Using nature as a starting point for the development of novel antimicrobial agents

Marriott, Christopher (2022) Using nature as a starting point for the development of novel antimicrobial agents. Doctoral thesis, University of East Anglia.

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Abstract

Antimicrobial resistance has caused an unprecedented need for the discovery of novel antimicrobial agents, especially those which are capable of acting against Gram-negative bacteria where strains have begun to emerge which have resistance pathways to all known antimicrobials. This can be achieved, broadly, by two means; either a new target, and hence a new class of antimicrobials, can be discovered and assessed, or by targeting an existing antimicrobial target but in such a way as to circumvent resistance. This project aimed to explore both means of overcoming resistance pathways, using two distinct targets.

Firstly, we investigated the inhibition of DNA gyrase, a topoisomerase enzyme found uniquely in bacteria which is essential for DNA replication. Using simocyclinone D8 (SD8), a natural product inhibitor of DNA gyrase that is not used therapeutically due to its poor in vivo activity, as a starting point, the work aimed to generate “pseudo-natural products” which were capable of emulating the activity of SD8 whilst being more readily synthetically prepared. Herein we illustrate an in silico fragment-based approach to the design of these mimics, with the selection of five angucyclinone-replacing alkyne fragments and five aminocoumarin-replacing amine fragments.

Secondly, a series of SD8-alkyne hybrids and “pseudo-natural products” were generated and examined in supercoiling assays against DNA gyrase, as well as other topoisomerase targets of SD8. Whilst these compounds did not possess any inhibitory activity, this work has furthered our understanding of DNA gyrase, and has laid the groundwork for future studies.

Finally, we investigated the inhibition of an important protein-protein interaction within the β-barrel assembly machinery (BAM) complex, an essential bacterial protein complex responsible for the insertion and correct folding of transmembrane β-barrel proteins in Gram-negative bacteria, using peptide fragments of important binding regions of BamA. The work aimed to use the peptide-directed binding methodology described in previous studies to generate small-molecule peptidomimetics capable of binding to BamD and inhibiting the complex. However, despite moderate success with the generation of these peptides, differential scanning fluorimetry studies revealed that the peptides selected were inefficient binders of BamD.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Pharmacy
Depositing User:	Chris White
Date Deposited:	22 Aug 2022 08:47
Last Modified:	22 Aug 2022 08:47
URI:	https://ueaeprints.uea.ac.uk/id/eprint/87536
DOI:

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