Discovery of Inhibitors of the Lipopolysaccharide Transporter MsbA: From a Screening Hit to Potent Wild-Type Gram-Negative Activity

The
dramatic increase in the prevalence of multi-drug resistant
Gram-negative bacterial infections and the simultaneous lack of new
classes of antibiotics is projected to result in approximately 10
million deaths per year by 2050. We report on efforts to target the
Gram-negative ATP-binding cassette (ABC) transporter MsbA, an essential
inner membrane protein that transports lipopolysaccharide from the
inner leaflet to the periplasmic face of the inner membrane. We demonstrate
the improvement of a high throughput screening hit into compounds
with on-target single digit micromolar (μM) minimum inhibitory
concentrations against wild-type uropathogenic Escherichia
coli, Klebsiella pneumoniae, and Enterobacter cloacae. A 2.98
Å resolution X-ray crystal structure of MsbA complexed with an
inhibitor revealed a novel mechanism for inhibition of an ABC transporter.
The identification of a fully encapsulated membrane binding site in
Gram-negative bacteria led to unique physicochemical property requirements
for wild-type activity.