DNA-encoded chemical library-based identification of novel inhibitors targeting the essential LpxH enzyme in Gram-negative bacteria

<jats:p>LpxH is a key enzyme in the lipid A biosynthesis pathway and a promising target for the development of new antibiotics against Gram-negative pathogens. We report the discovery and optimization of two structurally distinct LpxH inhibitor series discovered through DNA-encoded chemical library (DECL) screening. Our DECL affinity selections identified a known sulfonyl piperazine class (Series 1), and a novel biphenyl-pyrimidine scaffold (Series 2) that represented a new chemical starting point for LpxH inhibitor development. To overcome liabilities, like poor solubility and low potency, a structure-based drug design approach was used for downstream hit expansion. Optimization of Series 1 yielded compound 14, which achieved wild-type activity against E. coli. Optimization of Series 2 led to compounds 21 and 24, displaying a MIC of 16 µg/mL against efflux-defective and hyperpermeable E. coli and a MIC of 8 µg/mL against efflux-defective E. coli respectively. Target engagement was confirmed via bacterial genetic sensitization experiments, demonstrating a LpxH-mediated mechanism of action.</jats:p>