Structure-Based Optimization of a Series of Covalent, Cell Active Bfl‑1 Inhibitors

Bfl-1, a member of the Bcl-2 family of proteins, plays
a crucial
role in apoptosis regulation and has been implicated in cancer cell
survival and resistance to venetoclax therapy. Due to the unique cysteine
residue in the BH3 binding site, the development of covalent inhibitors
targeting Bfl-1 represents a promising strategy for cancer treatment.
Herein, the optimization of a covalent cellular tool from a lead-like
hit using structure based design is described. Informed by a reversible
X-ray fragment screen, the strategy to establish interactions with
a key glutamic acid residue (Glu78) and optimize binding in a cryptic
pocket led to a 1000-fold improvement in biochemical potency without
increasing reactivity of the warhead. Compound (R,R,S)-26 has a kinact/KI of 4600 M–1 s–1, shows <1 μM caspase activation in
a cellular assay and cellular target engagement, and has good physicochemical
properties and a promising in vivo profile.