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Design and use of chemical tools to modulate gene expression in cancer cells based on the targeting of DNA methyltransferase

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DNA methylation is involved in the regulation of gene expression and plays an important role in normal developmental processes and disease. In particular, the epigenetic landscape is altered in cancers where abnormal hypermethylation leads to silencing of certain genes such as tumor suppressor genes. In mammals, DNA methyltransferases are the enzymes responsible for DNA methylation on the position 5 of cytidine in a CpG context. Few direct enzyme inhibitors are known and those have several drawbacks. In order to identify novel inhibitors, we developed three chemical strategies. First a fluorescent High-Throughput Screening for the inhibition of the murine catalytic Dnmt3a/3L complex on the chemical library of the Muséum Naturelle d’Histoire Naturelle and found twelve hits with low micromolar activities. Two molecules efficiently reactivated YFP gene expression in a stable HEK293 cell line by promoter demethylation. Second, based on molecular modeling studies of quinoline inhibitor SGI1027 , we synthesized twenty-five new derivatives. Four compounds induced the reexpression of a reporter gene, controlled by a methylated CMV promoter, in leukemia KG-1 cells. Third, we carried out a modulation study of the non-nucleoside inhibitor N- Phthaloyl-L-tryptophan or RG108 . Two constrained compounds and two NPys derivatives were found at least 10-fold more potent than the reference compound. The cytotoxicity on the tumor DU145 cell line of the most potent inhibitors was correlated to their inhibitory potency. Finally, docking studies were conducted in order to understand their binding mode. The biological activity of the compounds was also addressed in solid and hematological cancer cells. Altogether, these studies provide insights for the design of the next-generation of DNMT inhibitors.

This talk is part of the Design and use of chemical tools to modulate gene expression in cancer cells based on the targeting of DNA methyltransferase series.

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