Analysis of Orthogonal Efflux and Permeation Properties of Compounds Leads to the Discovery of New Efflux Pump Inhibitors

Optimization of compound permeation into Gram-negative
bacteria
is one of the most challenging tasks in the development of antibacterial
agents. Two permeability barriersthe passive diffusion barrier
of the outer membrane (OM) and active drug effluxact synergistically
to protect cells from the antibacterial action of compounds. In Escherichia coli (E. coli) and relatives, these two barriers sieve compounds based on different
physicochemical properties that are defined by their interactions
with OM porins and efflux pumps, respectively. In this study, we critically
tested the hypothesis that the best substrates and inhibitors of efflux
pumps are compounds that can effectively permeate the OM and are available
at relatively high concentrations in the periplasm. For this purpose,
we filtered a large subset of the ZINC15 database of commercially
available compounds for compounds containing a primary amine, a chemical
feature known to facilitate the uptake through E. coli general porins. The assembled library was screened by ensemble docking
to AcrA, the periplasmic component of the AcrAB-TolC efflux pump,
followed by experimental testing of the top predicted binders for
antibacterial activities, efflux recognition, and inhibition. We found
that the filtered primary amine library is a rich source of compounds
with efflux-inhibiting activities and identified efflux pump inhibitors
with novel chemical scaffolds effective against E.
coli AcrAB-TolC and efflux pumps of multidrug-resistant
clinical isolates of Acinetobacter baumannii. However, primary amines are not required for the recognition of
compounds by efflux pumps and their efflux-inhibitory activities.