Modulating Protein-Protein Interactions Through Peptidomimetics Utilizing Thioether Oxidation States, Noncovalent Interactions & Epigenetic Regulation

Abstract

Interactions among proteins play a fundamental role in regulating all biological processes. Such interactions that dictate disease progression are viable regions to target with chemical probes and inhibitors. With an array of interacting sites that vary in size, polarity, and structure, these intransigent chemical targets have been termed undruggable due to the difficulties to target; however, advancements in the area of chemical biology now allow for exploration and progress of this formidable territory. With an estimated 650,000 protein-protein interactions (PPIs) found in the human interactome, probes that can target such interactions are highly sought after due to their significance in disease suppression. In Chapter 2, we explore the importance of a new non-covalent interaction between aromatic π-systems and sulfoxide moieties that contribute to binding energy. With an enrichment of aromatic amino acids at protein interfaces, the utility of this interaction can be exploited at protein interaction sites. We further probe protein interfaces in Chapter 3 by incorporating oxidizable thioether-bridged -helical peptidomimetics. These probes modulate the polarity, structure, stability, affinity, and permeability, thereby allowing the mimetics to disrupt native PPIs. We utilized a specific Protein Observed 19F (PrOF) NMR technique to monitor crosslinked peptide affinity, as well as circular dichroism, tryptic digests, HPLC, fluorescence microscopy, fluorescence polarization, and computational calculations to evaluate biophysical characteristics. We further probe perfluorinated sulfone crosslinks in collaboration with Ratimir Derda in Chapter 3 for interactions with human serum albumin. By using two different methods to incorporate thioether crosslinks, either with an SN2 dibromoalkylation or a thiol-ene reaction as discussed in Chapter 4, we can alter the oxidation states of either one or two sulfur groups within the macrocycle. Chapter 5 is an assessment of a histone variant, H2A.Z for specific acetylation patterns to interact with certain bromodomains, BPTF and PfGCN5. Using PrOF NMR, a ligand observed NMR technique CPMG, and photo-crosslinking, we identify from of a series of various acetylation patterns, that H2A.Z Ack4,11 shows the highest affinity towards the bromodomain BPTF. We further investigate a different bromodomain, CBP in collaboration with Stuart Conway for interactions with five previously identified small molecules. Using PrOF NMR, and fluorescence polarization, we identify affinity towards three bromodomains: CBP, Brd4 and BrdT.