New covalent technologies for PPI targeting and for protein precipitation in cells
The ability to covalently bind a target protein enables many novel applications in chemical biology. I will describe two different stories leveraging covalent chemistry. Installing a covalent electrophile on a peptide or protein-based scaffold with an extended binding footprint enables the targeting of shallow protein surfaces, not typically addressable using small molecules. We report protein-based thio-methacrylate esters – electrophiles with a diverse reactivity profile that can be installed easily on unprotected peptides and proteins via cysteine side chains, and react efficiently and selectively with cysteine and lysine side chains on the target.
In a second project, we introduce a novel chemical knockdown approach for homomeric proteins, which constitute up to 20% of the human proteome. Our strategy, Polymerization-Inducing Chimeras (PINCHs), leverages the inherent symmetry of homomeric proteins to induce polymerization and intracellular precipitation without requiring accessory proteins or post-translational modifications. PINCHs are bifunctional molecules that bind two monomeric subunits of a multimeric protein, bridging separate multimers and forming insoluble polymers. We demonstrate efficient intracellular precipitation of Keap1 and BCL6 homodimers, as well as in vitro polymerization of LDHA (homotetramer) and NQO2 (homodimeric). This results in functional knockdown, distinct from mere inhibition.