Structure-Based Inhibitors Exhibit Differential Activities against Helicobacter pylori and Escherichia coli Undecaprenyl Pyrophosphate Synthases

Helicobacter pylori colonizes the human gastric epithelium and causes diseases such as gastritis, peptic ulcers, and stomach cancer. Undecaprenyl pyrophosphate synthase (UPPS), which catalyzes consecutive condensation reactions of farnesyl pyrophosphate with eight isopentenyl pyrophosphate to form lipid carrier for bacterial peptidoglycan biosynthesis, represents a potential target for developing new antibiotics. In this study, we solved the crystal structure of H. pylori UPPS and performed virtual screening of inhibitors from a library of 58,635 compounds. Two hits were found to exhibit differential activities against Helicobacter pylori and Escherichia coli UPPS, giving the possibility of developing antibiotics specially targeting pathogenic H. pylori without killing the intestinal E. coli.

[1]  S. Colowick,et al.  Methods in Enzymology , Vol , 1966 .

[2]  Fujii Hiroshi,et al.  Efficient enzymatic hydrolysis of polyprenyl pyrophosphates. , 1982, Biochimica et biophysica acta.

[3]  A. Brünger.  Assessment of phase accuracy by cross validation: the free R value. Methods and applications. , 1993, Acta crystallographica. Section D, Biological crystallography.

[4]  L. Yang,et al.  Effect of site-directed mutagenesis of the conserved aspartate and glutamate on E. coli undecaprenyl pyrophosphate synthase catalysis. , 2000, Biochemistry.

[5]  C. O'Morain,et al.  Treatment of Helicobacter pylori , 2005, Helicobacter.

[6]  A. H. Wang,et al.  Mechanism of Product Chain Length Determination and the Role of a Flexible Loop in Escherichia coliUndecaprenyl-pyrophosphate Synthase Catalysis* , 2001, The Journal of Biological Chemistry.

[7]  T. Koyama,et al.  Enzymatic Aspects of Isoprenoid Chain Elongation. , 1998, Chemical reviews.

[8]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[9]  Yang-Sheng Sun,et al.  Substrate and product specificities of cis-type undecaprenyl pyrophosphate synthase. , 2005, The Biochemical journal.

[10]  A. H. Wang,et al.  Catalytic Mechanism Revealed by the Crystal Structure of Undecaprenyl Pyrophosphate Synthase in Complex with Sulfate, Magnesium, and Triton* , 2003, Journal of Biological Chemistry.

[11]  T. Koyama,et al.  Molecular Cloning, Expression, and Purification of Undecaprenyl Diphosphate Synthase , 1998, The Journal of Biological Chemistry.

[12]  A. H. Wang,et al.  Structure, mechanism and function of prenyltransferases. , 2002, European journal of biochemistry.

[13]  T. Koyama,et al.  Efficient enzymatic hydrolysis of polyprenyl pyrophosphates. , 1982, Biochimica et biophysica acta.

[14]  C. A. Thomas,et al.  Molecular cloning. , 1977, Advances in pathobiology.

[15]  P. Malfertheiner,et al.  Identification and characterization of an ATPase system of Helicobacter pylori and the effect of proton pump inhibitors. , 1993, The American journal of gastroenterology.

[16]  P. Kroon,et al.  Isoprenyl diphosphate synthases: Protein sequence comparisons, a phylogenetic tree, and predictions of secondary structure , 1994, Protein science : a publication of the Protein Society.

[17]  M. Uschold,et al.  Methods and applications , 1953 .

[18]  E A Merritt,et al.  Raster3D Version 2.0. A program for photorealistic molecular graphics. , 1994, Acta crystallographica. Section D, Biological crystallography.

[19]  R. Macarrón,et al.  The Effect of Triton Concentration on the Activity of Undecaprenyl Pyrophosphate Synthase Inhibitors , 2003, Journal of biomolecular screening.

[20]  J. Vederas,et al.  Synthesis and biological activity of isopentenyl diphosphate analogues. , 2004, Bioorganic & medicinal chemistry.

[21]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[22]  C. M. Allen.  Purification and characterization of undecaprenylpyrophosphate synthetase. , 1985, Methods in enzymology.

[23]  A. H. Wang,et al.  Crystal Structures of Undecaprenyl Pyrophosphate Synthase in Complex with Magnesium, Isopentenyl Pyrophosphate, and Farnesyl Thiopyrophosphate , 2005, Journal of Biological Chemistry.

[24]  E. Oldfield,et al.  Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases , 2007, Proceedings of the National Academy of Sciences.

[25]  P. Chyou,et al.  Helicobacter pylori Infection and the Risk for Duodenal and Gastric Ulceration , 1994, Annals of Internal Medicine.

[26]  M. Fountoulakis,et al.  Use of Genomics To Identify Bacterial Undecaprenyl Pyrophosphate Synthetase: Cloning, Expression, and Characterization of the Essential uppS Gene , 1999, Journal of bacteriology.

[27]  T. Ko,et al.  Substrate binding mode and reaction mechanism of undecaprenyl pyrophosphate synthase deduced from crystallographic studies , 2004, Protein science : a publication of the Protein Society.

[28]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[29]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.