Structure-based inhibitor discovery of Helicobacter pylori dehydroquinate synthase

Biochemical and Biophysical Research Communications

Volumn 373, Issue 1, 2008, Pages 1-7

  Liu, Jai Shin ^a   Cheng, Wen Chi ^a   Wang, Hung Jung ^a   Chen, Yen Cheng ^a   Wang, Wen Ching ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

Dehydroquinate synthase; Docking; Helicobacter pylori; Inhibitors; Shikimate pathway

Indexed keywords

BACTERIAL ENZYME; CARBAPHOSPHONATE; DEHYDROQUINATE SYNTHASE; DEHYDROQUINATE SYNTHASE INHIBITOR; ENZYME INHIBITOR; HTS 11955; NICOTINAMIDE ADENINE DINUCLEOTIDE; RH 00573; SYNTHETASE;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG IDENTIFICATION; DRUG SCREENING; DRUG STRUCTURE; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME CONFORMATION; ENZYME STRUCTURE; HELICOBACTER PYLORI; IC 50; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN;

AMINO ACID SEQUENCE; ANTI-BACTERIAL AGENTS; BINDING SITES; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ENZYME INHIBITORS; HELICOBACTER PYLORI; MICROBIAL SENSITIVITY TESTS; MOLECULAR SEQUENCE DATA; NAD; PHOSPHORUS-OXYGEN LYASES; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; STRUCTURE-ACTIVITY RELATIONSHIP;

FUNGI; HELICOBACTER PYLORI; MAMMALIA;

EID: 45849136334     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2008.05.070     Document Type: Article

References (32)

1. Warren J.R. Unidentified curved bacilli on gastric epithelium in active chronic gastritis. Lancet 1 (1983) 1273
2. Marshall B. Helicobacter pylori: 20 years on. Clin. Med. 2 (2002) 147-152
3. Lind T., Veldhuyzen van Zanten S., Unge P., Spiller R., Bayerdorffer E., O'Morain C., Bardhan K.D., Bradette M., Chiba N., Wrangstadh M., Cederberg C., and Idstrom J.P. Eradication of Helicobacter pylori using one-week triple therapies combining omeprazole with two antimicrobials: the MACH I Study. Helicobacter 1 (1996) 138-144
4. Graham D.Y. Antibiotic resistance in Helicobacter pylori: implications for therapy. Gastroenterology 115 (1998) 1272-1277
5. Shorr A.F. Epidemiology of staphylococcal resistance. Clin. Infect. Dis. 45 Suppl. 3 (2007) S171-S176
6. Haselbeck R., Wall D., Jiang B., Ketela T., Zyskind J., Bussey H., Foulkes J.G., and Roemer T. Comprehensive essential gene identification as a platform for novel anti-infective drug discovery. Curr. Pharm. Des. 8 (2002) 1155-1172
7. Steinrucken H.C., and Amrhein N. The herbicide glyphosate is a potent inhibitor of 5-enolpyruvyl-shikimic acid-3-phosphate synthase. Biochem. Biophys. Res. Commun. 94 (1980) 1207-1212
8. Gunel-Ozcan A., Brown K.A., Allen A.G., and Maskell D.J. Salmonella typhimurium aroB mutants are attentuated in BALB/c mice. Microb. Pathog. 23 (1997) 311-316
9. Carpenter E.P., Hawkins A.R., Frost J.W., and Brown K.A. Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis. Nature 394 (1998) 299-302
10. Nichols C.E., Ren J., Lamb H.K., Hawkins A.R., and Stammers D.K. Ligand-induced conformational changes and a mechanism for domain closure in Aspergillus nidulans dehydroquinate synthase. J. Mol. Biol. 327 (2003) 129-144
11. Nichols C.E., Ren J., Leslie K., Dhaliwal B., Lockyer M., Charles I., Hawkins A.R., and Stammers D.K. Comparison of ligand-induced conformational changes domain closure mechanisms, between prokaryotic and eukaryotic dehydroquinate synthases. J. Mol. Biol. 343 (2004) 533-546
12. Sugahara M., Nodake Y., Sugahara M., and Kunishima N. Crystal structure of dehydroquinate synthase from Thermus thermophilus HB8 showing functional importance of the dimeric state. Proteins 58 (2005) 249-252
13. Chen C.C., Liao C.C., and Hsu W.H. The cloning and nucleotide sequence of a Corynebacterium glutamicum 3-deoxy-d-arabinoheptulosonate-7-phosphate synthase gene. FEMS Microbiol. Lett. 107 (1993) 223-229
14. Mehdi S., Frost J.W., and Knowles J.R. Dehydroquinate synthase from Escherichia coli, and its substrate 3-deoxy-d-arabino-heptulosonic acid 7-phosphate. Methods Enzymol. 142 (1987) 306-314
15. 2+-dependent. Biochem. J. 226 (1985) 817-829
16. Noble M., Sinha Y., Kolupaev A., Demin O., Earnshaw D., Tobin F., West J., Martin J.D., Qiu C., Liu W.S., DeWolf Jr. W.E., Tew D., and Goryanin I.I. The kinetic model of the shikimate pathway as a tool to optimize enzyme assays for high-throughput screening. Biotechnol. Bioeng. 95 (2006) 560-573
17. Srinivasan P.R., and Sprinson D.B. 2-Keto-3-deoxy-d-arabo-heptonic acid 7-phosphate synthetase. J. Biol. Chem. 234 (1959) 716-722
18. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
19. Navaza J. AMoRE: an automated package for molecular replacement. Acta Crystallogr. A 50 (1994) 157-163
20. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53 (1997) 240-255
21. Lamzin V., and Wilson K.S. Automated refinement of protein models. Acta Crystallogr. D49 (1993) 127-147
22. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47 (1991) 110-119
23. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 (1993) 283-291
24. Gouet P., Courcelle E., Stuart D.I., and Metoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15 (1999) 305-308
25. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
26. Sali A., and Blundell T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234 (1993) 779-815
27. Raghuraman A., Mosier P.D., and Desai U.R. Finding a needle in a haystack: development of a combinatorial virtual screening approach for identifying high specificity heparin/heparan sulfate sequence(s). J. Med. Chem. 49 (2006) 3553-3562
28. Luthy R., Bowie J.U., and Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 356 (1992) 83-85
29. Melo F., Devos D., Depiereux E., and Feytmans E. ANOLEA: a www server to assess protein structures. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5 (1997) 187-190
30. Bahar I., Atilgan A.R., and Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des. 2 (1997) 173-181
31. Chiu W.C., You J.Y., Liu J.S., Hsu S.K., Hsu W.H., Shih C.H., Hwang J.K., and Wang W.C. Structure-stability-activity relationship in covalently cross-linked N-carbamoyl d-amino acid amidohydrolase and N-acylamino acid racemase. J. Mol. Biol. 359 (2006) 741-753
32. Montchamp J.-L., and Frost J.W. Cyclohexenyl and cyclohexylidene inhibitors of 3-dehydroquinate synthase: active site interactions relevant to enzyme mechanism and inhibitor design. J. Am. Chem. Soc. 119 (1997) 7645-7653