Enhancing De Novo Designed Peptides and Proteins via Irreversible Covalent Isoquinolinium Capture

Abstract

Irreversible covalent inhibitors have garnered significant attention in recent years. Despite encouraging progress, the vast majority contain electrophiles that target the least abundant amino acid cysteine, substantially limiting target inhibitor design for therapeutic intervention. Here, we generalize 2-ethynylbenzaldehyde as a proximity-induced electrophile for generating irreversible covalent peptide and protein inhibitors that specifically target native lysine residues. Leveraging this warhead, we design a covalent de novo peptide that potently engages MCL1 to block its interaction with Bak. We show it is faster, more selective, and increases potency 61-fold for MCL1 relative to a sulfonyl fluoride warhead. Additionally, with the guide of a computational script to predict ‘reactive hotspots’ at the protein level, we develop a minibinder that labels PD-L1 in vitro and in live cells, displays a slower off-rate, and potently blocks the native PD-1 and PD-L1. These results establish isoquinolinium capture as a promising strategy to inhibit protein-protein interactions and for the development of novel covalent peptide and protein therapeutics.