mRNA display selection of a high-affinity, Bcl-X_L-specific binding peptide

Bcl-X_L, an antiapoptotic member of the Bcl-2 family, is a mitochondrial protein that inhibits activation of Bax and Bak, which commit the cell to apoptosis, and it therefore represents a potential target for drug discovery. Peptides have potential as therapeutic molecules because they can be designed to engage a larger portion of the target protein with higher specificity. In the present study, we selected 16-mer peptides that interact with Bcl-X_L from random and degenerate peptide libraries using mRNA display. The selected peptides have sequence similarity with the Bcl-2 family BH3 domains, and one of them has higher affinity (IC₅₀=0.9 μM) than Bak BH3 (IC₅₀=11.8 μM) for Bcl-X_L in vitro. We also found that GFP fusions of the selected peptides specifically interact with Bcl-X_L, localize in mitochondria, and induce cell death. Further, a chimeric molecule, in which the BH3 domain of Bak protein was replaced with a selected peptide, retained the ability to bind specifically to Bcl-X _L. These results demonstrate that this selected peptide specifically antagonizes the function of Bcl-X_L and overcomes the effects of Bcl-X_L in intact cells. We suggest that mRNA display is a powerful technique to identify peptide inhibitors with high affinity and specificity for disease-related proteins.