naphthalenophanes has crucial influence on their intrinsic AP-site cleavage activity (i.e., ligand-catalyzed β- and β,δ-elimination reactions at the AP site), as illustrated by the compounds either having an exceptionally high AP-site cleavage activity (e.g., 2,7 BisNP-S, 125-fold more efficacious than spermine) or totally devoid of this activity (four compounds). Finally, we reveal the unprecedented formation of a stable covalent DNA adduct upon reaction of one ligand (2,7-BisNP-NH) with its own product of AP-site cleavage.

Pauline Gilson, Morgane Couvet, Laetitia Vanwonterghem, Maxime Henry, Julien Vollaire, Vladimir Baulin, Marco Werner, Anna Orlowska, Véronique Josserand, Florence Mahuteau-Betzer, Laurence Lafanechère, Jean-Luc Coll, Benoit Busser, Amandine Hurbin (2019 Feb 1)

The pyrrolopyrimidine colchicine-binding site agent PP-13 reduces the metastatic dissemination of invasive cancer cells in vitro and in vivo.

Biochemical pharmacology : 160 : 1-13 : DOI : S0006-2952(18)30503-3 En savoir plus

Standard chemotherapies that interfere with microtubule dynamics are a chemotherapeutic option used for the patients with advanced malignancies that invariably relapse after targeted therapies. However, major efforts are needed to reduce their toxicity, optimize their efficacy, and reduce cancer chemoresistance to these agents. We previously identified a pyrrolo[2,3d]pyrimidine-based microtubule-depolymerizing agent (PP-13) that binds to the colchicine site of β-tubulin and exhibits anticancer properties in solid human cancer cells, including chemoresistant subtypes. Here, we investigated the therapeutic potential of PP-13 in vitro and in vivo. PP-13 induced a mitotic blockade and apoptosis in several cancer cells cultured in two-dimensions or three-dimensions spheroids, in conjunction with reduced cell proliferation. Capillary-like tube formation assays using HUVECs showed that PP-13 displayed antiangiogenic properties. It also inhibited cancer cell motility and invasion, in in vitro wound-healing and transwell migration assays. Low concentration PP-13 (130 nmol.L) treatment significantly reduced the metastatic invasiveness of human cancer cells engrafts on chicken chorioallantoic membrane. In nude mice, 0.5 or 1 PP-13 intraperitoneally administered three-times a week reduced the sizes of paclitaxel-refractory orthotopic breast tumors, delayed the progression of metastasis, and decreased the global metastatic load compared to 0.5 paclitaxel or vehicle alone. PP-13 did not show any apparent early adverse effect in vivo. These data suggest that PP-13 is a promising alternative to standard chemotherapy in antimitotic drug-refractory tumors, especially through its impact on metastasis.

Delphine Naud-Martin, Corinne Landras-Guetta, Daniela Verga, Deepanjan Ghosh, Sylvain Achelle, Florence Mahuteau-Betzer, Sophie Bombard, Marie-Paule Teulade-Fichou (2019 Jan 26)

Selectivity of Terpyridine Platinum Anticancer Drugs for G-quadruplex DNA.

Molecules (Basel, Switzerland) : 24 : 404 : DOI : 10.3390/molecules24030404 En savoir plus

Guanine-rich DNA can form four-stranded structures called G-quadruplexes (G4s) that can regulate many biological processes. Metal complexes have shown high affinity and selectivity toward the quadruplex structure. Here, we report the comparison of a panel of platinum (II) complexes for quadruplex DNA selective recognition by exploring the aromatic core around terpyridine derivatives. Their affinity and selectivity towards G4 structures of various topologies have been evaluated by FRET-melting (Fluorescence Resonance Energy Transfert-melting) and Fluorescent Intercalator Displacement (FID) assays, the latter performed by using three different fluorescent probes (Thiazole Orange (TO), TO-PRO-3, and PhenDV). Their ability to bind covalently to the c-myc G4 structure in vitro and their cytotoxicity potential in two ovarian cancerous cell lines were established. Our results show that the aromatic surface of the metallic ligands governs, in vitro, their affinity, their selectivity for the G4 over the duplex structures, and platination efficiency. However, the structural modifications do not allow significant discrimination among the different G4 topologies. Moreover, all compounds were tested on ovarian cancer cell lines and normal cell lines and were all able to overcome cisplatin resistance highlighting their interest as new anticancer drugs.

M Schmidt-Cernohorska, I Zhernov, E Steib, M Le Guennec, R Achek, S Borgers, D Demurtas, L Mouawad, Z Lansky, V Hamel, P Guichard (2019 Jan 19)

Flagellar microtubule doublet assembly in vitro reveals a regulatory role of tubulin C-terminal tails.

Science (New York, N.Y.) : 363 : 285-288 : DOI : 10.1126/science.aav2567 En savoir plus

Microtubule doublets (MTDs), consisting of an incomplete B-microtubule at the surface of a complete A-microtubule, provide a structural scaffold mediating intraflagellar transport and ciliary beating. Despite the fundamental role of MTDs, the molecular mechanism governing their formation is unknown. We used a cell-free assay to demonstrate a crucial inhibitory role of the carboxyl-terminal (C-terminal) tail of tubulin in MTD assembly. Removal of the C-terminal tail of an assembled A-microtubule allowed for the nucleation of a B-microtubule on its surface. C-terminal tails of only one A-microtubule protofilament inhibited this side-to-surface tubulin interaction, which would be overcome in vivo with binding protein partners. The dynamics of B-microtubule nucleation and its distinctive isotropic elongation was elucidated by using live imaging. Thus, inherent interaction properties of tubulin provide a structural basis driving flagellar MTD assembly.

Michela Zuffo, Xiao Xie, Anton Granzhan (2018 Dec 6)

Strength in Numbers: Development of a Fluorescence Sensor Array for Secondary Structures of DNA.

Chemistry - A European Journal : 25 : 1812–1818 : DOI : 10.1002/chem.201805422 En savoir plus

GA-ChemEurJ-2018-3High-throughput assessment of secondary structures adopted by DNA oligonucleotides is currently hampered by the lack of suitable biophysical methods. Fluorescent sensors hold great potential in this respect; however, the moderate selectivity that they display for one DNA conformation over the others constitutes a major drawback to the development of accurate assays. Moreover, the use of single sensors impedes a comprehensive classification of the tested sequences. Herein, we propose to overcome these limitations through the development of a fluorescence sensor array constituted by easily accessible, commercial dyes. Multivariate analysis of the emission data matrix produced by the array allows to explore the conformational preferences of DNA sequences of interest, either by calculating the probability of group membership in the six predefined structural categories (three G-quadruplex groups, double-stranded, and two groups of single-stranded forms), or by revealing their particular structural features. The assay enables rapid screening of synthetic DNA oligonucleotides in a 96-wells plate format.