Biosensor-guided discovery of peptide inhibitors targeting the ribosomal protein uS5-PDCD2 chaperone interaction

Programmed cell death 2 (PDCD2) is an evolutionarily conserved protein essential for cell viability from yeast to humans. PDCD2 functions as a dedicated chaperone to the 40S ribosomal protein uS5, and loss of PDCD2 function impairs ribosome biogenesis. As cancer cells require a substantial supply of ribosomes to maintain elevated levels of protein synthesis, targeting the protein interaction interface between PDCD2 and uS5 is a promising modality to mitigate ribosome biogenesis. In this study, we used affinity purification assays and structural modeling to identify a stretch of 30 amino acids in the N-terminal region of uS5 that is necessary and sufficient for interaction with PDCD2. Our data also identified a conserved FxxGFG motif in uS5 that is important for association with PDCD2 via hydrophobic interactions. Notably, we developed a sensitive complementation-based biosensor that can monitor PDCD2-uS5 interaction in cell extracts and living human cells. Using this biosensor, we identified an 11-amino acid uS5-derived peptide that inhibits the PDCD2-uS5 interaction and impairs cancer cell viability. Such peptides provide a starting point in the development of peptidomimetic inhibitors capable of modulating ribosome biogenesis via disruption of ribosomal protein-dedicated chaperone complexes.