Investigations into foldameric inhibitors of protein-protein interactions: Studies of the Bcl-2 family of proteins and vascular endothelial growth factor

Protein-protein interactions govern most cellular processes, from intercellular communication to programmed cell death. Understanding how proteins recognize one another and developing inhibitors with both high affinity and specificity for their protein targets have been challenges in the field. In this thesis, I describe efforts to make progress in both areas. I investigated interactions within the Bcl-2 family of proteins through mutations to Bcl-xL in the BH3 binding cleft (A142L, V126L, and A93F). These Bcl-xL mutants were used to probe the binding location of a previously identified alpha/beta+alpha chimeric peptide, which contains both alpha- and beta-amino acid residues (a beta-amino acid has an additional carbon unit between the amine and carbonyl groups relative to an alpha-amino acid). Additionally, I have shown that cyclic beta-residue incorporation in Bim-derived alpha/beta-peptides can be helpful for promoting a helical structure and affinity for Bcl-x L and Mcl-1. I have also worked toward identifying the first alpha/beta-peptide inhibitor of the VEGF-VEGFR interaction. I have developed the first fluorescence polarization assay that can be used to screen molecules for binding to VEGF at the VEGFR-binding site. We identified a novel beta-peptide, designed to mimic VEGFR-1 residues, that bound to VEGF with Ki∼50 muM, but optimization attempts were unsuccessful. We have made progress toward developing an alpha/beta-peptide based on v114, a cyclic peptide previously identified by Genentech researchers. Employing a combination of beta 3-residue and cyclic beta-residue modifications to v114 M10NIe appears to be a promising approach for developing alpha/beta-peptides with high affinity for VEGF.