Discovering potent inhibitors against the beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Helicobacter pylori: structure-based design, synthesis, bioassay, and crystal structure determination

J Med Chem. 2009 Apr 23;52(8):2465-81. doi: 10.1021/jm8015602.


The discovery of HpFabZ inhibitors is now of special interest in the treatment of various gastric diseases. In this work, three series of derivatives (compounds 3, 4, and 5) were designed, synthesized, and their biological activities were investigated as potential HpFabZ inhibitors in a two phased manner. First, we designed and synthesized two series of derivatives (3a-r and 4a-u) and evaluated the enzyme-based assay against HpFabZ. Five compounds (3i-k, 3m, and 3q) showed potential inhibitory activity, with IC(50) values less than 2 muM. Second, a focused combinatorial library containing 280 molecules was designed employing the LD1.0 program. Twelve compounds (5a-l) were selected and synthesized. The activity of the most potent compound 5h (IC(50) = 0.86 muM) was 46 times higher than that of the hit 1. The high hit rate and the potency of the new HpFabZ inhibitors demonstrated the efficiency of the strategy for the focused library design and virtual screening.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crystallography, X-Ray
  • Helicobacter pylori / drug effects
  • Helicobacter pylori / enzymology*
  • Hydrazines / chemical synthesis*
  • Hydrazines / chemistry
  • Hydrazines / pharmacology
  • Hydro-Lyases / antagonists & inhibitors*
  • Hydro-Lyases / chemistry
  • Microbial Sensitivity Tests
  • Models, Molecular
  • Resorcinols / chemical synthesis*
  • Resorcinols / chemistry
  • Resorcinols / pharmacology
  • Solubility
  • Structure-Activity Relationship


  • 3-hydroxynaphthalene-2-carboxylic acid (3,5-dibromo-2,4-dihydroxy-benzylidene)hydrazide
  • Hydrazines
  • Resorcinols
  • Hydro-Lyases
  • beta-hydroxyacyl-(acyl-carrier-protein)dehydrase

Associated data

  • PDB/2GLL
  • PDB/3DOY
  • PDB/3DOZ
  • PDB/3DP0
  • PDB/3DP1
  • PDB/3DP2
  • PDB/3DP3