Intitulé du sujet: Design and synthesis of m6A methyltransferases inhibitors
Sujet
Codirection: Emmanuelle Braud et Laura Iannazzo
Nombre de mois: 48 mois
Ecole Doctorale: ED 563 - Médicament,Toxicologie, Chimie, Imageries
Unité de recherche et équipe:
Unité de recherche : Chimie et Biochimie Pharmacologiques et Toxicologiques - UMR8601 CNRS
Equipe: Chemistry of RNAs, Nucleosides, Peptides and Heterocycles
Coordonnées de l’équipe:
UFR des Sciences Fondamentales et Biomédicales
Université Paris Cité
45, rue des Saints-Pères
75006 Paris, France
Secteur: Sciences de la vie / Life Sciences
Langue attendue: Anglais
Niveau de langue attendu: B2
Description
Description du sujet:
The great majority of methyltransferases (MTases) use S-adenosyl-L-methionine (SAM) as the cofactor to transfer a methyl group to their substrates, leading to the methylation of nucleic acids, proteins or small-molecule metabolites and the release of the co-product S-adenosyl-L-homocysteine (SAH). Based on their substrates, MTases are divided into four main families, the DNA methyltransferases (DNMTs), protein methyltransferases (PMTs), MTases that catalyze the methylation of small molecules and RNA methyltransferases (RNA MTases). These enzymes are involved in important cell events such as epigenetics,[1] epitranscriptome,[2] signal transduction[3] or in the regulation of protein functions[4] and metabolism.[5] It has also been shown that deregulation of the methylation process leads to the development of human diseases such as cancers, metabolic disorders or neurodegenerative diseases.[2a,6] In RNA, m6A MTases catalyze the formation of N6-methyladenosine (m6A), which is the most prevalent internal mRNA modifications observed in a wide range of eukaryotes, viruses and bacteria. Recently, m6A RNA modification was defined as a dynamic process[7] and its disturbance correlated to human diseases thus emphasizing the importance of m6A RNA modification.[8]
In order to fully decipher the methylation process, chemical tools are needed to access structural data. In this context, our team has reported the design and synthesis of bisubstrate analogues of m6A MTases based on aromatic nucleophilic substitution (SNAr) and copper-catalyzed azide-alkyne cycloaddition (CuAAc). The chemical structure of these compounds is based on a SAM analogue covalently attached to a substrate surrogate via an appropriate linker that mimics the transition state of the SN2 mechanism.[9],[10],[11],[12],[13] Several crystallographic structures of complexes between bisubstrates and the bacterial MTase RlmJ were obtained and allowed us to propose a mechanism for the methylation process catalyzed by this enzyme.
We seek now to synthesize new bisubstrate analogues as inhibitors of m6A MTases. The design of the new structures will be guided by molecular modeling studies and crystallographic data.
The PhD program is divided into three main parts. First, the PhD student will be in charge of the synthesis of new SAM-adenosine conjugates by modifying the nature of the linker between the adenosine and the analogue of SAM. The importance of the amino acid side chain will also be assessed. Then, in situ click chemistry will be used to identify new inhibitors of m6A MTases. Finally, the PhD student will be involved in the design and synthesis of covalent inhibitors. All the inhibitors will be evaluated for their MTases inhibitory activity by the collaborators of the team.
Compétences requises:
Le candidat doit avoir de bonnes connaissances en chimie organique théorique et pratique. Une expérience en synthèse organique incluant des compétences dans les techniques chromatographiques de purification et les méthodes de caractérisation structurale des molécules organiques (RMN, spectrométrie de masse) est requise.
Références bibliographiques:
[1] a) S. L. Berger, T. Kouzarides, R. Shiekhattar, A. Shilatifard, Genes Dev 2009, 23, 781-783; b) T. K. Kelly, D. D. De Carvalho, P. A. Jones, Nat Biotechnol 2010, 28, 1069-1078.
[2] a) P. J. Batista, Genomics Proteomics Bioinformatics 2017, 15, 154-163; b) E. M. Harcourt, A. M. Kietrys, E. T. Kool, Nature 2017, 541, 339-346.
[3] S. Kirchner, Z. Ignatova, Nat Rev Genet 2015, 16, 98-112.
[4] R. Wang, M. Luo, Curr Opin Chem Biol 2013, 17, 729-737.
[5] H. S. Han, D. Choi, S. Choi, S. H. Koo, Endocrinol Metab (Seoul) 2014, 29, 435-440.
[6] a) P. A. Jones, S. B. Baylin, Cell 2007, 128, 683-692; b) D. Kraus, Q. Yang, D. Kong, A. S. Banks, L. Zhang, J. T. Rodgers, E. Pirinen, T. C. Pulinilkunnil, F. Gong, Y. C. Wang, Y. Cen, A. A. Sauve, J. M. Asara, O. D. Peroni, B. P. Monia, S. Bhanot, L. Alhonen, P. Puigserver, B. B. Kahn, Nature 2014, 508, 258-262; c) S. Espinoza, F. Manago, D. Leo, T. D. Sotnikova, R. R. Gainetdinov, CNS Neurol Disord Drug Targets 2012, 11, 251-263; d) T. Hamidi, A. K. Singh, T. Chen, Epigenomics 2015, 7, 247-265; e) C. J. Lewis, T. Pan, A. Kalsotra, Nat Rev Mol Cell Biol 2017, 18, 202-210.
[7] a) G. C. Cao, H. B. Li, Z. N. Yin, R. A. Flavell, Open Biol 2016, 6; b) R. R. Edupuganti, S. Geiger, R. G. H. Lindeboom, H. L. Shi, P. J. Hsu, Z. K. Lu, S. Y. Wang, M. P. A. Baltissen, P. W. T. C. Jansen, M. Rossa, M. Muller, H. G. Stunnenberg, C. He, T. Carell, M. Vermeulen, Nat Struct Mol Biol 2017, 24, 870; c) F. R. Traube, T. Carell, RNA Biol 2017, 14, 1099-1107.
[8] a) S. Blanco, M. Frye, Curr Opin Cell Biol 2014, 31, 1-7; b) N. Liu, T. Pan, Transl Res 2015, 165, 28-35.
[9] C. Atdjian, L. Iannazzo, E. Braud, M. Etheve-Quelquejeu, Eur J Org 2018, 4411-4425.
[10] S. Oerum, M. Catala, C. Atdjian, F. Brachet, L. Ponchon, P. Barraud, L. Iannazzo, L. Droogmans, E. Braud, M. Ethève-Quelquejeu, C. Tisné, RNA Biol 2019, 16, 798-808.
[11] Atdjian, D. Coelho, L. Iannazzo, M. Ethève-Quelquejeu, E. Braud, Molecules 2020, 25, 3241. [12] V. Meynier, L. Iannazzo, M. Catala, S. Oerum, E. Braud, C. Atdjian, P. Barraud, M. Fonvielle, C. Tisné, M. Ethève-Quelquejeu, Nucleic Acids Res 2022, 50, 5793-5806.
[13] D. Coelho, L. Le Corre, K. Bartosik, L. Iannazzo, E. Braud, M. Ethève-Quelquejeu, Chem Eur J 2023, e202301134.
