PD-L1 inhibitors, including macrocyclic peptide pAC65, converge on the same CC'FG β-sheet face

Targeting protein-protein interactions (PPIs) with large, flat interfaces, such as the programmed cell death protein-1 (PD-1)/programmed death ligand-1 (PD-L1) immune checkpoint, is notoriously challenging. This interaction is mediated by an extended β-sheet surface that lacks deep, druggable pockets. Despite this difficulty, PD-L1 has been successfully inhibited by diverse modalities, including antibodies, macrocyclic peptides, and small molecules, driving significant advancements in cancer immunotherapy. Understanding how these distinct inhibitors achieve their effect is crucial for next-generation drug design.

Researchers conducted a comparative, structure-driven analysis of PD-L1 complexes deposited in the Protein Data Bank. This involved visualizing and quantitatively comparing interface overlap, hotspot conservation, and buried surface area. The analysis encompassed various inhibitory modalities, including clinically tested antibodies, macrocyclic peptides (e.g., pAC65), and biphenyl small molecules, to identify common structural principles underlying their inhibitory mechanisms.

The analysis revealed a striking structural convergence among all effective PD-L1 inhibitors: they consistently engage the same CC'FG β-sheet face of PD-L1. While the target epitope is conserved, the mechanisms of neutralization differ significantly across modalities. Antibodies directly occlude this critical surface, preventing PD-1 binding. Macrocyclic peptides, such as pAC65, achieve antibody-like surface coverage through a compact and preorganized scaffold.

Biphenyl small molecules neutralize the same CC'FG epitope indirectly by inducing PD-L1 homodimerization, effectively sequestering the binding site. This unified structural framework highlights that despite employing fundamentally different mechanisms, diverse inhibitors converge on the same functional hotspot region.