Structure-Based Discovery of a New LpxH-Targeted Chemotype with Activity against Klebsiella pneumoniae

Gram-negative
pathogens are difficult to treat because their outer
membrane, enriched with lipid A–anchored lipopolysaccharide,
serves as a protective barrier to many antibiotics. LpxH, an essential
dimanganese hydrolase in lipid A biosynthesis, represents a promising
antimicrobial target, but its distinct L-shaped binding pocket has
limited inhibitor development, with only the sulfonylpiperazine chemotype
reported to date. To broaden the chemical space, we developed a multistage
virtual screening workflow combining HipHop-based pharmacophore modeling,
ROCS-based query matching, and FRED docking. This pipeline identified F523-0608, an acetylpiperazine-containing compound, as a moderate Klebsiella pneumoniae LpxH (KpLpxH)
inhibitor. Substructure searching and optimization yielded compound 7, a potent inhibitor (IC50: 0.17 μM) with
moderate antibacterial activity (MIC: 5.3 μg/mL). The crystal
structure of the KpLpxH–compound 7 complex revealed its binding mode, validating virtual screening
analysis. These studies establish acetylpiperazine derivatives as
a new class of LpxH inhibitors and provide a foundation for future
antibiotic development.