Design and Synthesis of Selective Bifunctional Nucleoside-based TET Enzyme Inhibitors as Epigenetic Modulators
Epigenetic regulation is achieved by equilibrium between DNA methylation and demethylation which regulates gene expression, genome stability, and genomic imprinting. DNA methylation marks (5-methylcytosine, 5-mC) are primarily found on the CpG sites of gene promoter regions. Cytosine is converted to 5-mC via DNA methyltransferase (DNMT), while a family of ten-eleven translocation dioxygenases (TET) catalyze local demethylation per an Fe(II)/alpha-ketoglutarate-dependent oxidation cascade on the C-5 position of 5-mC. However, the epigenetic equilibrium between methylation and demethylation is disrupted in many diseases including cancer, autism, and inflammatory diseases such as asthma and COPD. To investigate the role of TET proteins in human disease, we have designed and synthesized TET-specific small molecule inhibitors. Structure-based design was used to construct bifunctional nucleoside-based TET inhibitors that bind to both the substrate and cofactor binding sites. In silico docking studies revealed that docking scaffolds containing uridine as the substrate mimic covalently linked to a linear hydroxamic acid as the cofactor mimic have inhibitory potential against TET. Current synthetic approaches of AB-48 and similar analogs ultimately lead to the covalent linkage of the substrate and cofactor warheads via the Sonogashira cross-coupling reaction. Finally, similar amide-containing compounds have been synthesized and were tested in vitro which were determined to have IC50 values of ~21 µM.