NMR study on small proteins from helicobacter pylori for antibiotic target discovery: A review

Molecules

Volumn 18, Issue 11, 2013, Pages 13410-13424

  Kang, Su Jin ^a   Kim, Do Hee ^a   Lee, Bong Jin ^a  

^a Seoul National University   (South Korea)

Author keywords

Antibiotics; Antimicrobial peptides (AMPs); Helicobacter pylori; Nuclear magnetic resonance (NMR); Structure activity relationship (SAR)

Indexed keywords

ANTIINFECTIVE AGENT; BACTERIAL PROTEIN;

CHEMISTRY; DRUG DEVELOPMENT; DRUG EFFECT; HELICOBACTER PYLORI; METABOLISM; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; REVIEW;

ANTI-BACTERIAL AGENTS; BACTERIAL PROTEINS; DRUG DISCOVERY; HELICOBACTER PYLORI; MAGNETIC RESONANCE SPECTROSCOPY;

EID: 84888596236     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules181113410     Document Type: Review

References (56)

1. Waksman, S.A. What is an antibiotic or an antibiotic substance? Mycologia 1947, 39, 565-569.
2. Kohanski, M.A.; Dwyer, D.J.; Collins, J.J. How antibiotics kill bacteria: from targets to networks. Nat. Rev. Microbiol. 2010, 8, 423-435.
3. Walsh, C. Where will new antibiotics come from? Nat. Rev. Microbiol. 2003, 1, 65-70.
4. Fernandes, P. Antibacterial discovery and development-the failure of success? Nat. Biotechnol. 2006, 24, 1497-1503.
5. Fernandes, P.B. The ATCG of drug discovery. Curr. Opin. Mol. Ther. 2000, 2, 624-632.
6. Schmid, M.B. Crystallizing new approaches for antimicrobial drug discovery. Biochem. Pharmacol. 2006, 71, 1048-1056.
7. Waldor, M.K. Disarming pathogens-a new approach for antibiotic development. N. Engl. J. Med. 2006, 354, 296-297.
8. Casey, G. Antibiotics and the rise of superbugs. Nurs. N. Z. 2012, 18, 20-24.
9. Quinlivan, E.P.; Gregory, J.F.; Homocysteine, B vitamins, and cardiovascular disease. N. Engl. J. Med. 2006, 355, 209-211.
10. Tomb, J.F.; White, O.; Kerlavage, A.R.; Clayton, R.A.; Sutton, G.G.; Fleischmann, R.D.; Ketchum, K.A.; Klenk, H.P.; Gill, S.; Dougherty, B.A.; et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 1997, 388, 539-547.
11. Hessey, S.J.; Spencer, J.; Wyatt, J.I.; Sobala, G.; Rathbone, B.J.; Axon, A.T.; Dixon, M.F. Bacterial adhesion and disease activity in Helicobacter associated chronic gastritis. Gut 1990, 31, 134-138.
12. Kazi, J.L.; Sinniah, R.; Zaman, V.; Ng, M.L.; Jafarey, N.A.; Alam, S.M.; Zuberi, S.J.; Kazi, A.M. Ultrastructural study of Helicobacter pylori-associated gastritis. J. Pathol. 1990, 161, 65-70.
13. Krienitz, U. Über das Auftreten von Spirochäten verschiedener Form im Mageninhalt bei Carcinoma ventriculi. Dtsch. Med. Wochenschr. 1906, 32, 872.
14. Warren, J.R.; Marshall, B. Unidentified curved bacilli on gastric epithelium in active chronic gastritis. Lancet 1983, 1, 1273-1275.
15. Infection with Helicobacter pylori. In Schistosomes, Liver Flukes and Helicobacter pylori. International Agency for Research on Cancer, WHO: Lyon, France, 1994; Volume 61, pp. 177-240.
16. Eaton, K.A.; Gilbert, J.V.; Joyce, E.A.; Wanken, A.E.; Thevenot, T.; Baker, P.; Plaut, A.; Wright, A. In vivo complementation of ureB restores the ability of Helicobacter pylori to colonize. Infect. Immun. 2002, 70, 771-778.
17. Rothenbacher, D.; Brenner, H. Burden of Helicobacter pylori and H. pylori-related diseases in developed countries: Recent developments and future implications. Microbes Infect. 2003, 5, 693-703.
18. Wotherspoon, A.C.; Doglioni, C.; Diss, T.C.; Pan, L.; Moschini, A.; de Boni, M.; Isaacson, P.G. Regression of primary low-grade B-cell gastric lymphoma of mucosa-associated lymphoid tissue type after eradication of Helicobacter pylori. Lancet 1993, 342, 575-577.
19. Peek, R.M., Jr.; Blaser, M.J. Helicobacter pylori and gastrointestinal tract adenocarcinomas. Nat. Rev. Cancer 2002, 2, 28-37.
20. Parsonnet, J.; Friedman, G.D.; Vandersteen, D.P.; Chang, Y.; Vogelman, J.H.; Orentreich, N.; Sibley, R.K. Helicobacter pylori infection and the risk of gastric carcinoma. N. Engl. J. Med. 1991, 325, 1127-1131.
21. Suerbaum, S.; Achtman, M. Helicobacter pylori: recombination, population structure and human migrations. Int J. Med. Microbiol. 2004, 294, 133-139.
22. Malfertheiner, P.; Megraud, F.; O'Morain, C.; Bazzoli, F.; El-Omar, E.; Graham, D.; Hunt, R.; Rokkas, T.; Vakil, N.; Kuipers, E.J. Current concepts in the management of Helicobacter pylori infection: The Maastricht III Consensus Report. Gut 2007, 56, 772-781.
23. Gisbert, J.P.; Calvet, X.; Gomollon, F.; Mones, J. Eradication treatment of Helicobacter pylori. Recommendations of the II Spanish Consensus Conference. Med. Clin. 2005, 125, 301-316.
24. Gisbert, J.P.; Pajares, J.M. Treatment of Helicobacter pylori infection: the past and the future. Eur. J. Intern. Med. 2010, 21, 357-359.
25. Tominaga, K.; Higuchi, K.; Hamasaki, N.; Hamaguchi, M.; Takashima, T.; Tanigawa, T.; Watanabe, T.; Fujiwara, Y.; Tezuka, Y.; Nagaoka, T.; et al. In vivo action of novel alkyl methyl quinolone alkaloids against Helicobacter pylori. J. Antimicrob. Chemother. 2002, 50, 547-552.
26. Koga, T.; Inoue, H.; Ishii, C.; Okazaki, Y.; Domon, H.; Utsui, Y. Effect of plaunotol in combination with clarithromycin or amoxicillin on Helicobacter pylori in vitro in vitro and in vivo. J. Antimicrob. Chemother. 2002, 50, 133-136.
27. Alm, R.A.; Ling, L.S.; Moir, D.T.; King, B.L.; Brown, E.D.; Doig, P.C.; Smith, D.R.; Noonan, B.; Guild, B.C.; de Jonge, B.L.; et al. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 1999, 397, 176-180.
28. Salgado, F.; Garcia, A.; Onate, A.; Gonzalez, C.; Kawaguchi, F. Increased in vitro and in vivo biological activity of lipopolysaccharide extracted from clinical low virulence vacA genotype Helicobacter pylori strains. J. Med. Microbiol. 2002, 51, 771-776.
29. Selbach, M.; Moese, S.; Hauck, C.R.; Meyer, T.F.; Backert, S. Src is the kinase of the Helicobacter pylori CagA protein in vitro in vitro and in vivo. J. Biol. Chem. 2002, 277, 6775-6778.
30. Park, S.J.; Son, W.S.; Lee, B.J. Structural Analysis of Hypothetical Proteins from Helicobacter pylori: An Approach to Estimate Functions of Unknown or Hypothetical Proteins. Int J. Mol. Sci 2012, 13, 7109-7137.
31. Yeo, H.J.; Savvides, S.N.; Herr, A.B.; Lanka, E.; Waksman, G. Crystal structure of the hexameric traffic ATPase of the Helicobacter pylori type IV secretion system. Mol. Cell. 2000, 6, 1461-1472.
32. Lee, K.H.; Lee, D.G.; Park, Y.; Kang, D.I.; Shin, S.Y.; Hahm, K.S.; Kim, Y. Interactions between the plasma membrane and the antimicrobial peptide HP (2-20) and its analogues derived from Helicobacter pylori. Biochem. J. 2006, 394, 105-114.
33. Park, S.J.; Jung, Y.S.; Kim, J.S.; Seo, M.D.; Lee, B.J. Structural insight into the distinct properties of copper transport by the Helicobacter pylori CopP protein. Proteins 2008, 71, 1007-1019.
34. Kang, S.J.; Park, S.J.; Jung, S.J.; Lee, B.J. Solution structure of HP1242 from Helicobacter pylori. Proteins 2005, 61, 1111-1113.
35. Kang, S.J.; Park, S.J.; Jung, S.J.; Lee, B.J. Backbone 1H, 15N, and 13C resonance assignment of HP1242 from Helicobacter pylori. J. Biochem. Mol. Biol. 2005, 38, 591-594.
36. Lee, K.Y.; Kim, J.H.; Lee, J.; Lee, I.; Bae, Y.J.; Lee, B.J. Structural Characterization of HP1264 Reveals a Novel Fold for the Flavin Mononucleotide Binding Protein. Biochemistry 2013, 52, 1583-1593.
37. Seo, M.D.; Park, S.J.; Kim, H.J.; Lee, B.J. Solution structure of hypothetical protein, HP0495 (Y495-HELPY) from Helicobacter pylori. Proteins 2007, 67, 1189-1192.
38. Seo, M.D.; Park, S.J.; Kim, H.J.; Seok, S.H.; Lee, B.J. Backbone 1H, 15N, and 13C resonance assignment and secondary structure prediction of HP0495 from Helicobacter pylori. J. Biochem. Mol. Biol. 2007, 40, 839-843.
39. Han, K.D.; Park, S.J.; Jang, S.B.; Son, W.S.; Lee, B.J. Solution structure of conserved hypothetical protein HP0894 from Helicobacter pylori. Proteins 2005, 61, 1114-1116.
40. Han, K.D.; Park, S.J.; Lee, B.J. Backbone 1H, 15N, and 13C resonance assignments and secondary-structure of conserved hypothetical protein HP0894 from Helicobacter pylori. Mol. Cells 2005, 20, 442-445.
41. Jang, S.B.; Ma, C.; Lee, J.Y.; Kim, J.H.; Park, S.J.; Kwon, A.R.; Lee, B.J. NMR solution structure of HP0827 (O25501-HELPY) from Helicobacter pylori: model of the possible RNA-binding site. J. Biochem. 2009, 146, 667-674.
42. Kim, J.H.; Park, S.J.; Lee, K.Y.; Son, W.S.; Sohn, N.Y.; Kwon, A.R.; Lee, B.J. Solution structure of hypothetical protein HP1423 (Y1423-HELPY) reveals the presence of alphaL motif related to RNA binding. Proteins 2009, 75, 252-257.
43. Han, K.D.; Park, S.J.; Jang, S.B.; Lee, B.J. Backbone 1H, 15N, and 13C resonance assignments and secondary-structure of the conserved hypothetical protein HP0892 of Helicobacter pylori. Mol. Cells 2008, 25, 138-141.
44. Han, K.D.; Park, S.J.; Jang, S.B.; Lee, B.J. Solution structure of conserved hypothetical protein HP0892 from Helicobacter pylori. Proteins 2008, 70, 599-602.
45. Hong, E.; Lee, H.M.; Ko, H.; Kim, D.U.; Jeon, B.Y.; Jung, J.; Shin, J.; Lee, S.A.; Kim, Y.; Jeon, Y.H.; et al. Structure of an atypical orphan response regulator protein supports a new phosphorylation-independent regulatory mechanism. J. Biol. Chem. 2007, 282, 20667-20675.
46. Popescu, A.; Karpay, A.; Israel, D.A.; Peek, R.M., Jr.; Krezel, A.M. Helicobacter pylori protein HP0222 belongs to Arc/MetJ family of transcriptional regulators. Proteins 2005, 59, 303-311.
47. Gupta, S.S.; Borin, B.N.; Cover, T.L.; Krezel, A.M. Structural analysis of the DNA-binding domain of the Helicobacter pylori response regulator ArsR. J. Biol. Chem. 2009, 284, 6536-6545.
48. Xia, W.; Li, H.; Sze, K.H.; Sun, H. Structure of a nickel chaperone, HypA, from Helicobacter pylori reveals two distinct metal binding sites. J. Am. Chem. Soc. 2009, 131, 10031-10040.
49. Borin, B.N.; Krezel, A.M. Structure of HP0564 from Helicobacter pylori identifies it as a new transcriptional regulator. Proteins 2008, 73, 265-268.
50. Han, K.D.; Matsuura, A.; Ahn, H.C.; Kwon, A.R.; Min, Y.H.; Park, H.J.; Won, H.S.; Park, S.J.; Kim, D.Y.; Lee, B.J. Functional identification of toxin-antitoxin molecules from Helicobacter pylori 26695 and structural elucidation of the molecular interactions. J. Biol. Chem. 2011, 286, 4842-4853.
51. Han, K.D.; Ahn, D.H.; Lee, S.A.; Min, Y.H.; Kwon, A.R.; Ahn, H.C.; Lee, B.J. Identification of chromosomal HP0892-HP0893 toxin-antitoxin proteins in Helicobacter pylori and structural elucidation of their protein-protein interaction. J. Biol. Chem. 2013, 288, 6004-6013.
52. Engelberg-Kulka, H.; Amitai, S.; Kolodkin-Gal, I.; Hazan, R. Bacterial programmed cell death and multicellular behavior in bacteria. PLoS Genet. 2006, 2, e135.
53. Van Melderen, L.; Saavedra De Bast, M. Bacterial toxin-antitoxin systems: More than selfish entities? PLoS Genet. 2009, 5, e1000437.
54. Yamaguchi, Y.; Park, J.H.; Inouye, M. Toxin-antitoxin systems in bacteria and archaea. Annu. Rev. Genet. 2011, 45, 61-79.
55. Park, S.J.; Son, W.S.; Lee, B.J. Structural overview of toxin-antitoxin systems in infectious bacteria:Atargetfordevelopingantimicrobialagents. Biochim. Biophys. Acta 2013, 1834, 1155-1167.
56. Gerdes, K.; Christensen, S.K.; Lobner-Olesen, A. Prokaryotic toxin-antitoxin stress response loci. Nat. Rev. Microbiol. 2005, 3, 371-382.