The goal of the proposed research is to developed methods for the design of biologically active compounds based on a knowledge of the structure and conformation of oligopeptide ligands and protein binding sites. Five distinct systems will be explored through the synthesis, evaluation, and refinement of a series of peptide mimics. The compounds to be synthesized include: Inhibitors of alpha-Amylase: Tricyclic molecules incorporating tyrosine, arginine, and tryptophan sidechains of the key triad of amino acids of the amylase inhibitor tendamistat. Serine Protease Inhibitors: Macrocyclic mimics of the active loop of bovine pancreatic trypsin inhibitor, incorporating elements of residues 13-17, the lysine-15 side chain, and a reactive ketone in place of the scissile amide. This series of inhibitor mimics can be readily extended to other serine proteases. Alpha-Helix Mimics: A pair of bicyclic molecules containing three hydrogen bonding groups fixed in the orientation found within a peptide alpha-helix. These molecules will be appended to oligopeptides as their N- or C-terminal residues and evaluated for their ability to induce or stabilize the alpha-helical conformation. Thermolysin Inhibitors: Macrocyclic derivatives of high affinity phosphonate inhibitors which adopt a specific loop conformation in the active site of thermolysin. These compounds will be used to explore in a structurally verifiable manner the effect of conformational restriction on protein-ligand binding. Haloalkene Isosteres of the Peptide Bond: Dipeptide analogs in which the amide linkage is replaced with a fluorine- or chlorine- substituted double bond. Such analogs will be prepared for enkephalin, thyrotropin releasing hormone, aspartame, and as ground-state substrate analogs for peptidases. The synthetic methodology will also be adapted for the stereospecific synthesis of ketomethylene dipeptide isoteres. In addition to direct evaluation of the ability of the above compounds to exert their intended biochemcial or biophysical effect, collaborative studies will be undertaken to determine their solution structure through 2-D NMR or their bound conformation through X-ray crystallography, where appropriate.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Method to Extend Research in Time (MERIT) Award (R37)
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University of California Berkeley
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