Discovery of D-Miniprotein Inhibitors of PD-1/PD-L1 Interaction via Mirror-Image Phage Display against Synthetic D-PD-1

Abstract

As a member of the immune checkpoint, PD-1 is acknowledged as a key player in immune regulation and a hot target for cancer immunotherapy. The broad and flat binding interface of PD-1 to PD-L1 poses a challenge to non-antibody inhibitor discovery. In this work, through mirror-image phage display, we developed the first d-miniprotein inhibitor of PD-1/PD-L1 interaction, ^DPDI-49, with nanomolar affinity to PD-1 and single-digit micromolar EC50 in a cell-based inhibition assay. The binding mode between ^DPDI-49 and PD-1 was studied by NMR and MD simulations. For comparison, we screened several commercial and in-house short peptide libraries against synthetic d-PD-1. The failure in identifying a hit structure with inhibition activity using those libraries underpins the superiority of the well-folded miniprotein library in PPI inhibitor development for challenging protein targets.