The Quantification of Drug Accumulation within Gram-Negative Bacteria

Intrabacterial drug accumulation, mediated by the bacterial permeability barrier, efflux, and intrabacterial drug metabolism, is of general significance to the interaction between small molecules and bacteria. For example, the ability of a small molecule to accumulate within a bacterium influences its ability to serve as a chemical probe of an intracellular protein target and/or its efficacy as an antibacterial drug discovery entity. A general method to quantitatively interrogate both intrabacterial drug accumulation and metabolism (IBDM) is presented for Gram-negative bacteria and exemplified with Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa in both single-compound and high-throughput formats. The liquid chromatography–mass spectrometry-based platform does not depend on drug labeling, and its utility is highlighted through the exploration of the relationship between drug accumulation and drug minimum inhibitory concentration (MIC) for both wild-type and efflux-deficient strains of E. coli and K. pneumoniae clinical and laboratory strains of varying degrees of drug resistance. Furthermore, an investigation of drug synergy implicates the selective enhancement of the accumulation of one drug by its partner therapy. Finally, a high-throughput format is validated and deployed, which provides a readily adaptable approach to screening assays. We anticipate the further applications of this platform to both the translational and the fundamental studies of the interactions of small molecules with bacteria.