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

Abstract 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.