General Platform for Systematic Quantitative Evaluation of Small-Molecule Permeability in Bacteria

The
chemical features that impact small-molecule permeability across
bacterial membranes are poorly understood, and the resulting lack
of tools to predict permeability presents a major obstacle to the
discovery and development of novel antibiotics. Antibacterials are
known to have vastly different structural and physicochemical properties
compared to nonantiinfective drugs, as illustrated herein by principal
component analysis (PCA). To understand how these properties influence
bacterial permeability, we have developed a systematic approach to
evaluate the penetration of diverse compounds into bacteria with distinct
cellular envelopes. Intracellular compound accumulation is quantitated
using LC-MS/MS, then PCA and Pearson pairwise correlations are used
to identify structural and physicochemical parameters that correlate
with accumulation. An initial study using 10 sulfonyladenosines in Escherichia coli, Bacillus subtilis, and Mycobacterium smegmatis has identified nonobvious correlations
between chemical structure and permeability that differ among the
various bacteria. Effects of cotreatment with efflux pump inhibitors
were also investigated. This sets the stage for use of this platform
in larger prospective analyses of diverse chemotypes to identify global
relationships between chemical structure and bacterial permeability
that would enable the development of predictive tools to accelerate
antibiotic drug discovery.