Small-molecule inhibitors of the RNA m⁶A demethylase FTO potently support the survival of dopamine neurons

Abstract

The fat mass and obesity-associated protein (FTO), an RNA N6-methyladenosine (m6A) demethylase, is an important regulator of central nervous system development, neuronal signalling and disease. We present here the target-tailored development and biological characterization of small-molecule inhibitors of FTO. The active compounds were identified using high-throughput molecular docking and molecular dynamics screening of the ZINC compound library. In FTO binding and activity-inhibition assays the two best inhibitors demonstrated Kd = 185 nM; IC50 = 1.46 mkM (compound 2) and Kd = 337 nM; IC50 = 28.9 mkM (compound 3). Importantly, the treatment of mouse midbrain dopamine neurons with the compounds promoted cellular survival and rescued them from growth factor deprivation induced apoptosis already at nanomolar concentrations. Moreover, these inhibitors demonstrated good blood-brain-barrier penetration in the model system, 31.7% and 30.8%, respectively. The compounds 2 and 3 protected dopamine neurons with greater potency than our recently developed alkylation repair homolog protein 5 (AlkBH5) m6A demethylase inhibitors. Inhibition of m6A RNA demethylation by small-molecule drugs, as presented here, has therapeutic potential and provides tools for the identification of disease-modifying m6A RNAs in neurogenesis and neuroregeneration. Further refinement of the lead compounds identified in this study, can also lead to unprecedented breakthroughs in the treatment of neurodegenerative diseases.

Exploring the brain epitranscriptome: perspectives from the NSAS summit

“…Currently, several therapeutic strategies have been proposed involving m 6 A demethylase inhibitors for various diseases, including glioblastoma and neurodegenerative conditions (Selberg et al, 2021;Huff et al, 2022;You et al, 2022). However, due to the diverse effects of m 6 A modification on RNA metabolism, generally manipulating m 6 A levels could result in potential side effects.…”