Characterization of LpxC inhibitors and resistant mutants

LpxC, the deacetylase that catalyzes the second and committed step of lipid A biosynthesis in E. coli, is an essential enzyme for virtually all Gram-negative bacteria and one of the most promising novel antibiotic targets for the treatment of multidrug-resistant Gram-negative infections. Here, we report the characterization of two novel LpxC inhibitors that have apparent binding affinities for E. coli LpxC in the picomolar range. Furthermore, these compounds display broad spectrum activity against a plethora of Gram-negative pathogens.

In anticipation for the advancement of LpxC inhibitors in clinical trials, we undertook studies to probe potential bacterial resistance mechanisms to these compounds. In this study, we report a two-step isolation of spontaneously resistant E. coli mutants that have > 200-fold resistance to LpxC inhibitors. These mutants have two chromosomal point mutations that account for resistance additively and independently: one in fabZ, a dehydrase in fatty acid biosynthesis, and the other in thrS, the Thr-tRNA ligase.

For both enzymes, the isolated mutations result in reduced enzymatic activities in vitro. Most unexpectedly, we observed a decreased level of LpxC in bacterial cells harboring fabZ mutations, suggesting that the biosyntheses of fatty acids and lipid A are tightly regulated to maintain balance between phospholipid and lipid A. Additionally, we show that the mutation in thrS slows protein production and cellular growth, providing the first example that reduced protein biosynthesis confers a suppressive effect on inhibition of membrane biosynthesis. Altogether, our studies reveal an impressive compensatory ability of bacteria to overcome inhibition of lipid A biosynthesis by rebalancing cellular homeostasis, a unique mechanism of antibiotic resistance.