Design and synthesis of peptide substrates as probes of structure activity relationship of biomolecules

This thesis describes the design and synthesis of peptides as tools for investigating the interaction of biomolecules with substrates. Chapter 1 gives a brief overview of some basic concepts of molecular recognition and defines relevant terminology.; In chapter 2, the Penn-Penn State catalytic antibody endeavor is discussed. The design and synthesis of substrates for antibody 16G3 resulted in the preparation and purification of linear hexapeptides containing p-nitrophenyl esters at the C-terminus and a free amino group (protected only as a salt) at the N-terminus. We have recently reported that the antibody ligase catalyzes the cyclization of hexapeptides without epimerization of the C-terminus amino acid.; Chapters 3 and 4 involved the design and synthesis of peptide ligands for two G-coupled protein receptors, in particular the neurokinin (NK) and opioid receptors, respectively. It had been discovered by former members of the research group that a β-D-glycoside designed to bind the somatostatin (SRIF) receptor as an agonist can also bind the NK-1 receptor, but as an antagonist. That the sugar scaffold can bind both SRIF and NK-1 receptors indicated that the two receptors have much in common in the way they bind ligands. This is supported by the fact that a c-hexapeptide which is a potent and specific agonist for the SRIF receptor can be readily converted Into a potent and specific NK-1 receptor antagonist.; Chapter 3 describes the extension of this approach from a cyclic hexapeptide, L-363,301 to a tetradecapeptide (SRIF) via the design and synthesis of three SRIF analogues. The conversion of the SRIF-14 scaffold, associated with agonism, to a neurokinin antagonist was achieved. Significantly, the switch from SRIF agonism to NK antagonism via one mutation of [D-Trp8]SRIF is uncommon since it demonstrates a complete change of function of a ligand and not merely an improvement in ligand selectivity.; Finally, it has been widely accepted that among the pharmacophores responsible for binding to the opioid receptor, a basic nitrogen is a requirement. Nevertheless, believing cyclic hexapeptides to be privileged scaffolds, five randomly selected peptides from the NK-1 program were assayed at the opioid receptor. Two of the five c-hexapeptides, one lacking a primary amino group and the other lacking both primary amino and phenolic hydroxyl groups, were shown to be δ opiate antagonists. Chapter 4 describes the design and synthesis of other cyclic hexapeptides in an effort to understand the interactions of the opioid receptor with cyclic hexapeptides.