Thesis (Ph.D.) - University of Queensland, 2003. / Includes bibliography.

Peptides are short, sequence and length specific oligomers composed of small amino acid residues. Nature has refined these peptide sequences and their endogenous function through evolution. In addition, peptides have played an important role in medicine, which has lead to further research into developing peptides as lead pharmaceuticals (therapeutic peptides). Unfortunately, therapeutic peptides are inferior as drug candidates due to their low oral bioavailability; immunogenicity and potential to be attacked by peptidases. Fortunately, peptides can be modified by steric constraints, cyclization, and/or replacement of the peptide backbone itself creating a mimic (peptidomimetic) of the original peptide. Peptidomimetics are deliberately designed to have increased protease resistance, reduced immunogenicity and improved bioavailability when compared to the original endogenous peptide. One such peptide, Magainin is a O One such peptide, Magainin is a well-studied, a-helical peptide found in African clawed frogs. This peptide has antibiotic properties (against pathogenic bacteria), which partly arises from the hydrophilic portion of the peptide having basic amino acid side chains periodically disposed on one side of the a-helix. This property of magainin causes its attraction to negatively charged bacteria cell membranes. Unfortunately, as in the case of other antibiotics, pathogenic bacteria have developed effective countermeasures against magainin. We designed a peptidomimetic based on magainin and implemented a plan to determine what type of molecules could be assembled for a magainin mimic. We successfully utilized molecular modeling (Monte Carlo conformational search), as well as results from previous experiments to elucidate what type of molecules, as well as how many molecules would be necessary to create a novel helical-like magainin peptidomimetic. It was discovered that C2 symmetric diamines would be best at generating the helical-like motif and the amino acid lysine to generate the basic side chain. The next step was the successful connection of two C2 symmetric molecules via a urea linkage and then one more connection to a lysine (a-amino group) residue, creating a short sequence of oligoureas (trimers). Finally, attempts to connect the oligoureas trimers were attempted using a solid-phase synthesis approach to generate a functional magainin mimic.

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Protein modification is an essential tool in Chemical Biology, allowing a functional biomolecule to be equipped with a small molecule tag or label. However, as proteins are constructed from a limited palette of around 20 canonical amino acids, achieving selective modification can be problematic. Previously reported methods for protein modification will be discussed in Chapter 1; these often rely on alteration of the protein sequence to introduce a uniquely reactive (often non-canonical) amino acid which may then be covalently modified in a bioorthogonal manner. An alternative approach is to identify a uniquely reactive site within the native protein sequence, such as the protein N-terminus or the reactive side chain of an amino acid with low frequency, and modify this using selective chemistry. In this project, modification of a native sequence protein was achieved by targeting a low abundance residue, tyrosine (Tyr), in a selective manner. Tyr was identified as the ideal candidate as it displays only ~3% frequency in the proteome and, due to its electron-rich aryl ring, it can be selectively modified by electrophilic aromatic substitution. Using a diazonium salt as the tuned electrophile, modification results in formation of an azobenzene motif which may be orthogonally cleaved under mild reducing conditions. The resulting cleavage product bears an o-aminophenol modification on the Tyr side chain, which can then be conjugated to a fluorescent label using established chemistry. This system has been developed on a solid-phase platform to give further control over the extent of modification achieved. In Chapter 2, the component parts of this method are developed through reactions performed in-solution on small molecule substrates. In Chapter 3, this work is then moved onto a solid-phase resin in order to 'catch-and-release' small molecule and peptide substrates. Finally in Chapter 4, the resin-based catch-and-release system is optimised for use in protein modification, and analysis of the modification site is explored.

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