Application of Dynamic Combinatorial Chemistry to Identify New Compounds that Bind G-Quadruplex DNA & Probing the Role of the Cation-π Interaction Between the HP1 Chromodomain and Methylated Lysine Using Unnatural Amino Acids

Abstract

This dissertation discusses two different projects. The first project involves the development of cyclic-peptide acridine conjugates in the effort to identify molecules that can selectively bind to and stabilize G-quadruplex DNA. The second project seeks to probe the role of the cation-π interaction in the binding of the HP1 chromodomain to trimethylated lysine 9 of histone 3 (H3). In recent years, interest in the G-quadruplex DNA structure has increased enormously due to the unique physical properties of this secondary DNA structure as well as the presence of guanine-rich sequences in biologically functional regions of many genomes. Given the propensity of G-quadruplex structures to control many biological functions, it has become desirable to identify small molecules that can bind to and stabilize G-quadruplexes. This work aims to develop quadruplex ligands that exhibit selectively over not only duplex DNA but also over various quadruplex sequences. It was believed that cyclic peptides could deliver selectivity for the quadruplex structure over duplex DNA while also providing the added advantages of mimicking native protein structure, displaying enhanced metabolic stability and possessing structural preorganization. Using a strategy that has been developed in our lab, we propose screening libraries of cyclic peptides generated in situ using thiol-thioester exchange for dynamic combinatorial chemistry (DCC). These libraries can efficiently be screen against different quadruplex sequences as well as duplex DNA in order to determine the selectivity of each species. In the second project, we sought to characterize the noncovalent interactions responsible for the recognition of trimethylated lysine 9 of histone 3 by the aromatic pocket of the HP1 chromodomain. Lysine can exist in three distinct methylation states under the control of highly specific methyl transferases or demethylases. These methylation states serve to turn on specific protein-protein interactions with partners that specifically recognize the methylated side chain. Recognition and affinity is mainly derived from cation-π interactions between the positively charged cationic side chain and the electron rich π surfaces of nearby aromatic rings. This interaction can be quantified by incorporation of fluorinated derivatives of the aromatic amino acids responsible for the binding of H3K9Me3 to the HP1 chromodomain. The cation-π interaction between the aromatic pocket of the HP1 chromodomain and H3K9Me3 can be revealed by incorporation of a series of fluorinated amino acid analogues. A linear correlation between binding affinity and the calculated magnitude of the cation-pi interaction of those groups indicates a cation-π interaction. Because many reader proteins for methylated lysine have an aromatic cage in their binding pockets, findings from the investigation of the HP1 chromodomain will provide broad insight into this class of proteins.Doctor of Philosoph