Characterization of small-molecule accumulation trends and novel antibiotics in Gram-negative bacteria

Novel antibiotics are urgently needed to combat multidrug resistant Gram-negative bacterial infections. A major challenge in antibiotic development is that the impermeable outer membrane of Gram-negative bacteria precludes the intracellular accumulation of many potential antibiotics, and an improved understanding of what physicochemical properties promote compound accumulation would be beneficial. A recent unbiased study of compound accumulation in Escherichia coli led to the development of predictive guidelines for accumulation, called the eNTRy rules, which suggest that primary amine-containing compounds that meet specific shape parameters are most likely to accumulate in E. coli. The eNTRy rules have proved to be generalizable in some additional Gram-negative species, but the opportunistic pathogen Pseudomonas aeruginosa is particularly impermeable, and requires the development of species-specific accumulation guidelines. With the goal of developing predictive guidelines for small-molecule accumulation in P. aeruginosa, here we evaluate 345 diverse compounds for accumulation in P. aeruginosa. It was identified that while an amphiphilic molecule containing a sterically accessible primary amine was more likely to accumulate in P. aeruginosa, the eNTRy rules were not predictive. Instead, structure-activity relationships and computational analyses revealed that hydrogen bond donor surface area and positive charge descriptors were much more predictive and were generalizable across different strains of P. aeruginosa. Further mode of uptake studies demonstrated the importance of porin-independent compound uptake. Application of these findings led to the discovery of a fusidic acid derivative with good antipseudomonal activity. Even with the development of the eNTRy rules, there is much to be learned about accumulation in Gram-negative bacteria. Further work has been performed using novel Gram-negative antibiotics to understand why amines accumulate to a greater extent, rates of compound uptake, and the role that compound localization plays in antibiotic activity. Enantioselective compound uptake and efflux in E. coli has also been evaluated. We anticipate that this work will aid in the discovery and development of antibiotics active against P. aeruginosa, while also improving our understanding of the mechanistic underpinnings of compound accumulation.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Chemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2022

Author dc:creator

• Geddes, Emily Jane

Contributors dc:contributor

• Hergenrother, Paul J
• Mitchell, Douglas A
• Metcalf, William W
• Chan, Jefferson

• Gram-negative bacteria
• accumulation
• antibiotics

Statement dc:rights

• Copyright 2022 Emily Geddes

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/115688

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F115688