Structure-based design of a phosphotyrosine-masked covalent ligand targeting the E3 ligase SOCS2

The Src homology 2 (SH2) domain recognises phosphotyrosine (pY) post translational modifications in partner proteins to trigger downstream signalling. Drug discovery efforts targeting the SH2 domains have long been stymied by the poor drug-like properties of phosphate and its mimetics. Here, we have used structure-based design to target the SH2 domain of the E3 ligase suppressor of cytokine signalling 2 (SOCS2). Starting from the highly ligand-efficient pY amino acid, a fragment growing approach led to a serendipitous observation of covalent modification of Cys111 in a co-crystal structure, which we leveraged to rationally design a cysteine-directed electrophilic covalent inhibitor MN551. We developed the prodrug MN714 containing a pivaloyloxymethyl (POM) protecting group and evidence its cell permeability and capping group unmasking using cellular target engagement and in cell 19F NMR spectroscopy. Covalent engagement and modification of Cys111 of cellular SOCS2 was confirmed using mass spectrometry. The qualified covalent inhibitors of SOCS2 could find attractive applications as chemical probes to understand the biology of SOCS2 and its CRL5 complex, and as covalent E3 ligase handles in proteolysis targeting chimera (PROTACs) to induce targeted protein degradation.