Side-Chain Engineering Guides the Design of β-Sheet Inhibitor to Anchor Protein-Protein Interaction Interfaces

Customizing inhibitors for β-sheet mediated protein-protein interactions (PPIs) remains a challenge in medicinal chemistry research. Directly separating β-sheet elements from the PPI interface as inhibitors represents a feasible strategy. Although useful, peptides derived from PPIs typically lose their natural secondary structure, resulting in low affinity. How to construct stable β-sheet inhibitors remains elusive, mainly due to the lack of reliable strategies to guide the design of β-sheet backbones. In this study, we propose an amino acid side-chain engineering strategy (AASE) to design of β-sheet inhibitors. Specifically, this strategy was based on the amino acid pairing (AAP) principle observed in the β-sheets of natural proteins, and further integrates the complementarity of various non-covalent interactions between β-strand side chains. When combined with high-throughput peptide screening technology, above strategy can generate structurally defined β-sheet inhibitors. We validated the physicochemical properties of the β-sheet structures obtained under the aforementioned strategy and prioritized the peptide EH. The β-sheet inhibitor formed by EH exhibits potent biological functions, enabling high-resolution imaging of tumors in the NIR window and guiding tumor resection. In addition, EH can inhibit tumor growth as a PD-1/PD-L1 checkpoint blockade. This strategy provides valuable guidance for the design of PPI inhibitors with β-sheet structures.