Peptide Tethering: Pocket-Directed Fragment Screening for Peptidomimetic Inhibitor Discovery

Constrained peptides have proven to be a rich source of ligands for protein surfaces, but are often limited in their binding potency. Deployment of nonnatural side chains that access unoccupied crevices on the receptor surface offers a potential avenue to enhance binding affinity. We recently described a computational approach to create topographic maps of protein surfaces to guide the design of nonnatural side chains [J. Am. Chem. Soc. 2017, 139, 15560]. The computational method, AlphaSpace, was used to predict peptide ligands for the KIX domain of the p300/CBP coactivator. KIX has been the subject of numerous ligand discovery strategies, but potent inhibitors of its interaction with transcription factors remain difficult to access. Although the computational approach provided a significant enhancement in the binding affinity of the peptide, fine-tuning of nonnatural side chains required an experimental screening method. Here we implement a peptide-tethering strategy to screen fragments as nonnatural side chains on conformationally defined peptides. The combined computational-experimental approach offers a general framework for optimizing peptidomimetics as inhibitors of protein-protein interactions.

Automated summary

Constrained peptides are a valuable source of ligands for protein surfaces, but their binding affinity is often limited. This study proposes the use of nonnatural side chains to enhance binding affinity by accessing unoccupied crevices on the receptor surface. The computational method, AlphaSpace, was used to predict peptide ligands for the KIX domain of the p300/CBP coactivator, and experimental screening was performed to fine-tune the nonnatural side chains. The combined computational-experimental approach offers a general framework for optimizing peptidomimetics as inhibitors of protein-protein interactions.