Targeting Des1: Syntheses of ceramide analogues with a rigid scaffold, inhibitory assays, and AF2-assisted structural insights reveal PR280 as a potent inhibitor

Identifier:  TDX:4408

Handle: https://hdl.handle.net/20.500.11797/TDX4408

Authors:  Rivero Prieto, Pablo

Abstract:
Dihydroceramide desaturase 1 (Des1) catalyzes the formation of a C-C double bond in dihydroceramide to furnish ceramide. Inhibition of Des1 is related to cell cycle arrest and programmed cell death. The lack of the Des1 crystalline structure, as well as that of a close homologue, hampers the detailed understanding of its inhibition mechanism and difficult the design of new inhibitors, thus making Des1 a challenging target. Based on previous structure-activity studies, different ceramides containing rigid scaffolds were designed. The synthesis and evaluation of these compounds as Des1 inhibitors allowed the identification of PR280 as a better Des 1 inhibitor in vitro (IC50 = 0.7 µM) than GT11 and XM462, the current reference inhibitors. This cyclopropenone ceramide was obtained in a 6-step synthesis with a 24 % overall yield. The highly confident 3D structure of Des1, recently predicted by AlphaFold2, served as the basis for conducting docking studies of known Des1 inhibitors and the ceramide derivatives synthesized in this work. For this purpose, a complete holoprotein structure was previously constructed. This study has allowed a better knowledge of key ligand-enzyme interactions for Des1 inhibitory activity.