Download MendeleyStructure-Based Discovery of a New LpxH-Targeted Chemotype with Activity against Klebsiella pneumoniae.
Zhang, G., Cochrane, C.S., Yang, B., Zhao, J., Jin, H., Wu, S., Zhou, P., Xia, J.(2026) J Med Chem 69: 6691-6705
- PubMed: 41784176 Search on PubMed
- DOI: https://doi.org/10.1021/acs.jmedchem.5c02939
- Primary Citation Related Structures:
9PAQ - PubMed Abstract:
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 ( Kp LpxH) inhibitor. Substructure searching and optimization yielded compound 7 , a potent inhibitor (IC 50 : 0.17 μM) with moderate antibacterial activity (MIC: 5.3 μg/mL). The crystal structure of the Kp LpxH-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.
- State Key Laboratory of Bioactive Substance and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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