Structurally constrained peptides as protein-protein interaction modulators

A limited number of drug targets can be exploited by conventional drug-like compounds as the vast majority of disease-associated targets are involved in protein-protein interactions (PPI). PPI targets possess binding surfaces that lack a well-defined hydrophobic pocket amenable for binding to small drug-like compounds. A new class of therapeutics that has shown great potential at modulating PPI are macrocyclic peptides, particularly for their ability to bind to large and topologically complex protein surfaces as well as their potential to access intracellular targets. However, the efficiency of macrocyclic peptides at mediating PPIs and permeating cell membranes is conformation dependent. Here, I describe the role of peptide conformation on target recognition using three clinically relevant PPI targets: the Kelch like ECH Associated Protein-1 (KEAP1), (Chapter Two and Chapter Three); the RET receptor tyrosine kinase (Chapter Four); and β-catenin (Chapter Five). Guided by published X-ray crystal structures, peptides derived from PPI epitopes were designed and structurally constrained to mimic the conformation of the natural PPI recognition motif. In Chapter Two, I report the development of a cyclic heptapeptide derived from the transcription factor Nuclear Factor (Erythroid-derived 2)-Like 2 (Nrf2) with similar affinity for KEAP1 as native Nrf2 through conformational optimization of a linear Nrf2-derived heptapeptide. Efforts to improve the potency and physicochemical properties of the cyclic heptapeptide are discussed in Chapter Three. In Chapter Four, I describe the design of dimeric peptides as tool compounds to investigate the mechanism by which the interaction between glial cell-line derived neurotrophic factor family ligands (GFLs) and GPI-linked co-receptors, GFRα, induce RET signaling. These peptides were derived from the β-sheet regions of GFLs, GDNF and ART, that interact with GFRα1 and GFRα3, respectively. Peptide cyclization and the introduction of a β-turn promoting motif yielded GFL mimetic peptides with stronger affinity for GFRα. Lastly, Chapter Five focuses on exploring the scope of i, i+4 carbamate and amino-staples as a novel peptide stapling system to stabilize α-helical peptides. An axin-derived α-helical peptide that disrupts the β-catenin/TCF4 interaction was used as a model to determine the effect of peptide α-helical stabilization on binding affinity for β-catenin.2023-07-07T00:00:00