Identification of Loop Mediated Protein-Protein Interactions and Design of Cyclic Peptide Locked Loop Inhibitors
Siegert, Timothy.
2017-04-19T18:08:14.939Z
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Abstract: The landscape of drug discovery has recently begun to shift from traditionally druggable enzymes to protein-protein interactions (PPIs). Enzymes possess well defined active sites, while PPIs often have large and flat surface areas that small molecules can not interrupt. As this landscape shifts, it is essential that the tools used to target these proteins change to meet these demands. On... read moree class of molecules particularly adept at binding proteins are peptides. While rational design of substrate transition state mimics as inhibitors has led to successful targeting of enzymes, an analogous approach for rational design PPI inhibitors using peptides is a difficult task. The identification of hot spot residues at protein interfaces has enabled the characterization of essential amino acid residues at protein interfaces amenable to targeting or mimicry using peptides. Much previous work on this subject has used computational approaches to identify epitopes on proteins that facilitate PPIs containing either well-defined secondary structure, such as α-helices and β-sheets or have disregarded any structural information searching for purely extended linear regions. This thesis work describes LoopFinder, a computational tool developed to identify loops and turns at protein interfaces for design and development of synthetic cyclic peptide inhibitors of PPIs. This program was used to identify a hot loop residing on the protein stonin2 at its interface with Eps15, a complex essential for clathrin-mediated endocytosis. The hot loop was used to inspire the development of a cyclic peptide "locked loop library". Libraries were prepared using a panel of bis-bromomethy-aryl linkers for bis-alkylation of cysteine residues introduced to flank the hot loop. Using this approach, we were able to identify sub-micromolar binding peptides to the Eps15-EH2. This peptide was then used to develop a novel biochemical assay for Eps15 binding molecules enabling the search for new inhibitors of endocytosis.
Thesis (Ph.D.)--Tufts University, 2016.
Submitted to the Dept. of Chemistry.
Advisor: Joshua Kritzer.
Committee: David Walt, Krishna Kumar, and Adrian Whitty.
Keyword: Chemistry.read less - ID:
- 76537c86n
- Component ID:
- tufts:21305
- To Cite:
- DCA Citation Guide EndNote
