Table of Contents Author Guidelines Submit a Manuscript
Journal of Biomedicine and Biotechnology
Volume 2012, Article ID 735368, 11 pages
http://dx.doi.org/10.1155/2012/735368
Research Article

Characterization of Flavonol Inhibition of DnaB Helicase: Real-Time Monitoring, Structural Modeling, and Proposed Mechanism

1Department of Biomedical Sciences, Chung Shan Medical University, No. 110, Section 1, Chien-Kuo N. Road, Taichung City 40201, Taiwan
2Department of Medical Research, Chung Shan Medical University Hospital, No. 110, Section 1, Chien-Kuo N. Road, Taichung City 40201, Taiwan

Received 1 February 2012; Revised 18 April 2012; Accepted 22 May 2012

Academic Editor: S. L. Mowbray

Copyright © 2012 Hsin-Hsien Lin and Cheng-Yang Huang. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. R. Reyes-Lamothe, D. J. Sherratt, and M. C. Leake, “Stoichiometry and architecture of active DNA replication machinery in Escherichia coli,” Science, vol. 328, no. 5977, pp. 498–501, 2010. View at Publisher · View at Google Scholar · View at Scopus
  2. M. L. Mott and J. M. Berger, “DNA replication initiation: mechanisms and regulation in bacteria,” Nature Reviews Microbiology, vol. 5, no. 5, pp. 343–354, 2007. View at Publisher · View at Google Scholar · View at Scopus
  3. K. J. Marians, “Prokaryotic DNA replication,” Annual Review of Biochemistry, vol. 61, pp. 673–719, 1992. View at Google Scholar · View at Scopus
  4. T. A. Baker and S. P. Bell, “Polymerases and the replisome: machines within machines,” Cell, vol. 92, no. 3, pp. 295–305, 1998. View at Publisher · View at Google Scholar · View at Scopus
  5. M. R. Singleton, M. S. Dillingham, and D. B. Wigley, “Structure and mechanism of helicases and nucleic acid translocases,” Annual Review of Biochemistry, vol. 76, pp. 23–50, 2007. View at Publisher · View at Google Scholar · View at Scopus
  6. S. S. Patel and K. M. Picha, “Structure and function of hexameric helicases,” Annual Review of Biochemistry, vol. 69, pp. 651–697, 2000. View at Publisher · View at Google Scholar · View at Scopus
  7. Y. H. Lo, K. L. Tsai, Y. J. Sun, W. T. Chen, C. Y. Huang, and C. D. Hsiao, “The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA,” Nucleic Acids Research, vol. 37, no. 3, pp. 804–814, 2009. View at Publisher · View at Google Scholar · View at Scopus
  8. H. W. Boucher, G. H. Talbot, J. S. Bradley et al., “Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America,” Clinical Infectious Diseases, vol. 48, no. 1, pp. 1–12, 2009. View at Publisher · View at Google Scholar
  9. K. K. Kumarasamy, M. A. Toleman, T. R. Walsh et al., “Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study,” The Lancet Infectious Diseases, vol. 10, no. 9, pp. 597–602, 2010. View at Publisher · View at Google Scholar · View at Scopus
  10. K. Bush, “Alarming β-lactamase-mediated resistance in multidrug-resistant Enterobacteriaceae,” Current Opinion in Microbiology, vol. 13, no. 5, pp. 558–564, 2010. View at Publisher · View at Google Scholar · View at Scopus
  11. R. Podschun and U. Ullmann, “Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors,” Clinical Microbiology Reviews, vol. 11, no. 4, pp. 589–603, 1998. View at Google Scholar · View at Scopus
  12. P. Soultanas, “The bacterial helicase-primase interaction: a common structural/functional module,” Structure, vol. 13, no. 6, pp. 839–844, 2005. View at Publisher · View at Google Scholar · View at Scopus
  13. C. C. Chen and C. Y. Huang, “Inhibition of Klebsiella pneumoniae dnab helicase by the flavonol galangin,” Protein Journal, vol. 30, no. 1, pp. 59–65, 2011. View at Publisher · View at Google Scholar · View at Scopus
  14. J. A. Ross and C. M. Kasum, “Dietary flavonoids: bioavailability, metabolic effects, and safety,” Annual Review of Nutrition, vol. 22, pp. 19–34, 2002. View at Publisher · View at Google Scholar · View at Scopus
  15. F. Teillet, A. Boumendjel, J. Boutonnat, and X. Ronot, “Flavonoids as RTK inhibitors and potential anticancer agents,” Medicinal Research Reviews, vol. 28, no. 5, pp. 715–745, 2008. View at Publisher · View at Google Scholar · View at Scopus
  16. K. L. Wolfe and R. H. Liu, “Structure-activity relationships of flavonoids in the cellular antioxidant activity assay,” Journal of Agricultural and Food Chemistry, vol. 56, no. 18, pp. 8404–8411, 2008. View at Publisher · View at Google Scholar · View at Scopus
  17. S. Burda and W. Oleszek, “Antioxidant and antiradical activities of flavonoids,” Journal of Agricultural and Food Chemistry, vol. 49, no. 6, pp. 2774–2779, 2001. View at Google Scholar · View at Scopus
  18. T. P. T. Cushnie and A. J. Lamb, “Antimicrobial activity of flavonoids,” International Journal of Antimicrobial Agents, vol. 26, no. 5, pp. 343–356, 2005. View at Publisher · View at Google Scholar · View at Scopus
  19. C. C. Wang, H. W. Tsau, W. T. Chen, and C. Y. Huang, “Identification and characterization of a putative dihydroorotase, KPN01074, from Klebsiella pneumoniae,” Protein Journal, vol. 29, no. 6, pp. 445–452, 2010. View at Publisher · View at Google Scholar · View at Scopus
  20. H. C. Jan, Y. L. Lee, and C. Y. Huang, “Characterization of a single-stranded DNA-binding protein from Pseudomonas aeruginosa PAO1,” Protein Journal, vol. 30, no. 1, pp. 20–26, 2011. View at Publisher · View at Google Scholar · View at Scopus
  21. Y. H. Huang, Y. L. Lee, and C. Y. Huang, “Characterization of a single-stranded DNA binding protein from Salmonella enterica serovar typhimurium LT2,” Protein Journal, vol. 30, no. 2, pp. 102–108, 2011. View at Publisher · View at Google Scholar · View at Scopus
  22. Y. H. Huang and C. Y. Huang, “Characterization of a single-stranded DNA binding protein from Klebsiella pneumoniae: mutation at either Arg73 or Ser76 causes a less cooperative complex on DNA,” Genes to Cells, vol. 17, pp. 146–157, 2012. View at Publisher · View at Google Scholar
  23. H. C. Hsieh and C. Y. Huang, “Identification of a novel protein, PriB, in Klebsiella pneumoniae,” Biochemical and Biophysical Research Communications, vol. 404, no. 1, pp. 546–551, 2011. View at Publisher · View at Google Scholar · View at Scopus
  24. C. Y. Huang, C. H. Hsu, Y. J. Sun, H. N. Wu, and C. D. Hsiao, “Complexed crystal structure of replication restart primosome protein PriB reveals a novel single-stranded DNA-binding mode,” Nucleic Acids Research, vol. 34, no. 14, pp. 3878–3886, 2006. View at Publisher · View at Google Scholar · View at Scopus
  25. J. H. Liu, T. W. Chang, C. Y. Huang et al., “Crystal structure of PriB, a primosomal DNA replication protein of Escherichia coli,” Journal of Biological Chemistry, vol. 279, no. 48, pp. 50465–50471, 2004. View at Publisher · View at Google Scholar · View at Scopus
  26. P. P. Van Veldhoven and G. P. Mannaerts, “Inorganic and organic phosphate measurements in the nanomolar range,” Analytical Biochemistry, vol. 161, no. 1, pp. 45–48, 1987. View at Google Scholar · View at Scopus
  27. M. A. Larkin, G. Blackshields, N. P. Brown et al., “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, 2007. View at Publisher · View at Google Scholar · View at Scopus
  28. K. Arnold, L. Bordoli, J. Kopp, and T. Schwede, “The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling,” Bioinformatics, vol. 22, no. 2, pp. 195–201, 2006. View at Publisher · View at Google Scholar · View at Scopus
  29. C. Knox, V. Law, T. Jewison et al., “DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs,” Nucleic Acids Research, vol. 39, no. 1, pp. D1035–D1041, 2011. View at Publisher · View at Google Scholar · View at Scopus
  30. D. Schneidman-Duhovny, Y. Inbar, R. Nussinov, and H. J. Wolfson, “PatchDock and SymmDock: servers for rigid and symmetric docking,” Nucleic Acids Research, vol. 33, no. 2, pp. W363–W367, 2005. View at Publisher · View at Google Scholar · View at Scopus
  31. A. Roychowdhury, M. R. Szymanski, M. J. Jezewska, and W. Bujalowski, “Mechanism of NTP hydrolysis by the Escherichia coli primary replicative helicase DnaB protein. 2. Nucleotide and nucleic acid specificities,” Biochemistry, vol. 48, no. 29, pp. 6730–6746, 2009. View at Publisher · View at Google Scholar · View at Scopus
  32. S. Bailey, W. K. Eliason, and T. A. Steitz, “Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase,” Science, vol. 318, no. 5849, pp. 459–463, 2007. View at Publisher · View at Google Scholar · View at Scopus
  33. E. E. Biswas and S. B. Biswas, “Mechanism of DnaB helicase of Escherichia coli: structural domains involved in ATP hydrolysis, DNA binding, and oligomerization,” Biochemistry, vol. 38, no. 34, pp. 10919–10928, 1999. View at Publisher · View at Google Scholar · View at Scopus
  34. H. Tani, O. Fujita, A. Furuta et al., “Real-time monitoring of RNA helicase activity using fluorescence resonance energy transfer in vitro,” Biochemical and Biophysical Research Communications, vol. 393, no. 1, pp. 131–136, 2010. View at Publisher · View at Google Scholar · View at Scopus
  35. A. Koul, E. Arnoult, N. Lounis, J. Guillemont, and K. Andries, “The challenge of new drug discovery for tuberculosis,” Nature, vol. 469, no. 7331, pp. 483–490, 2011. View at Publisher · View at Google Scholar · View at Scopus
  36. B. D. Bax, P. F. Chan, D. S. Eggleston et al., “Type IIA topoisomerase inhibition by a new class of antibacterial agents,” Nature, vol. 466, no. 7309, pp. 935–940, 2010. View at Publisher · View at Google Scholar · View at Scopus
  37. M. T. Black and K. Coleman, “New inhibitors of bacterial topoisomerase GyrA/ParC subunits,” Current Opinion in Investigational Drugs, vol. 10, no. 8, pp. 804–810, 2009. View at Google Scholar · View at Scopus
  38. K. L. Hopkins, R. H. Davies, and E. J. Threlfall, “Mechanisms of quinolone resistance in Escherichia coli and Salmonella: recent developments,” International Journal of Antimicrobial Agents, vol. 25, no. 5, pp. 358–373, 2005. View at Publisher · View at Google Scholar · View at Scopus
  39. A. Srivastava, M. Talaue, S. Liu et al., “New target for inhibition of bacterial RNA polymerase: `switch region',” Current Opinion in Microbiology, vol. 14, no. 5, pp. 532–543, 2011. View at Publisher · View at Google Scholar
  40. K. Chono, K. Katsumata, T. Kontani et al., “ASP2151, a novel helicase-primase inhibitor, possesses antiviral activity against varicella-zoster virus and herpes simplex virus types 1 and 2,” Journal of Antimicrobial Chemotherapy, vol. 65, no. 8, Article ID dkq198, pp. 1733–1741, 2010. View at Publisher · View at Google Scholar · View at Scopus
  41. S. Li, T. Hattori, and E. N. Kodama, “Epigallocatechin gallate inhibits the HIV reverse transcription step,” Antiviral Chemistry and Chemotherapy, vol. 21, no. 6, pp. 239–243, 2011. View at Publisher · View at Google Scholar
  42. S. C. Chu, Y. S. Hsieh, and J. Y. Lin, “Inhibitory effects of flavonoids on moloney murine leukemia virus reverse transcriptase activity,” Journal of Natural Products, vol. 55, no. 2, pp. 179–183, 1992. View at Google Scholar · View at Scopus
  43. M. K. Chahar, N. Sharma, M. P. Dobhal, and Y. C. Joshi, “Flavonoids: a versatile source of anticancer drugs,” Pharmacognosy Reviews, vol. 5, no. 9, pp. 1–12, 2011. View at Publisher · View at Google Scholar · View at Scopus
  44. S. Holder, M. Zemskova, C. Zhang et al., “Characterization of a potent and selective small-molecule inhibitor of the PIM1 kinase,” Molecular Cancer Therapeutics, vol. 6, no. 1, pp. 163–172, 2007. View at Publisher · View at Google Scholar · View at Scopus
  45. E. H. Walker, M. E. Pacold, O. Perisic et al., “Structural determinants of phosphoinositide 3-kinase inhibition by wortmannin, LY294002, quercetin, myricetin, and staurosporine,” Molecular Cell, vol. 6, no. 4, pp. 909–919, 2000. View at Google Scholar · View at Scopus
  46. M. A. Griep, S. Blood, M. A. Larson, S. A. Koepsell, and S. H. Hinrichs, “Myricetin inhibits Escherichia coli DnaB helicase but not primase,” Bioorganic and Medicinal Chemistry, vol. 15, no. 22, pp. 7203–7208, 2007. View at Publisher · View at Google Scholar · View at Scopus
  47. M. J. Jezewska, U. S. Kim, and W. Bujalowski, “Interactions of Escherichia coli primary replicative helicase DnaB protein with nucleotide cofactors,” Biophysical Journal, vol. 71, no. 4, pp. 2075–2086, 1996. View at Google Scholar · View at Scopus
  48. M. J. Jezewska and W. Bujalowski, “Global conformational transitions in Escherichia coli primary replicative helicase DnaB protein induced by ATP, ADP, and single-stranded DNA binding: multiple conformational states of the helicase hexamer,” Journal of Biological Chemistry, vol. 271, no. 8, pp. 4261–4265, 1996. View at Google Scholar · View at Scopus