Design, synthesis, and characterization of biomimetic oligomers

Peptides and proteins made from the 20 canonical amino acids are responsible for many processes necessary for organisms to function. Beside their composition, proteins obtain their activity and unique selectivity through an ability to display functionalities accurately in the three-dimensional space.

These properties are highly sought after in pharmaceutical agents, where the interest in this class of compounds is increasing. However, due to susceptibility to proteolytic degradation in cellular environments and often poor cell-penetrating properties, this class of compounds has traditionally been considered unsuitable for drug discovery.

Circumventing the inherent stability problems, non-natural peptide analogues have shown significant potential for the development of new materials and pharmacologically active ligands. Mimics of natural amino acids have received considerable attention, for their ability to mimic the structural elements seen in proteins.

Two prominent peptidomimetics are ß-peptides and a-peptoids (N-alkylglycines), which have been shown to fold into helical and sheet-like arrangements. To expand the chemical space available for mimicking protein structure their features have been combined to give the ß-peptoids, which has found use in biologically active compounds but has been sparsely studied with respect to folding propensity.

Thus, an aim of this Ph.D. project has been to investigate the effect of structural variations, including side chain substitution, introduction of thioamides, and trifluoroacetylation, on the cis-trans amide bond rotamer equilibria in monomer model systems. The latter systems revealed an increase in the preference for cis-amides as compared to their parent compounds and thus provide novel strategies for affecting the folding of peptoid constructs.

Using NMR spectroscopy, X-ray crystallographic analysis, and density functional theory (DFT) calculations, we found evidence for the presence of thioamide–aromatic interactions through Csp2-H···Samide hydrogen bonding. Based on these studies we designed a ß-peptoid oligomer from residues prone to fit a helical arrangement found by DFT calculations.

The designed oligomer indeed proved the existence of a ß-peptoid helical conformation by X-ray. Further studies of these compounds indicated a structured display in solution. These helices thus definitively show that the ß-peptoids should be considered a valid addition to the already existing ensemble of foldamer designs.

Sequences of alternating a-peptides and ß-peptoids, containing basic a-amino acid residues have been shown to possess antimicrobial activity. Using X-ray surface scattering techniques the interaction of two oligomers, containing different basic moieties, and model lipid membranes of Gram-positive and Gram-negative bacteria, respectively, were investigated.

We also synthesized fluorophore labeled analogues of the hybrid oligomers, which during a preliminary biological screening, showed cases of enhanced antimicrobial activity. The X-ray scattering studies confirmed earlier findings, showing that the guanidino-group binds more deeply into the membranes of Gram-positive bacteria, and that the nitrobenzoxadiazole-fluorophore enhanced this interaction.