Homology model of the DNA gyrase enzyme of Helicobacter pylori, a target of quinolone-based eradication therapy

Journal of Gastroenterology and Hepatology (Australia)

Volumn 25, Issue SUPPL. 1, 2010, Pages

  Matsuzaki, Juntaro ^a   Suzuki, Hidekazu ^a   Tsugawa, Hitoshi ^a   Nishizawa, Toshihiro ^a   Hibi, Toshifumi ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

DNA gyrase; Helicobacter pylori; Quinolones

Indexed keywords

DNA TOPOISOMERASE (ATP HYDROLYSING); QUINOLONE; ANTIINFECTIVE AGENT; ESCHERICHIA COLI PROTEIN; QUINOLONE DERIVATIVE;

CONFERENCE PAPER; DNA BINDING MOTIF; ERADICATION THERAPY; HELICOBACTER PYLORI; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; AMINO ACID SEQUENCE; ANTIBIOTIC RESISTANCE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; DRUG EFFECTS; ENZYMOLOGY; GENETICS; MUTATION; PROTEIN CONFORMATION; STRUCTURAL HOMOLOGY; STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; ANTI-BACTERIAL AGENTS; COMPUTER SIMULATION; DNA GYRASE; DRUG RESISTANCE, BACTERIAL; ESCHERICHIA COLI PROTEINS; HELICOBACTER PYLORI; MODELS, MOLECULAR; MUTATION; PROTEIN CONFORMATION; QUINOLONES; STRUCTURAL HOMOLOGY, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77951584716     PISSN: 08159319     EISSN: 14401746     Source Type: Journal    
DOI: 10.1111/j.1440-1746.2010.06245.x     Document Type: Conference Paper

References (45)

1. Suzuki H, Hibi T, Marshall BJ. Helicobacter pylori: present status and future prospects in Japan. J. Gastroenterol. 2007 42 : 1 15. (Pubitemid 46357245)
2. Amieva MR, El-Omar EM. Host-bacterial interactions in Helicobacter pylori infection. Gastroenterology 2008 134 : 306 323. (Pubitemid 350309334)
3. Correa P, Houghton J. Carcinogenesis of Helicobacter pylori. Gastroenterology 2007 133 : 659 672. (Pubitemid 47187360)
4. Shi R, Xu S, Zhang H et al. Prevalence and risk factors for Helicobacter pylori infection in Chinese populations. Helicobacter 2008 13 : 157 165. (Pubitemid 351347659)
5. Suzuki H, Iwasaki E, Hibi T. Helicobacter pylori and gastric cancer. Gastric Cancer 2009 12 : 79 87.
6. Kato M, Yamaoka Y, Kim JJ et al. Regional differences in metronidazole resistance and increasing clarithromycin resistance among Helicobacter pylori isolates from Japan. Antimicrob. Agents Chemother. 2000 44 : 2214 2216. (Pubitemid 30484458)
7. Osato MS, Reddy R, Graham DY. Metronidazole and clarithromycin resistance amongst Helicobacter pylori isolates from a large metropolitan hospital in the United States. Int. J. Antimicrob. Agents 1999 12 : 341 347. (Pubitemid 29397499)
8. Nishizawa T, Suzuki H, Umezawa A et al. Rapid detection of point mutations conferring resistance to fluoroquinolone in gyrA of Helicobacter pylori by allele-specific PCR. J. Clin. Microbiol. 2007 45 : 303 305. (Pubitemid 46272036)
9. Nishizawa T, Suzuki H, Nakagawa I, Iwasaki E, Masaoka T, Hibi T. Gatifloxacin-based triple therapy as a third-line regimen for Helicobacter pylori eradication. J. Gastroenterol. Hepatol. 2008 23 (Suppl. 2 S167 70.
10. Suzuki S, Suzuki H, Nishizawa T et al. Past rifampicin dosing determines rifabutin resistance of Helicobacter pylori. Digestion 2009 79 : 1 4.
11. Gisbert JP, Castro-Fernandez M, Bermejo F et al. Third-line rescue therapy with levofloxacin after two H. pylori treatment failures. Am. J. Gastroenterol. 2006 101 : 243 247. (Pubitemid 43381662)
12. Cianci R, Montalto M, Pandolfi F, Gasbarrini GB, Cammarota G. Third-line rescue therapy for Helicobacter pylori infection. World J. Gastroenterol. 2006 12 : 2313 2319.
13. Nishizawa T, Suzuki H, Hibi T. Quinolone-based third-line therapy for Helicobacter pylori eradication. J. Clin. Biochem. Nutr. 2009 44 : 119 124.
14. Sharara AI, Chaar HF, Aoun E, Abdul-Baki H, Araj GF, Kanj SS. Efficacy and safety of rabeprazole, amoxicillin, and gatifloxacin after treatment failure of initial Helicobacter pylori eradication. Helicobacter 2006 11 : 231 236. (Pubitemid 44051348)
15. Tanaka M, Isogai E, Isogai H et al. Synergic effect of quinolone antibacterial agents and proton pump inhibitors on Helicobacter pylori. J. Antimicrob. Chemother. 2002 49 : 1039 1040. (Pubitemid 34692903)
16. Shen LL, Kohlbrenner WE, Weigl D, Baranowski J. Mechanism of quinolone inhibition of DNA gyrase. Appearance of unique norfloxacin binding sites in enzyme-DNA complexes. J. Biol. Chem. 1989 264 : 2973 2978. (Pubitemid 19057797)
17. Reece RJ, Maxwell A. DNA gyrase: structure and function. Crit. Rev. Biochem. Mol. Biol. 1991 26 : 335 375. (Pubitemid 21892761)
18. Wang G, Wilson TJ, Jiang Q, Taylor DE. Spontaneous mutations that confer antibiotic resistance in Helicobacter pylori. Antimicrob. Agents Chemother. 2001 45 : 727 733. (Pubitemid 32182016)
19. Megraud F. Epidemiology and mechanism of antibiotic resistance in Helicobacter pylori. Gastroenterology 1998 115 : 1278 1282. (Pubitemid 28485621)
20. Moore RA, Beckthold B, Wong S, Kureishi A, Bryan LE. Nucleotide sequence of the gyrA gene and characterization of ciprofloxacin-resistant mutants of Helicobacter pylori. Antimicrob. Agents Chemother. 1995 39 : 107 111.
21. Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 2003 31 : 3381 3385. (Pubitemid 37442164)
22. Bordoli L, Kiefer F, Arnold K, Benkert P, Battey J, Schwede T. Protein structure homology modeling using SWISS-MODEL workspace. Nat. Protoc. 2009 4 : 1 13.
23. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modelling. Electrophoresis 1997 18 : 2714 2723. (Pubitemid 28059943)
24. Arnold K, Bordoli L, Kopp J, Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 2006 22 : 195 201. (Pubitemid 43205406)
25. Morais Cabral JH, Jackson AP, Smith CV, Shikotra N, Maxwell A, Liddington RC. Crystal structure of the breakage-reunion domain of DNA gyrase. Nature 1997 388 : 903 906. (Pubitemid 27377066)
26. Ruthenburg AJ, Graybosch DM, Huetsch JC, Verdine GL. A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. J. Biol. Chem. 2005 280 : 26177 26184.
27. Swanberg SL, Wang JC. Cloning and sequencing of the Escherichia coli gyrA gene coding for the A subunit of DNA gyrase. J. Mol. Biol. 1987 197 : 729 736.
28. Tankovic J, Lascols C, Sculo Q, Petit JC, Soussy CJ. Single and double mutations in gyrA but not in gyrB are associated with low- and high-level fluoroquinolone resistance in Helicobacter pylori. Antimicrob. Agents Chemother. 2003 47 : 3942 3944. (Pubitemid 37485011)
29. Glocker E, Kist M. Rapid detection of point mutations in the gyrA gene of Helicobacter pylori conferring resistance to ciprofloxacin by a fluorescence resonance energy transfer-based real-time PCR approach. J. Clin. Microbiol. 2004 42 : 2241 2246. (Pubitemid 38637854)
30. Nishizawa T, Suzuki H, Kurabayashi K et al. Gatifloxacin resistance and mutations in gyra after unsuccessful Helicobacter pylori eradication in Japan. Antimicrob. Agents Chemother. 2006 50 : 1538 1540.
31. Drlica K, Zhao X. DNA gyrase, topoisomerase IV, and the 4-quinolones. Microbiol. Mol. Biol. Rev. 1997 61 : 377 392. (Pubitemid 28090230)
32. Heisig P, Kratz B, Halle E et al. Identification of DNA gyrase A mutations in ciprofloxacin-resistant isolates of Salmonella typhimurium from men and cattle in Germany. Microb. Drug Resist. 1995 1 : 211 218.
33. Willmott CJ, Maxwell A. A single point mutation in the DNA gyrase A protein greatly reduces binding of fluoroquinolones to the gyrase-DNA complex. Antimicrob. Agents Chemother. 1993 37 : 126 127. (Pubitemid 23019183)
34. Williams NL, Maxwell A. Locking the DNA gate of DNA gyrase: investigating the effects on DNA cleavage and ATP hydrolysis. Biochemistry 1999 38 : 14157 14164. (Pubitemid 29513831)
35. Siegmund K, Maheshwary S, Narayanan S et al. Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. Nuclei. Acids Res. 2005 33 : 4838 4848. (Pubitemid 41418883)
36. Barnard FM, Maxwell A. Interaction between DNA gyrase and quinolones: effects of alanine mutations at GyrA subunit residues Ser(83) and Asp(87). Antimicrob. Agents Chemother. 2001 45 : 1994 2000. (Pubitemid 32591689)
37. Suzuki H, Nishizawa T, Muraoka H, Hibi T. Sitafloxacin and garenoxacin may overcome the antibiotic resistance of Helicobacter pylori with gyrA mutation. Antimicrob. Agents Chemother. 2009 53 : 1720 1721.
38. Akasaka T, Kurosaka S, Uchida Y, Tanaka M, Sato K, Hayakawa I. Antibacterial activities and inhibitory effects of sitafloxacin (DU-6859a) and its optical isomers against type II topoisomerases. Antimicrob. Agents Chemother. 1998 42 : 1284 1287. (Pubitemid 28227939)
39. Yoshida H, Bogaki M, Nakamura M, Yamanaka LM, Nakamura S. Quinolone resistance-determining region in the DNA gyrase gyrB gene of Escherichia coli. Antimicrob. Agents Chemother. 1991 35 : 1647 1650. (Pubitemid 20177394)
40. Heddle J, Maxwell A. Quinolone-binding pocket of DNA gyrase: role of GyrB. Antimicrob. Agents Chemother. 2002 46 : 1805 1815. (Pubitemid 34535201)
41. Ferrero L, Cameron B, Manse B et al. Cloning and primary structure of Staphylococcus aureus DNA topoisomerase IV: a primary target of fluoroquinolones. Mol. Microbiol. 1994 13 : 641 653. (Pubitemid 24266200)
42. Khodursky AB, Cozzarelli NR. The mechanism of inhibition of topoisomerase IV by quinolone antibacterials. J. Biol. Chem. 1998 273 : 27668 27677. (Pubitemid 28500492)
43. Alm RA, Ling LS, Moir DT et al. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 1999 397 : 176 180. (Pubitemid 29050924)
44. Tomb JF, White O, Kerlavage AR et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 1997 388 : 539 547. (Pubitemid 27339996)
45. Bina JE, Alm RA, Uria-Nickelsen M, Thomas SR, Trust TJ, Hancock RE. Helicobacter pylori uptake and efflux: basis for intrinsic susceptibility to antibiotics in vitro. Antimicrob. Agents Chemother. 2000 44 : 248 254. (Pubitemid 30060714)