Multifunctional Scaffolds for Selective Protein-Protein Inhibition

Protein-protein interactions (PPIs) play an important role in numerous biological processes. Consequently, modulating PPIs is fundamental for understanding and manipulating mechanisms that govern many diseases. Among the wide range of topographies that PPIs display, the α-helix is the most common secondary structure in nature and thus represents a good generic template for inhibitor design.1 Some of the most relevant approaches in this field are the proteomimetic approach, which recapitulate the key binding residues of an α-helix on a non-peptidic scaffold; and the constrained peptides, which aim to reproduce the helical structure by stabilising a helical peptide. Both approaches have generated potent inhibitors of a great diversity of α-helix mediated PPIs. However, developing a better understanding of the key features that govern the modulation of protein recognition is necessary to further advance the field and fully exploit each class of foldamer. In that context, we developed functionalised aromatic oligoamide backbones to mimic residues located on multiple faces of an -helix to target the ER/co-activator PPI. The novel scaffolds are based on bis-benzamide and N-(4-aminophenyl)terephthalamidic acid backbones functionalised with isobutyl groups to reproduce the key side chains of the co-activator α-helix. Conformational studies in combination with molecular modeling and docking analysis provide evidence that the new oligomers can adopt conformations that mimic the residues at i, i+3 and i+4 positions of the native co-activator α-helix. In addition, the rules that govern molecular recognition of protein surfaces were further investigated through the optimisation of the oligobenzamide hybrid scaffold using a structure-activity relationship (SAR) study. A library of compound analogues has been synthesised incorporating five variable sites. The modifications focused on size, polarity and stereochemistry to obtain more potent and selective proteomimetic inhibitors of the p53/hDM2 and Mcl-1/NOXA B PPIs. Finally, using existing methodologies a 3-O-alkylated proteomimetic scaffold and hydrocarbon stapling peptide strategy, have been used to design inhibitors of the Asf1/H3 interaction. The application of both approaches allowed the different inhibitor designs to be directly compared when targeting the same PPI.