Synthèse de Molécules et de Macromolécules
pour le Vivant et l’Environnement
Chemical tools for the study of epigenetic modifications
Epigenetics defines the changes in gene expression that are not coded by the DNA sequence and are inheritable. The main epigenetic factors are chemical modification of histones (methylation and acetylation) and DNA methylation, but new modifications have recently expanded the epigenetic landscape. Considering the potential of “druggability” of proteins involved in epigenetics, the precise characterization of their activity might offer new opportunity for therapeutic intervention. In recent years, the study of chromatin biology has greatly benefited from chemical biology tools to address fundamental structure/function problems in epigenetics. We recently developed both chemical tools and proteomic approaches based on photolabeling or bioorthogonal labeling coupled to mass spectrometry to study several epigenetic modifications.
Identification of Novel Inhibitors of DNA methylation by Screening of a Chemical Library. ACS Chem Biol. 2013, 8 (3), pp 543–548.
Synthesis and Evaluation of Analogues of N-Phthaloyl-L-tryptophan (RG108) as Inhibitors of DNA Methyltransferase 1. Journal of Medicinal Chemistry. 2014, 57(2), 421-34.
Combined analysis of DNA methylation cell cycle in cancer celles. Epigenetics. 2015, 10(1), 82-91.
A direct label-free MALDI-TOF mass spectrometry based assay for the characterization of inhibitors of protein lysine methyltransferases. Analytical and Bioanalytical Chemistry. 2017, 409(15), 3767–3777.
Rational design of bisubstrate-type analogs as inhibitors of DNA methyltransferases in cancer cells. Journal of Medicinal Chemistry. 2017, 60 (11), 4665–4679.
Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors. Philos Trans R Soc Lond B Biol Sci. 2018, 5, 373(1748)
Recently, chemical-biology-based strategies have emerged for the study of bacterial pathogens, giving biologists the opportunity to have powerful new tools for probing bacteria. Actually, probes for the study of mycobacterial envelope remains challenging since Mycobacteria and Corynebacteria have an atypical organization being composed of complex glycolipids (mycolic acids esterified to α,α-D-trehalose). They form a very impermeable and rigid barrier that might contribute to the exceptional resistance of mycobacteria towards chemotherapeutic molecules. The biosynthesis of these cell wall mycolate esters has been studied during the last decade but the mechanisms of their assembly in the bacterial envelope is largely unknown.
In this context, we study the specificity and the interplay between several enzymes named mycoloytransferases in the biogenesis of the envelope of these mycobacteria, using our expertise in trehalose chemistry including the synthesis of complex fatty acids and selective modifications of trehalose. We work in this project in close collaboration with Prof. Nicolas Bayan (Institut de Biologie Intégrative de la Cellule, Université Paris Sud), Dr. Boris Vauzeilles (Chemical Biology Department, Institut de Chimie des Substances Naturelles) and with Prof. Federica Migliardo (University of Messina).
"First access to a mycolic acid-based bioorthogonal reporter for the study of the mycomembrane and mycoloyltransferases in Corynebacteria". E. Lesur, A. Baron, C. Dietrich, M. Buchotte, G. Doisneau, D. Urban, J.-M. Beau, N. Bayan, B. Vauzeilles, D. Guianvarc’h, Y. Bourdreux, Chem. Commun., 2019, 55, 13074-13077.
"Study of the conformational behaviour of trehalose mycolates by FT-IR spectroscopy". F. Migliardo, Y. Bourdreux, M. Buchotte, G. Doisneau, J.-M. Beau, N. Bayan, Chem. Phys. Lipids, 2019, 223, 104789
For the selective synthesis of Mycobacterium tuberculosis sulfoglycolipids, see:
"Synthesis of a Mycobacterium tuberculosis Tetra-acylated Sulfolipid Analogue and Characterization of the Chiral Acyl Chains Using Anisotropic NAD 2D-NMR Spectroscopy"" A. Lemétais, Y. Bourdreux, P. Lesot, J. Farjon, J.-M. Beau, J. Org. Chem. 2013, 78, 7648–7657.
"Simplified Deoxypropionate Acyl Chains for Mycobacterium tuberculosis Sulfoglycolipid Analogues: Chain Length is Essential for High Antigenicity" B. Gau, A. Lemétais, M. Lepore, L. F. Garcia-Alles, Y. Bourdreux, L. Mori, M. Gilleron, G. De Libero, G. Puzo, J.-M. Beau, J. Prandi, ChemBioChem 2013, 14, 2413–2417.
"Recent results in synthetic glycochemistry with iron salts at Orsay-Gif" J.-M. Beau, Y. Bourdreux, F.-D. Boyer, S. Norsikian, D. Urban, G. Doisneau, B. Vauzeilles, A. Gouasmat, A. Lemétais, A. Mathieu, J.-F. Soul., A. Stévenin, A. Xolin, in Carbohydrate Chemistry, vol. 40 (Eds.: A. P. Rauter, T. K. Lindhorst, Y. Queneau), The Royal Society of Chemistry, Cambridge, UK, 2014, pp. 118–139.
Metabolic glycan labeling
Our group pioneered the use of specific carbohydrate analogues for the quick detection of living bacteria, using metabolic glycan labeling. The use of a carbohydrate modified by a chemical reporter group deceives bacterial metabolism, leading to the incorporation of this carbohydrate into surface glycans. The reporter (e.g. azido) group can then be detected by conjugation with a fluorophore, therefore labeling the bacterial surface. For example, the detection and numeration of Gram-negative bacteria can be performed via the assimilation of a 3-deoxy-d-manno-octulosonic acid (Kdo) derivative (Kdo-N3), since Kdo is an essential component of lipopolysaccharides (LPS), glycolipids which are present only at the surface of Gram-negative bacteria. This approach allows for rapid detection of the presence of living Gram-negative bacteria, and finds applications in different domains including microbiological quality control. Beyond labeling and imaging, when used in combination with streptavidin-coated magnetic beads, this strategy allows the concentration of a target, biotin-labeled bacterium from a mixture or complex medium.
Another development of this strategy uses a carbohydrate (Legionaminic acid), which is specifically present at the surface of Legionella pneumophila, a bacterium responsible for most cases of legionellosis. Legionellosis is a serious disease presenting a relatively high fatality rate, and leading to epidemic events attracting high media attention. The main prevention strategy is based on regular control of installations, which are susceptible to allow development of the bacterium. The classical detection method relies on bacterial culture and requires more than ten days. The new method should significantly shorten this delay, since different strains of Legionella pneumophila have been labeled in the lab in less than 24 hours. This was the first time that metabolic glycan labeling could be used for direct species identification.
A strategy to specifically label Legionella pneumophila
More recent applications of this strategy resulted in specific labeling of plant cell wall by incorporation of Kdo-N3 within rhamnogalacturonan II, a Kdo-containing parietal polysaccharide. Further applications to tumor cell labeling are also under study.
Click-mediated labeling of bacterial membranes through metabolic modification of the Lipopolysaccharide inner-core, A. Dumont, A. Malleron, M. Awwad, S. Dukan, B. Vauzeilles, Angew. Chem. Int. Ed., 2012, 51, 3143-3146.
Identification of living Legionella pneumophila using species-specific metabolic lipopolysaccharide labeling. J. Mas Pons, A. Dumont, G. Sautejeau, E. Fugier, A. Baron, S. Dukan, B. Vauzeilles, Angew. Chem. Int. Ed. 2014, 53, 1275-1278
Rapid and Specific Enrichment of Culturable Gram Negative Bacteria Using Non-Lethal Copper-Free Click Chemistry Coupled with Magnetic Beads Separation, E. Fugier, A. Dumont, A. Malleron, E. Poquet, J. Mas Pons, A. Baron, B. Vauzeilles, S. Dukan, PLoS ONE, 2015, 10(6): e0127700.
Inhibition of fucosylation of cell wall components by 2-fluoro 2-deoxy-L-fucose induces defects in root cell elongation, M. Dumont, A. Lehner, M. Bardor, C. Burel, B. Vauzeilles, O. Lerouxel, C. T. Anderson, J.-C. Mollet, Patrice Lerouge, Plant J., 2015, 84, 1137-1151.
Plant cell wall imaging by metabolic click-mediated labelling of rhamnogalacturonan II using azido 3-deoxy-D-manno-oct-2-ulosonic acid, M. Dumont, A. Lehner, B. Vauzeilles, J. Malassis, A. Marchant, K. Smyth, B. Linclau, A. Baron, J. Mas Pons, C. T. Anderson, D. Schapman, L. Galas, J.-C. Mollet, P. Lerouge, Plant J., 2016, 85, 437–447.