Chemical Building Blocks and Models for Studying Peptides

Chemical building blocks and models can serve as useful tools and surrogates for mimicking peptides in a biological system. In the following chapters of my thesis, I introduce two noncanonical amino acid building blocks that I have synthesized for incorporation into peptides and evaluate their secondary structure formation or biological activity (chapter 1 and chapter 3). I will also describe the use of chemical models derived from the β-amyloid peptide Aβ to investigate and probe the chiral selectivity in β-sheet assembly in aqueous solution (chapter 2). These three chapters of my thesis represent my passion for organic synthesis and NMR spectroscopy, and are linked by a theme of using building blocks and models to investigate peptide folding, assembly, and activity.Chapter 1 describes the design, synthesis, and evaluation of an improved turn structure for inducing β-hairpin formation in peptides. This project builds upon a previous finding from our laboratory that δ-linked-ornithine (δOrn) can be used as suitable turn unit for stabilizing macrocyclic β-sheet peptides. Development of β-turn units as peptidomimetic tools are important for stabilizing the secondary structure of peptides and have led to the design of biomaterials and potential biomedical therapeutics. Chapter 1 details the development and characterization of γ-methylornithine — a methylated version of δOrn — and shows its propensity to induce a β-hairpin conformation in comparison to the established turn, D-Pro-Gly. The utility provided by this improved turn structure will add to the existing toolbox of ways to create stabilized macrocyclic β-sheet peptides.Chapter 2 seeks to answer a basic question: do enantiomeric β-sheet peptides prefer to self-assemble to form pleated β-sheets or co-assemble to form rippled β-sheets? In the past decade, a theory has emerged that enantiomeric β-sheets prefer to co-assemble in a heterochiral fashion to form rippled β-sheets. Our laboratory has previously found that enantiomeric β-sheet pentapeptides strongly prefer to self-assemble. To address this discrepancy, equimolar amounts of L- and D-chemical model peptides derived from Aβ were mixed and studied by solution-phase NMR spectroscopy. These NMR spectroscopic studies reveal that β-sheet peptide models derived from Aβ prefer to self-assemble in a homochiral fashion in aqueous solution. Chapter 2 ends with concluding remarks about our interpretation of the different forces that drive the formation of heterochiral rippled β-sheets vs. homochiral pleated β-sheets.Chapter 3 is an ongoing collaborative project with members of the lab, on the synthesis and stereochemical determination of Novo29, a new Gram-positive peptide antibiotic discovered by Novobiotic Pharmaceuticals. Novo29 is an 8-residue peptide that contains a noncanonical hydroxyasparagine amino acid at position 5; the stereochemistry of this amino acid is undetermined. Chapter 3 begins with the syntheses of two diastereomers of hydroxyasparagine containing either the R,R or the R,S stereochemistry at the α- and β-positions. Incorporation of the hydroxyasparagine amino acids into peptides enabled the stereochemical determination of the natural Novo29 through NMR spectroscopic studies and functional correlation assays. At the end of chapter 3, a 1.13 Å X-ray crystallographic structure of the synthetic peptide containing the R,S stereochemistry is presented and discussed in further detail. Future directions for this project will aim to generate a molecular model of the peptide containing R,R stereochemistry in order to provide an explanation into the potential mechanism of action of the natural Novo29 antibiotic