Covalent modification of a glutamic acid inspired by HaloTag technology

For targeted covalent protein modification at low-reactivity aspartates and glutamates, new methods are in high demand. We report a technique inspired by the HaloTag technology, which employs nucleophilic substitution at chloroalkane-functionalised ligands by a specific aspartate residue. Embedding of alkyl bromide warheads into non-covalent inhibitors enables covalent modification of a glutamate in the lipoprotein binding chaperone - phosphodiesterase of retinal rod subunit delta (PDEδ), which shuttles prenylated lipoproteins between cellular membranes and thereby mediates their activity. Its hydrophobic ligand-binding pocket contains p.E88 as the only accessible nucleophile for covalent targeting. We show that a covalent inhibitor, termed DeltaTag, overcomes limitations of non-covalent inhibitors. DeltaTag labels PDEδ at its p.E88 under biologically relevant conditions, modulates mammalian target of rapamycin (mTOR) signalling by disrupting the PDEδ-Rheb (Ras homologue enriched in brain)-mTORC1 (mTOR complex 1) axis and inhibits cancer cell proliferation. This proof-of-concept study demonstrates that the design strategy holds promise for the covalent modification of proteins with lipophilic binding sites that lack accessible reactive amino acids but contain specific carboxylates.