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BioMed Research International
Volume 2013, Article ID 390920, 15 pages
http://dx.doi.org/10.1155/2013/390920
Research Article

Molecular Dynamic Simulation and Inhibitor Prediction of Cysteine Synthase Structured Model as a Potential Drug Target for Trichomoniasis

1Department of Computational Biology and Bioinformatics, JSBB, SHIATS, Allahabad 211007, India
2Department of Biodiversity and Molecular Ecology, Research and Innovation Center, Fondazione Edmund Mach (FEM), Istituto Agrario San Michele (IASMA), Via Mach 1, 38010 San Michele all'Adige, Italy
3Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
4Bioinformatics Centre, Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, India

Received 26 April 2013; Accepted 14 July 2013

Academic Editor: Stavros J. Hamodrakas

Copyright © 2013 Satendra Singh et al. 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. M. F. Rein and M. Muller, Trichomonas Vaginalis and Sexually Transmitted Diseases, McGraw-Hill, New York, NY, USA, 1990.
  2. World Health Organization, An Overview of Selected Curable Sexually Transmitted Diseases, in Global Program on AIDS, World Health Organization, Geneva, Switzerland, 1995.
  3. E. W. Hook, “Trichomonas vaginalis-no longer a minor STD,” Sexually Transmitted Diseases, vol. 26, no. 7, pp. 388–389, 1999. View at Publisher · View at Google Scholar · View at Scopus
  4. A. Donne, “Weekly reports of sittings of the Academy of Sciences Paris,” 3, 385, 1836.
  5. J. G. Lossick, “Therapy of urogenital trichomoniasis,” in Trichomonads Parasitic in Humans, B. M. Honigberg, Ed., pp. 324–341, Springer, New York, NY, USA, 1990. View at Google Scholar
  6. J. G. Meingassner and H. Mieth, “Cross resistance of trichomonads to 5 nitroimidazole derivatives,” Experientia, vol. 32, no. 2, pp. 183–184, 1976. View at Google Scholar · View at Scopus
  7. E. M. Narcisi and W. E. Secor, “In vitro effect of tinidazole and furazolidone on metronidazole-resistant Trichomonas vaginalis,” Antimicrobial Agents and Chemotherapy, vol. 40, no. 5, pp. 1121–1125, 1996. View at Google Scholar · View at Scopus
  8. P. Upcroft and J. A. Upcroft, “Drug targets and mechanisms of resistance in the anaerobic protozoa,” Clinical Microbiology Reviews, vol. 14, no. 1, pp. 150–164, 2001. View at Publisher · View at Google Scholar · View at Scopus
  9. D. V. Quon, C. E. d'Oliveira, and P. J. Johnson, “Reduced transcription of the ferredoxin gene in metronidazole-resistant Trichomonas vaginalis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 89, no. 10, pp. 4402–4406, 1992. View at Publisher · View at Google Scholar · View at Scopus
  10. J. M. Carlton, P. R. Hirt, J. C. Silva et al., “Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis,” Science, vol. 315, no. 5809, pp. 207–212, 2007. View at Publisher · View at Google Scholar
  11. G. D. Westrop, G. Goodall, J. C. Mottram, and G. H. Coombs, “Cysteine biosynthesis in Trichomonas vaginalis involves Cysteine synthase utilizing O-phosphoserine,” Journal of Biological Chemistry, vol. 281, no. 35, pp. 25062–25075, 2006. View at Publisher · View at Google Scholar · View at Scopus
  12. T. Nozaki, V. Ali, and M. Tokoro, “Sulfur-containing amino acid metabolism in parasitic protozoa,” Advances in Parasitology, vol. 60, pp. 1–99, 2005. View at Publisher · View at Google Scholar · View at Scopus
  13. S. Singh, G. Singh, B. Gautam, P. A. Jain, and P. K. Yadav, “In silico metabolic pathway analysis of Trichomonas vaginalis for potential drug targets,” Elixir Bio Physics, vol. 32, pp. 1991–1994, 2011. View at Google Scholar
  14. J. E. Ellis, N. Yarlett, D. Cole, M. J. Humphreys, and D. Lloyd, “Antioxidant defences in the microaerophilic protozoan Trichomonas vaginalis: comparison of metronidazole-resistant and sensitive strains,” Microbiology, vol. 140, no. 9, pp. 2489–2494, 1994. View at Google Scholar · View at Scopus
  15. S. Satendra, S. Gurmit, G. Budhayash, V. Pritish, and F. Rohit, “Trichomonas vaginalis genome analysis using Bioinformatics approaches,” International Journal of Pharmaceutical Sciences Review and Research, vol. 3, no. 1, pp. 38–42, 2010. View at Google Scholar · View at Scopus
  16. E. Gasteiger, A. Gattiker, C. Hoogland, I. Ivanyi, R. D. Appel, and A. Bairoch, “ExPASy: the proteomics server for in-depth protein knowledge and analysis,” Nucleic Acids Research, vol. 31, no. 13, pp. 3784–3788, 2003. View at Publisher · View at Google Scholar · View at Scopus
  17. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990. View at Publisher · View at Google Scholar · View at Scopus
  18. H. M. Bermen, J. Westbrook, Z. Feng et al., “The protein data bank,” Nucleic Acids Research, vol. 28, no. 1, pp. 235–242, 2000. View at Publisher · View at Google Scholar
  19. J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994. View at Google Scholar · View at Scopus
  20. A. Sali and T. L. Blundell, “Comparative protein modelling by satisfaction of spatial restraints,” Journal of Molecular Biology, vol. 234, no. 3, pp. 779–815, 1993. View at Publisher · View at Google Scholar · View at Scopus
  21. A. Sali and J. P. Overington, “Derivation of rules for comparative protein modeling from a database of protein structure alignments,” Protein Science, vol. 3, no. 9, pp. 1582–1596, 1994. View at Google Scholar · View at Scopus
  22. A. Sali, L. Potterton, F. Yuan, H. Van Vlijmen, and M. Karplus, “Evaluation of comparative protein modeling by MODELLER,” Proteins, vol. 23, no. 3, pp. 318–326, 1995. View at Publisher · View at Google Scholar · View at Scopus
  23. R. A. Laskoswki, M. W. MacArthur, D. S. Moss, and J. M. Thornton, “PROCHECK: a program to check the sterochemical quality of protein structures,” Journal of Applied Crystallography, vol. 26, pp. 283–291, 1993. View at Publisher · View at Google Scholar
  24. D. Eisenberg, R. Lüthy, and J. U. Bowie, “VERIFY3D: assessment of protein models with three-dimensional profiles,” Methods in Enzymology, vol. 277, pp. 396–406, 1997. View at Publisher · View at Google Scholar · View at Scopus
  25. C. Colovos and T. O. Yeates, “Verification of protein structures: patterns of nonbonded atomic interactions,” Protein Science, vol. 2, no. 9, pp. 1511–1519, 1993. View at Google Scholar · View at Scopus
  26. G. Vriend, “WHAT IF: a molecular modeling and drug design program,” Journal of Molecular Graphics, vol. 8, no. 1, pp. 52–56, 1990. View at Google Scholar · View at Scopus
  27. M. Wiederstein and M. J. Sippl, “ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins,” Nucleic Acids Research, vol. 35, pp. W407–W410, 2007. View at Publisher · View at Google Scholar · View at Scopus
  28. M. J. Sippl, “Recognition of errors in three-dimensional structures of proteins,” Proteins, vol. 17, no. 4, pp. 355–362, 1993. View at Publisher · View at Google Scholar · View at Scopus
  29. B. Hess, C. Kutzner, D. Van Der Spoel, and E. Lindahl, “GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation,” Journal of Chemical Theory and Computation, vol. 4, no. 3, pp. 435–447, 2008. View at Publisher · View at Google Scholar · View at Scopus
  30. C. Oostenbrink, A. Villa, A. E. Mark, and W. F. Van Gunsteren, “A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6,” Journal of Computational Chemistry, vol. 25, no. 13, pp. 1656–1676, 2004. View at Publisher · View at Google Scholar · View at Scopus
  31. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, “A smooth particle mesh Ewald method,” The Journal of Chemical Physics, vol. 103, no. 19, pp. 8577–8593, 1995. View at Google Scholar · View at Scopus
  32. B. Hess, H. Bekker, H. J. C. Berendsen, and J. G. E. M. Fraaije, “LINCS: a linear constraint solver for molecular simulations,” Journal of Computational Chemistry, vol. 18, no. 12, pp. 1463–1472, 1997. View at Google Scholar · View at Scopus
  33. H. J. C. Berendsen, J. P. M. Postma, W. F. Van Gunsteren, A. Dinola, and J. R. Haak, “Molecular dynamics with coupling to an external bath,” The Journal of Chemical Physics, vol. 81, no. 8, pp. 3684–3690, 1984. View at Google Scholar · View at Scopus
  34. O. Trott and A. J. Olson, “Software news and update AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading,” Journal of Computational Chemistry, vol. 31, no. 2, pp. 455–461, 2010. View at Publisher · View at Google Scholar · View at Scopus
  35. J. J. Irwin and B. K. Shoichet, “ZINC-a free database of commercially available compounds for virtual screening,” Journal of Chemical Information and Modeling, vol. 45, no. 1, pp. 177–182, 2005. View at Publisher · View at Google Scholar · View at Scopus
  36. A. C. Wallace, R. A. Laskowski, and J. M. Thornton, “LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions,” Protein Engineering, vol. 8, no. 2, pp. 127–134, 1995. View at Google Scholar · View at Scopus
  37. D. Burstein, S. B. Gould, V. Zimorski et al., “A machine learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis,” Eukaryotic Cell, vol. 11, no. 2, pp. 217–228, 2012. View at Publisher · View at Google Scholar · View at Scopus
  38. A. C. Gerbase, J. T. Rowley, D. H. L. Heymann, S. F. B. Berkley, and P. Piot, “Global prevalence and incidence estimates of selected curable STDS,” Sexually Transmitted Infections, vol. 74, supplement 1, pp. S12–S16, 1998. View at Google Scholar · View at Scopus
  39. D. A. Lewis, L. Habgood, R. White, K. F. Barker, and S. M. Murphy, “Managing vaginal trichomoniasis resistant to high-dose metronidazole therapy,” International Journal of STD and AIDS, vol. 8, no. 12, pp. 780–784, 1997. View at Publisher · View at Google Scholar · View at Scopus
  40. S. L. Baldauf, A. J. Roger, I. Wenk-Siefert, and W. F. Doolittle, “A kingdom-level phylogeny of eukaryotes based on combined protein data,” Science, vol. 290, no. 5493, pp. 972–977, 2000. View at Publisher · View at Google Scholar · View at Scopus
  41. D. S. Horner and T. M. Embley, “Chaperonin 60 phylogeny provides further evidence for secondary loss of mitochondria among putative early-branching eukaryotes,” Molecular Biology and Evolution, vol. 18, no. 10, pp. 1970–1975, 2001. View at Google Scholar · View at Scopus
  42. W. Martin and M. Müller, “The hydrogen hypothesis for the first eukaryote,” Nature, vol. 392, pp. 937–941, 1998. View at Google Scholar