Targeting a Glutamic Acid in PDEδ with Fluoromethyl-Aryl Electrophiles Impairs K‑Ras Signaling

For targeted covalent
modification at low-reactivity carboxylates
with biocompatible electrophiles, new approaches are in high demand.
Engineering of the HaloTag protein facilitates such a covalent reaction
between chloroalkanes and an aspartate residue. We demonstrate that
conversely, engineering stable ligands can also enable covalent targeting
of an acid residue in a protein binding site. Using the chaperone
PDEδ, which shuttles lipidated oncoproteins and thereby mediates
their signaling activity, we show that equipping noncovalent inhibitors
with a benzyl fluoride-based electrophile leads to covalent modification
of a specific glutamate p.E88 in the ligand binding site. The best
inhibitor, Deltafluorine, embodies a 3-fluoromethyl-pyridyl group
and is stable to nucleophiles like glutathione, phosphate, acetate,
and citrate. In cells, Deltafluorine combines noncovalent and covalent
reactivity to demonstrate distinct cellular profiles and inhibits
signaling through the MAP-kinase and Akt-mTOR pathways. In an autochthonous
mouse model of highly aggressive KrasG12D-driven lung adenocarcinoma,
Deltafluorine treatment significantly reduces tumor volume.