Discovery and characterization of orally bioavailable 4-chloro-6-fluoroisophthalamides as covalent PPARG inverse-agonists

PPAR gamma (PPARG) is a ligand-activated transcription factor pivotal in regulating genes involved in inflammation, bone biology, lipid homeostasis, and adipogenesis, and it is implicated as a potential driver in luminal bladder cancer. PPARG agonists activate canonical target genes, whereas inverse agonists exert an opposite effect by inducing a repressive transcriptional complex that suppresses canonical target gene expression. Despite extensive research on agonists, inverse agonists represent an underexplored approach to modulate PPARG biology in vivo. Currently available inverse agonists have limitations in vivo. Here, we report the discovery and characterization of a series of orally bioavailable 4-chloro-6-fluoroisophthalamides as covalent PPARG inverse agonists, namely BAY-5516, BAY-5094, and BAY-9683.

Structural studies of this series identified distinct pre- and post-covalent binding positions. It was hypothesized that interactions in the pre-covalent conformation primarily drive affinity, while interactions in the post-covalent state enhance PPARG interactions with corepressors, exerting cellular functional effects. The challenge of optimizing for two distinct states may explain the observed steep structure-activity relationship (SAR). These compounds exhibit exquisite selectivity over related nuclear receptors within the subfamily, achieved partly through a covalent warhead with low reactivity via an SNAr mechanism and specific binding to a reactive cysteine in the PPARG LBD.

In vivo, BAY-5516, BAY-5094, and BAY-9683 regulate PPARG target gene expression comparably to the known inverse agonist SR10221. These findings introduce new tools for future studies investigating their potential therapeutic utility in disorders associated with hyperactivated PPARG, including luminal bladder cancer and other conditions.