Development of Antimicrobial Peptidomimetics

Abstract

Peptoids (oligomers of N-substituted glycines, NSGs) represent a class of peptidomimetics that offers notable advantages over peptides, including proteolytic stability and enhanced biological function, all while maintaining the capability to target the intricate landscape of protein-protein interactions. This thesis aimed to establish links between peptoid structure, physical properties, and antimicrobial efficacy while minimising toxicity to mammalian cells. Novel peptoid frameworks were developed to expand the chemical diversity with therapeutic promise, including long peptoid chains and macrocycles.
Chapter 1 introduces peptoids and focuses on their secondary structures, pharmacokinetics, and their biological properties. It also summarises peptoid limitations such as unfavourable hydrophobicities and amide bond heterogeneity.
In Chapter 2, a library of dodecamer peptoids incorporating fluorinated alkyl, 31 and 32, and cationic quaternary ammonium peptoid (49 – 51) building blocks. The biological evaluation of this library unveiled that the incorporation of these monomers led to peptoids showcasing the highest SI values reported thus far for clinically relevant pathogens, including E. coli and S. aureus. Notably, Pep. 27 and Pep. 31 exhibited SI values of 16 and 32, respectively, for these two species. It was further observed that the inclusion of tertiary cationic ammonium monomers decreased peptoid cytotoxicity.
Chapter 3 focused on the design and synthesis of polar tyrosine-type peptoid monomers, outlining the synthetic strategies employed in their development. Detailed discussions include the determination of amide bond geometry through NMR and X-ray crystallography. The incorporation of hydrogen bond donors in the ortho position of the hydroxy(aryl) moiety of 104 (NoTyr) resulted in hydrogen bonding between the hydroxyl and the backbone Oi-1, yielding a Kcis/trans value of 8.70 in CD3CN and thereby inducing α-helical peptoid structures. Surprisingly, the o-amino(aryl)-containing acetamide 170 exhibited a full cisoid amide bond population, attributed to hydrogen bonding between the ortho amino substituent and the Oi-1.
The tyrosine-type and amino(aryl) monomers were employed in peptoid synthesis in Chapter 4, wherein eight nonamer peptoids were synthesised and their biological activities against Gram-positive and gram-negative bacteria were assessed. In addition, the partition coefficients between octanol and water were evaluated for these peptoids and revealed that increasing the number of hydroxyl groups decreased peptoid partitioning into octanol. Pep. 54 containing the cis inducing 104 monomer showed the highest SI values for E. coli (SI of 16), S. aureus (SI of 64) and B. subilitis (SI of 64) whilst being non-toxic.
Finally, development of a novel TFP-based peptoid cyclisation method is discussed in Chapter 5. This method explores the employment of NTyr and NLys residues in the formation of cyclic peptoid structures. Furthermore, the methodology was extended to the formation of cyclic peptides. Pep. 93 displayed significant efficacies against Gram-positive bacteria with its MIC and ED50 values indicating potential therapeutic applications for TFP-stapled structures (S. aureus MIC of 12.5 μM; B. subtilis MIC of μM 3.13 μM; HepG2 ED50 of 100 μM).
Partitioning experiments were carried out for all the linear and cyclic peptoids studied in this thesis. Peptoids with log D values close to 0 exhibited the highest efficacy against pathogens, whilst reducing peptoid hydrophobicity correlates with decreased toxicity.