Synthesis and translation of novel gram-negative antibacterial agents

Pathogenic bacteria have been, and always will be, a scourge to mankind. Efforts to develop new drugs have been traditionally stymied by a lack of understanding about what properties are correlated with enhanced permeation into bacteria, with gram-negatives especially being a problem due to their characteristic dual membrane. This dissertation describes the use of general permeation guidelines for enhancing small molecule accumulation in gram-negative bacteria to inform the discovery and advancement of new drugs. Here, these rules have been applied to three separate antibiotic scaffolds—acrylamide-linked naphthyridinones (FabI inhibitors), phenyl-thiazolylurea-sulfonamides (phenylalanyl-tRNA synthetase inhibitors), and 2,4-diaminopyrimidines (dihydrofolate reductase inhibitors). The acrylamide-linked naphthyridinones campaign has been successful, culminating in the discovery of fabimycin which has broad spectrum activity versus problematic clinical pathogens while sparing healthy gut microbes. The phenyl-thiazolylurea-sulfonamides were largely unsuccessful in achieving wild-type gram-negative activity; however, they largely accumulate to a higher extent, reinforcing the predictive power of the permeation guidelines. Dozens of 2,4-diaminopyrimidines analogues were prepared and tested versus P. aeruginosa, enabling a basic structure-activity-relationship to be established. Combination testing with new permeation-enhanced sulfonamide drugs––another antifolate antibiotic––have led to cell culture synergy in wild-type P. aeruginosa with single-digit µg/mL concentrations. Furthermore, they have been found to be very well-tolerated orally, inviting further experimentation to flesh out other dosing regiments and pharmacokinetic studies to enable in-vivo efficacy. Aside from implementing general permeation guidelines, this dissertation describes the synthetic scale-up and in-vivo testing of a promising fusidic acid analogue, dubbed FA-Oxane. It was found to possess notable activity versus Mycobacterium tuberculosis (Mtb) in cell culture, as well as an improved pharmacokinetic profile in mice. A new synthetic route was devised to synthesize multi-gram levels of the drug to enable a preliminary in-vivo efficacy model in collaboration with the Bill and Melinda Gates Foundation. While the initial results were inconclusive, using the drug in combination with another established Mtb drug could drastically improve efficacy.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Chemistry

Grantor

University of Illinois Urbana-Champaign

Year dc:date

2025

Author dc:creator

• Cain, Brett Nelson

Contributors dc:contributor

• Hergenrother, Paul J
• White, M Christina
• Lau, Gee
• Silverman, Scott K

• Antibacterials
• gram-negative

Statement dc:rights

• Copyright 2025 Brett Nelson Cain

Language dc:language

en

Handle dc:identifier

https://hdl.handle.net/2142/132749

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/132749