Phenotype-Directed Discovery of Antibacterials

With antibacterial resistance on the rise, there is an urgent need for new, effective, and safe antibiotics to be brought to clinic as quickly as possible. Although many antibiotics have been developed using conventional drug development approaches, these have their limitations, with drug attrition rates >95%. Activity-directed synthesis (ADS) is one technique developed to speed up early drug development and reduce the time invested in the development of inactive compounds. Catalytic reactions are harnessed, as they can form multiple different products from common substrates, and reactions are performed in a microscale format, with mixtures being screened, without purification, against the selected target.
This thesis initially shows how ADS, driven by a phenotypic assay, can be harnessed to expand the structure-activity relationships (SAR) of a class of antibacterials by designing, executing, and screening an array of 200 reactions based on Pd-catalysed carbonylation chemistry, without purification of individual products. LC-MS analysis of a random 10% of reaction wells confirmed significant conversion to bioactive products. Results show the discovery of new micromolar active antibacterial ligands based on a 4(3H)-quinazolinone core that possess antibacterial activity against multiple strains of S. aureus. Scale-up reactions were prioritised according to activity, and the structure of these products was elucidated. This approach therefore enabled rapid and efficient expansion of the SAR of antibacterials.
ADS was also utilised to aid in the discovery of novel antibacterial chemotypes. This was possible as arrays were designed with no known antibacterial fragments incorporated into them. Two arrays, with a total of 375 reactions based on Rh carbenoid chemistry were performed and mixtures were screened directly against S. aureus. After scale-up and purification, novel antibacterial compounds with micromolar activity were identified, confirming this approach could aid in antibacterial drug development. Active compounds were further assessed for both eukaryotic toxicity and activity against different bacterial strains to assess their use as an antibacterial. It was demonstrated that ADS also aided in the discovery of new chemosynthetic pathways to antibacterials. This project confirmed ADS has the potential to be of more general value in the discovery of new antibacterial classes.