Identification of highly selective covalent inhibitors by phage display

Covalent inhibitors with high selectivity are rapidly identified by phage display. Molecules that covalently bind macromolecular targets have found widespread applications as activity-based probes and as irreversibly binding drugs. However, the general reactivity of the electrophiles needed for covalent bond formation makes control of selectivity difficult. There is currently no rapid, unbiased screening method to identify new classes of covalent inhibitors from highly diverse pools of candidate molecules. Here we describe a phage display method to directly screen for ligands that bind to protein targets through covalent bond formation. This approach makes use of a reactive linker to form cyclic peptides on the phage surface while simultaneously introducing an electrophilic 'warhead' to covalently react with a nucleophile on the target. Using this approach, we identified cyclic peptides that irreversibly inhibited a cysteine protease and a serine hydrolase with nanomolar potency and exceptional specificity. This approach should enable rapid, unbiased screening to identify new classes of highly selective covalent inhibitors for diverse molecular targets.

Automated summary

A phage display method was developed to screen for covalent inhibitors that bind to protein targets by introducing a reactive linker to form cyclic peptides and an electrophilic 'warhead' to react with target nucleophiles. This approach identified cyclic peptides that irreversibly inhibited cysteine protease and serine hydrolase with high specificity and potency. It enables rapid, unbiased screening to identify new classes of highly selective covalent inhibitors for diverse molecular targets.