Structure of the deacetylase LpxC bound to the antibiotic CHIR-090: Time-dependent inhibition and specificity in ligand binding.
The UDP-3-O-(R-3-hydroxyacyl)-N-acetylglucosamine deacetylase LpxC is an essential enzyme of lipid A biosynthesis in Gram-negative bacteria and a promising antibiotic target. CHIR-090, the most potent LpxC inhibitor discovered to date, displays two-step time-dependent inhibition and kills a wide range of Gram-negative pathogens as effectively as ciprofloxacin or tobramycin. In this study, we report the solution structure of the LpxC-CHIR-090 complex. CHIR-090 exploits conserved features of LpxC that are critical for catalysis, including the hydrophobic passage and essential active-site residues. CHIR-090 is adjacent to, but does not occupy, the UDP-binding pocket of LpxC, suggesting that a fragment-based approach may facilitate further optimization of LpxC inhibitors. Additionally, we identified key residues in the Insert II hydrophobic passage that modulate time-dependent inhibition and CHIR-090 resistance. CHIR-090 shares a similar, although previously unrecognized, chemical scaffold with other small-molecule antibiotics such as L-161,240 targeting LpxC, and provides a template for understanding the binding mode of these inhibitors. Consistent with this model, we provide evidence that L-161,240 also occupies the hydrophobic passage.
Barb
Adam W
AW
Department of Biochemistry, Duke University Medical Center, Durham NC 27710.
Jiang
Ling
L
Raetz
Christian R H
CR
Zhou
Pei
P
D000114:Acetylene / Q000737:chemistry; D000115:Acetylesterase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001713:Biphenyl Compounds / Q000737:chemistry; D002384:Catalysis; D017124:Conserved Sequence; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D006877:Hydroxamic Acids / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009025:Morpholines / Q000737:chemistry; D009154:Mutation / Q000235:genetics; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D013379:Substrate Specificity; D013912:Threonine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D013997:Time Factors
D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D001713:Biphenyl Compounds; C525369:CHIR 090; D004791:Enzyme Inhibitors; D006877:Hydroxamic Acids; D008024:Ligands; D009025:Morpholines; D013912:Threonine; C037574:morpholine; D000115:Acetylesterase; D000114:Acetylene